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- PDB-6wa3: Solution NMR structure of the myristoylated feline immunodeficien... -

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Basic information

Entry
Database: PDB / ID: 6wa3
TitleSolution NMR structure of the myristoylated feline immunodeficiency virus matrix protein
ComponentsMatrix protein
KeywordsVIRAL PROTEIN / FIV
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / viral capsid / viral nucleocapsid / structural constituent of virion / nucleic acid binding / zinc ion binding
Similarity search - Function
: / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
MYRISTIC ACID / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesFeline immunodeficiency virus
MethodSOLUTION NMR / na
AuthorsBrown, J.B. / Summers, H.R. / Brown, L.A. / Marchant, J. / Canova, P.N. / O'Hern, C.T. / Abbott, S. / Nyaunu, C. / Maxwell, S. / Johnson, T. ...Brown, J.B. / Summers, H.R. / Brown, L.A. / Marchant, J. / Canova, P.N. / O'Hern, C.T. / Abbott, S. / Nyaunu, C. / Maxwell, S. / Johnson, T. / Moser, M. / Ablan, S.D. / Carter, H. / Freed, E.O. / Summers, M.F.
Funding support United States, 9items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM066706 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM042561 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)IMSD R25 GM-055036-18 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM103297 United States
National Science Foundation (NSF, United States)DGE-1144243 United States
National Science Foundation (NSF, United States)1460653 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 AI30917 United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural and Mechanistic Studies of the Rare Myristoylation Signal of the Feline Immunodeficiency Virus.
Authors: Brown, J.B. / Summers, H.R. / Brown, L.A. / Marchant, J. / Canova, P.N. / O'Hern, C.T. / Abbott, S.T. / Nyaunu, C. / Maxwell, S. / Johnson, T. / Moser, M.B. / Ablan, S.D. / Carter, H. / ...Authors: Brown, J.B. / Summers, H.R. / Brown, L.A. / Marchant, J. / Canova, P.N. / O'Hern, C.T. / Abbott, S.T. / Nyaunu, C. / Maxwell, S. / Johnson, T. / Moser, M.B. / Ablan, S.D. / Carter, H. / Freed, E.O. / Summers, M.F.
History
DepositionMar 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.0May 17, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.label_seq_id / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_site_gen.label_seq_id
Revision 2.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 2.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9402
Polymers13,7121
Non-polymers2281
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area650 Å2
ΔGint4 kcal/mol
Surface area7630 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Matrix protein


Mass: 13711.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Gene: GAG / Production host: Escherichia coli (E. coli) / References: UniProt: Q66971, UniProt: P16087*PLUS
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
315isotropic12D 1H-1H NOESY
221isotropic12D 1H-15N HSQC
234isotropic13D CBCA(CO)NH
244isotropic13D HN(CA)CB
254isotropic13D HNCO
264isotropic13D HN(CA)CO
271isotropic13D 1H-15N NOESY
2114isotropic14D HSQC-NOESY-HMQC
3102isotropic14D HMQC-NOESY-HMQC
392isotropic12D 1H-13C HMQC
383isotropic12D 1H-13C HMQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution150 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-15N] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 90% H2O/10% D2O1H/15N90% H2O/10% D2O
solution250 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L ammonium chloride, 300 uM [U-13C] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 100% D2O1H/13C_1100% D2O
solution350 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L ammonium chloride, 50 mg/L Myristoyl coenzyme A, 300 uM [U-13C] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 100% D2O1H/13C_2100% D2O
solution450 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Feline Immunodeficiency Virus Myristoylated Matrix Protein, 90% H2O/10% D2O1H/15N/13C90% H2O/10% D2O
solution550 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 4 g/L glucose, 1 g/L ammonium chloride, 300 uM Feline Immunodeficiency Virus Myristoylated Matrix Protein, 100% D2O1H100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphatenatural abundance1
10 mMDTTnatural abundance1
5 mMsodium chloridenatural abundance1
4 g/Lglucosenatural abundance1
1 g/Lammonium chloride[U-99% 15N]1
300 uMFeline Immunodeficiency Virus Myristoylated Matrix Protein[U-15N]1
50 mMsodium phosphatenatural abundance2
10 mMDTT[U-98% 2H]2
5 mMsodium chloridenatural abundance2
4 g/Lglucose[U-99% 13C]2
1 g/Lammonium chloridenatural abundance2
300 uMFeline Immunodeficiency Virus Myristoylated Matrix Protein[U-13C]2
50 mMsodium phosphatenatural abundance3
10 mMDTT[U-98% 2H]3
5 mMsodium chloridenatural abundance3
4 g/Lglucose[U-99% 13C]3
1 g/Lammonium chloridenatural abundance3
50 mg/LMyristoyl coenzyme Anatural abundance3
300 uMFeline Immunodeficiency Virus Myristoylated Matrix Protein[U-13C]3
50 mMsodium phosphatenatural abundance4
10 mMDTTnatural abundance4
5 mMsodium chloridenatural abundance4
4 g/Lglucose[U-99% 13C]4
1 g/Lammonium chloride[U-99% 15N]4
300 uMFeline Immunodeficiency Virus Myristoylated Matrix Protein[U-13C; U-15N]4
50 mMsodium phosphatenatural abundance5
10 mMDTT[U-98% 2H]5
5 mMsodium chloridenatural abundance5
4 g/Lglucosenatural abundance5
1 g/Lammonium chloridenatural abundance5
300 uMFeline Immunodeficiency Virus Myristoylated Matrix Proteinnatural abundance5
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
25 mMconditions_181 atm298 K
35 mMconditions_28 pD1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRFxJohnson, One Moon Scientificprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
NMRViewJohnson, One Moon Scientificpeak picking
TopSpinBruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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