data_5815 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the coat protein in fd filamentous bacteriophage particles ; _BMRB_accession_number 5815 _BMRB_flat_file_name bmr5815.str _Entry_type original _Submission_date 2003-06-03 _Accession_date 2003-06-04 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zeri A. C. . 2 Mesleh M. F. . 3 Nevzorov A. A. . 4 Opella S. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 residual_dipolar_couplings 1 stop_ loop_ _Data_type _Data_type_count "15N chemical shifts" 43 "residual dipolar couplings" 43 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-10-17 original author . stop_ _Original_release_date 2003-10-17 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure of the Coat Protein in fd Filamentous Bacteriophage Particles Determined by Solid-state NMR Spectroscopy ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22656956 _PubMed_ID 12750469 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zeri A. C. . 2 Mesleh M. F. . 3 Nevzorov A. A. . 4 Opella S. J. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U. S. A.' _Journal_volume 100 _Journal_issue 11 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6458 _Page_last 6463 _Year 2003 _Details . loop_ _Keyword 'ALPHA HELIX' bacteriophage 'solid-state NMR' PISEMA stop_ save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _Citation_full ; Zeri AC, Mesleh MF, Nevzorov AA, Opella SJ. Proc Natl Acad Sci U S A. 2003 May 27;100(11) ; _Citation_title 'Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state NMR spectroscopy.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 12750469 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zeri 'Ana Carolina' C. . 2 Mesleh 'Michael F' F. . 3 Nevzorov 'Alexander A' A. . 4 Opella 'Stanley J' J. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_name_full 'Proceedings of the National Academy of Sciences of the United States of America' _Journal_volume 100 _Journal_issue 11 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 6458 _Page_last 6463 _Year 2003 _Details ; The atomic resolution structure of fd coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles differs from that previously determined by x-ray fiber diffraction. Most notably, the 50-residue protein is not a single curved helix, but rather is a nearly ideal straight helix between residues 7 and 38, where there is a distinct kink, and then a straight helix with a different orientation between residues 39 and 49. Residues 1-5 have been shown to be mobile and unstructured, and proline 6 terminates the helix. The structure of the coat protein in virus particles, in combination with the structure of the membrane-bound form of the same protein in bilayers, also recently determined by solid-state NMR spectroscopy, provides insight into the viral assembly process. In addition to their roles in molecular biology and biotechnology, the filamentous bacteriophages continue to serve as model systems for the development of experimental methods for determining the structures of proteins in biological supramolecular assemblies. New NMR results include the complete sequential assignment of the two-dimensional polarization inversion spin-exchange at the magic angle spectrum of a uniformly 15N-labeled 50-residue protein in a 1.6 x 107 Da particle in solution, and the calculation of the three-dimensional structure of the protein from orientational restraints with an accuracy equivalent to an rms deviation of approximately 1A. ; save_ ################################## # Molecular system description # ################################## save_system_p8 _Saveframe_category molecular_system _Mol_system_name 'Major coat protein' _Abbreviation_common p8 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'p8 monomer' $p8 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state 'virus particle' _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'bacteriophage coat protein' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_p8 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'bacteriophage fd major coat protein' _Abbreviation_common p8 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 50 _Mol_residue_sequence ; AEGDDPAKAAFDSLQASATE MIGYAWAMVVVIVGATIGIK LFKKFTSKAS ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 GLU 3 GLY 4 ASP 5 ASP 6 PRO 7 ALA 8 LYS 9 ALA 10 ALA 11 PHE 12 ASP 13 SER 14 LEU 15 GLN 16 ALA 17 SER 18 ALA 19 THR 20 GLU 21 MET 22 ILE 23 GLY 24 TYR 25 ALA 26 TRP 27 ALA 28 MET 29 VAL 30 VAL 31 VAL 32 ILE 33 VAL 34 GLY 35 ALA 36 THR 37 ILE 38 GLY 39 ILE 40 LYS 41 LEU 42 PHE 43 LYS 44 LYS 45 PHE 46 THR 47 SER 48 LYS 49 ALA 50 SER stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value SWISS-PROT P69539 'Coat protein B precursor (Major coat protein)' 100.00 73 98.00 98.00 3.96e-19 SWISS-PROT P69540 'Coat protein B precursor (Major coat protein)' 100.00 73 98.00 98.00 3.96e-19 GenBank AAF75598 'major coat protein pVIII precursor [Filamentous phage cloning vector fd-tet]' 100.00 73 98.00 98.00 3.96e-19 PRF 0812197K DNA,phage 100.00 73 98.00 98.00 3.96e-19 GenBank AAA32308 'VIII [Enterobacteria phage fd]' 100.00 73 98.00 98.00 3.96e-19 GenBank AAB24445 'gene-8 protein, g8p=major coat protein [bacteriophage fd, Peptide, 50 aa]' 100.00 50 98.00 98.00 7.86e-19 GenBank AAA32214 'protein VIII' 100.00 73 98.00 98.00 3.96e-19 GenBank AAA32220 'major coat protein B' 100.00 73 98.00 98.00 3.96e-19 PDB 2HI5 'Model For Bacteriophage Fd From Cryo-Em' 100.00 50 98.00 98.00 7.86e-19 EMBL CAA23871 'unnamed protein product [Enterobacteria phage f1]' 100.00 73 98.00 98.00 3.96e-19 PDB 2C0W 'Molecular Structure Of Fd Filamentous Bacteriophage Refined With Respect To X-Ray Fibre Diffraction' 100.00 50 100.00 100.00 1.34e-19 PDB 2C0X 'Molecular Structure Of Fd Filamentous Bacteriophage Refined With Respect To X-Ray Fibre Diffraction And Solid-State Nmr Data' 100.00 50 100.00 100.00 1.34e-19 PDB 1MZT 'Nmr Structure Of The Fd Bacteriophage Pviii Coat Protein In Lipid Bilayer Membranes' 100.00 50 98.00 98.00 7.86e-19 PDB 1NH4 'Structure Of The Coat Protein In Fd Filamentous Bacteriophage Particles' 100.00 50 100.00 100.00 1.34e-19 PDB 1IFI 'Molecular Models And Structural Comparisons Of Native And Mutant Class I Filamentous Bacteriophages Ff (Fd, F1, M13), If1 And Ike' 100.00 50 98.00 98.00 7.86e-19 PDB 1IFJ 'Molecular Models And Structural Comparisons Of Native And Mutant Class I Filamentous Bacteriophages Ff (Fd, F1, M13), If1 And Ike' 100.00 50 98.00 98.00 7.86e-19 PDB 1FDM 'Fd Major Coat Protein In Sds Micelles, Nmr, 20 Structures' 100.00 50 98.00 98.00 7.86e-19 PDB 1IFD 'Model-Building Studies Of Inovirus: Genetic Variations On A Geometric Theme' 100.00 50 98.00 98.00 7.86e-19 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $p8 bacteriophage 12420 virus . Filamentous bacteriophage stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $p8 'purified from the natural source' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'bacteriophage particles were suspended in aqueous buffer' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $p8 50 mg/ml [U-15N] 'sodium borate buffer' 5 mM . stop_ save_ ############################ # Computer software used # ############################ save_tecmag _Saveframe_category software _Name tecmag _Version libra loop_ _Task collection stop_ _Details tecmag save_ save_FELIX _Saveframe_category software _Name FELIX _Version 97 loop_ _Task processing stop_ _Details MSI save_ save_SCWRL _Saveframe_category software _Name SCWRL _Version 2.1 loop_ _Task refinement stop_ _Details 'Dunbrack, R.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer homebuilt _Model . _Field_strength 550 _Details . save_ ############################# # NMR applied experiments # ############################# save_PISEMA-Polarization_1 _Saveframe_category NMR_applied_experiment _Experiment_name PISEMA-Polarization _Sample_label $sample_1 save_ save_Inversion_and_Spin_Exchange_at_the_Magic_Angle_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'Inversion and Spin Exchange at the Magic Angle' _Sample_label $sample_1 save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name PISEMA-Polarization _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'Inversion and Spin Exchange at the Magic Angle' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details ; at the concentration used for the experiment, 50 mg/ml, the virus particles orient spontaneously in the magnetic field ; loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 8.0 0.2 na temperature 338 1 K pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis AMS N 15 ammonium ppm 26.8 external direct cylindrical external_to_the_sample perpendicular_to_Bo stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label PISEMA-Polarization 'Inversion and Spin Exchange at the Magic Angle' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'p8 monomer' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 7 ALA N N 179.4 . 1 2 . 8 LYS N N 217 . 1 3 . 9 ALA N N 219.6 . 1 4 . 10 ALA N N 159.5 . 1 5 . 11 PHE N N 197.2 . 1 6 . 12 ASP N N 216.7 . 1 7 . 13 SER N N 172.3 . 1 8 . 14 LEU N N 183.5 . 1 9 . 15 GLN N N 216.5 . 1 10 . 16 ALA N N 217.9 . 1 11 . 17 SER N N 169.8 . 1 12 . 18 ALA N N 200 . 1 13 . 19 THR N N 211.5 . 1 14 . 20 GLU N N 203.8 . 1 15 . 21 MET N N 179 . 1 16 . 22 ILE N N 199 . 1 17 . 23 GLY N N 211.8 . 1 18 . 24 TYR N N 190.4 . 1 19 . 25 ALA N N 175 . 1 20 . 26 TRP N N 207.7 . 1 21 . 27 ALA N N 214.6 . 1 22 . 28 MET N N 166.2 . 1 23 . 29 VAL N N 185.3 . 1 24 . 30 VAL N N 217 . 1 25 . 31 VAL N N 210 . 1 26 . 32 ILE N N 164 . 1 27 . 33 VAL N N 193.2 . 1 28 . 34 GLY N N 216 . 1 29 . 35 ALA N N 192 . 1 30 . 36 THR N N 159.6 . 1 31 . 37 ILE N N 202 . 1 32 . 38 GLY N N 210.8 . 1 33 . 39 ILE N N 209.2 . 1 34 . 40 LYS N N 201.5 . 1 35 . 41 LEU N N 216.6 . 1 36 . 42 PHE N N 229 . 1 37 . 43 LYS N N 206.3 . 1 38 . 44 LYS N N 192.5 . 1 39 . 45 PHE N N 215.7 . 1 40 . 46 THR N N 210.5 . 1 41 . 47 SER N N 196.2 . 1 42 . 48 LYS N N 190.2 . 1 43 . 49 ALA N N 205.4 . 1 stop_ save_ save_Dipolar_couplings _Saveframe_category residual_dipolar_couplings loop_ _Sample_label $sample_1 stop_ _Details . _Sample_conditions_label $sample_cond_1 _Spectrometer_frequency_1H 550 _Text_data_format . _Text_data . loop_ _Residual_dipolar_coupling_ID _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name _Residual_dipolar_coupling_value _Atom_one_mol_system_component_name _Atom_two_mol_system_component_name _Residual_dipolar_coupling_min_value _Residual_dipolar_coupling_max_value _Residual_dipolar_coupling_value_error 1DHN 7 ALA H 7 ALA N 2.7 ? ? . . . 1DHN 8 LYS H 8 LYS N 7.1 ? ? . . . 1DHN 9 ALA H 9 ALA N 10.1 ? ? . . . 1DHN 10 ALA H 10 ALA N 5.6 ? ? . . . 1DHN 11 PHE H 11 PHE N 4 ? ? . . . 1DHN 12 ASP H 12 ASP N 8.6 ? ? . . . 1DHN 13 SER H 13 SER N 9.1 ? ? . . . 1DHN 14 LEU H 14 LEU N 5.1 ? ? . . . 1DHN 15 GLN H 15 GLN N 6.3 ? ? . . . 1DHN 16 ALA H 16 ALA N 9.7 ? ? . . . 1DHN 17 SER H 17 SER N 8.3 ? ? . . . 1DHN 18 ALA H 18 ALA N 5.3 ? ? . . . 1DHN 19 THR H 19 THR N 7.5 ? ? . . . 1DHN 20 GLU H 20 GLU N 9.9 ? ? . . . 1DHN 21 MET H 21 MET N 7.6 ? ? . . . 1DHN 22 ILE H 22 ILE N 4.3 ? ? . . . 1DHN 23 GLY H 23 GLY N 7.1 ? ? . . . 1DHN 24 TYR H 24 TYR N 9.3 ? ? . . . 1DHN 25 ALA H 25 ALA N 6 ? ? . . . 1DHN 26 TRP H 26 TRP N 5.4 ? ? . . . 1DHN 27 ALA H 27 ALA N 9.5 ? ? . . . 1DHN 28 MET H 28 MET N 7.9 ? ? . . . 1DHN 29 VAL H 29 VAL N 5.4 ? ? . . . 1DHN 30 VAL H 30 VAL N 6 ? ? . . . 1DHN 31 VAL H 31 VAL N 9.9 ? ? . . . 1DHN 32 ILE H 32 ILE N 7.7 ? ? . . . 1DHN 33 VAL H 33 VAL N 4.9 ? ? . . . 1DHN 34 GLY H 34 GLY N 8.4 ? ? . . . 1DHN 35 ALA H 35 ALA N 9.6 ? ? . . . 1DHN 36 THR H 36 THR N 7.5 ? ? . . . 1DHN 37 ILE H 37 ILE N 5.6 ? ? . . . 1DHN 38 GLY H 38 GLY N 8.5 ? ? . . . 1DHN 39 ILE H 39 ILE N 10.3 ? ? . . . 1DHN 40 LYS H 40 LYS N 8.5 ? ? . . . 1DHN 41 LEU H 41 LEU N 6.9 ? ? . . . 1DHN 42 PHE H 42 PHE N 9.5 ? ? . . . 1DHN 43 LYS H 43 LYS N 10 ? ? . . . 1DHN 44 LYS H 44 LYS N 8 ? ? . . . 1DHN 45 PHE H 45 PHE N 8 ? ? . . . 1DHN 46 THR H 46 THR N 9.6 ? ? . . . 1DHN 47 SER H 47 SER N 9.6 ? ? . . . 1DHN 48 LYS H 48 LYS N 7.9 ? ? . . . 1DHN 49 ALA H 49 ALA N 7.7 ? ? . . . stop_ save_