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- PDB-6axw: Structure of the I124A mutant of the HIV-1 capsid protein -

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Basic information

Entry
Database: PDB / ID: 6axw
TitleStructure of the I124A mutant of the HIV-1 capsid protein
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / I124A mutant
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane ...viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain ...Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsGres, A.T. / Kirby, K.A. / Sarafianos, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120860 United States
CitationJournal: MBio / Year: 2018
Title: Identification of a Structural Element in HIV-1 Gag Required for Virus Particle Assembly and Maturation.
Authors: Novikova, M. / Adams, L.J. / Fontana, J. / Gres, A.T. / Balasubramaniam, M. / Winkler, D.C. / Kudchodkar, S.B. / Soheilian, F. / Sarafianos, S.G. / Steven, A.C. / Freed, E.O.
History
DepositionSep 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 14, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,97220
Polymers25,4751
Non-polymers1,49719
Water2,846158
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)161,831120
Polymers152,8516
Non-polymers8,980114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area31950 Å2
ΔGint-741 kcal/mol
Surface area59990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.611, 92.611, 57.954
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein HIV-1 capsid protein


Mass: 25475.188 Da / Num. of mol.: 1 / Fragment: UNP residues 133-362 / Mutation: I124A
Source method: isolated from a genetically manipulated source
Details: 469008 / Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6DRA0, UniProt: P12493*PLUS
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.32 % / Mosaicity: 0.19 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, MIB, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000031 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.4→57.95 Å / Num. obs: 10933 / % possible obs: 97.2 % / Redundancy: 10.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.036 / Rrim(I) all: 0.119 / Net I/σ(I): 15.8 / Num. measured all: 115437 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.498.40.7511360.8080.2670.79796.8
8.97-57.9510.10.0552330.9980.0190.05898.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.44 Å46.31 Å
Translation5.44 Å46.31 Å

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
Blu-Icedata collection
REFMACREFMAC 5.8.0158refinement
PDB_EXTRACT3.22data extraction
Aimless0.5.31data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 2.4→57.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 15.102 / SU ML: 0.188 / SU R Cruickshank DPI: 0.3839 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.248
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 644 5.9 %RANDOM
Rwork0.1894 ---
obs0.1925 10280 97.05 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 94.82 Å2 / Biso mean: 48.192 Å2 / Biso min: 22.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å2-0 Å2
2--0.44 Å20 Å2
3----1.44 Å2
Refinement stepCycle: final / Resolution: 2.4→57.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1660 0 19 158 1837
Biso mean--62.6 47.28 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191722
X-RAY DIFFRACTIONr_bond_other_d0.0020.021612
X-RAY DIFFRACTIONr_angle_refined_deg1.061.9592348
X-RAY DIFFRACTIONr_angle_other_deg0.88133760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0235219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48524.59574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50515298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5791511
X-RAY DIFFRACTIONr_chiral_restr0.0550.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02319
X-RAY DIFFRACTIONr_sphericity_free34.62757
X-RAY DIFFRACTIONr_sphericity_bonded30.535512
LS refinement shellResolution: 2.398→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 37 -
Rwork0.238 740 -
all-777 -
obs--95.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0754-1.1363-0.64185.74041.30984.3733-0.0871-0.00570.33970.322-0.03550.0533-0.2093-0.30410.12260.055-0.0007-0.01520.0468-0.00250.24571.3088-16.09010.2323
22.3543-1.01090.15512.6476-0.59384.7202-0.1921-0.1569-0.04320.22450.14110.07610.25730.02260.0510.0643-0.00790.02060.057-0.00910.2002-3.4911-30.31464.7782
31.54121.3876-2.39341.5566-2.13248.09870.2613-0.2601-0.00880.4864-0.06250.076-0.3963-0.1919-0.19880.25340.09960.06330.22990.05250.111-6.7507-28.663220.8646
45.6157-0.7139-5.76611.10110.96076.1438-0.13350.091-0.1267-0.04640.03990.07060.16710.00310.09360.04490.0143-0.00620.05760.01420.14637.3994-30.7698-3.0681
56.5451-0.0516-3.42932.582-0.29327.8998-0.03530.0942-0.0608-0.17350.02950.12660.30570.19350.00580.11410.0296-0.04460.02910.01710.127423.0079-25.6323-15.6444
613.94676.9358-11.96969.1959-5.504414.13130.20790.4850.32370.6468-0.382-0.2176-0.10510.38790.17410.24210.0455-0.05150.31540.1470.10724.8565-35.3704-4.7977
78.9170.4784-0.04772.38852.51984.4838-0.12340.15020.0302-0.15220.2183-0.1109-0.04090.3568-0.09490.05870.05910.02460.13860.03430.132535.018-26.6097-14.7478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A44 - 86
3X-RAY DIFFRACTION3A87 - 126
4X-RAY DIFFRACTION4A127 - 153
5X-RAY DIFFRACTION5A154 - 176
6X-RAY DIFFRACTION6A177 - 188
7X-RAY DIFFRACTION7A189 - 220

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