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- PDB-6axr: Structure of the P122A mutant of the HIV-1 capsid protein -

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Basic information

Entry
Database: PDB / ID: 6axr
TitleStructure of the P122A mutant of the HIV-1 capsid protein
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / P122A 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 / virion membrane / structural molecule activity ...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 / virion membrane / structural molecule activity / RNA binding / zinc ion 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: 2.3 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)26,79714
Polymers25,6041
Non-polymers1,19213
Water93752
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)160,78184
Polymers153,6266
Non-polymers7,15578
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 area27050 Å2
ΔGint-424 kcal/mol
Surface area60010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.728, 92.728, 57.791
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: 25604.389 Da / Num. of mol.: 1 / Fragment: UNP residues 133-363 / Mutation: P122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / 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 / Iodide


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.8 Å3/Da / Density % sol: 56.09 % / Mosaicity: 0.15 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, Sodium cacodylate, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033203 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033203 Å / Relative weight: 1
ReflectionResolution: 2.3→46.91 Å / Num. obs: 12735 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 59.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.028 / Rrim(I) all: 0.066 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.385.60.63312510.8330.2930.699100
8.91-46.915.50.0462410.9980.0220.05199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.43 Å46.91 Å
Translation5.43 Å46.91 Å

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
Blu-Icedata collection
PHENIX1.11.1-2575_1692refinement
PDB_EXTRACT3.22data extraction
Aimless0.5.32data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 2.3→46.907 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.95
RfactorNum. reflection% reflection
Rfree0.2678 704 5.53 %
Rwork0.2398 --
obs0.2415 12730 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.3 Å2 / Biso mean: 77.7982 Å2 / Biso min: 44.95 Å2
Refinement stepCycle: final / Resolution: 2.3→46.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 13 52 1747
Biso mean--79.77 69.94 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021719
X-RAY DIFFRACTIONf_angle_d0.5082336
X-RAY DIFFRACTIONf_chiral_restr0.039263
X-RAY DIFFRACTIONf_plane_restr0.004303
X-RAY DIFFRACTIONf_dihedral_angle_d9.4241051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3002-2.47780.34671330.328124062539
2.4778-2.72720.33221670.31623602527
2.7272-3.12170.35821200.324124002520
3.1217-3.93270.29081200.25324212541
3.9327-46.9170.22961640.195124392603
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)
1-0.02370.11850.1707-0.1581-0.0911-0.06920.82090.0358-0.20450.51911.13131.2549-0.13670.2058-00.92250.1703-0.03410.83330.0791.0207-1.8018-12.487814.5997
20.28590.58160.02730.33990.29280.9301-0.1380.18650.8236-0.3293-0.2073-0.3378-0.09920.221-00.51240.0042-0.03080.54840.1010.97712.6556-17.0861-3.6022
30.1679-0.40350.27690.8304-0.52210.3381-0.35680.1370.4310.16340.1464-0.05070.17090.191600.50570.0229-0.09780.44770.04120.543-4.2064-21.01843.4166
40.2352-0.6113-0.5210.23940.15560.4546-0.63010.24550.1889-0.15790.0494-0.27771.3958-0.213100.67590.04870.16310.39870.05820.5059-2.8236-36.04623.9791
5-0.203-0.0886-0.27420.1825-0.15770.06010.1828-0.3806-0.01010.061-0.4299-0.0567-0.03240.1474-00.84450.00070.08810.65230.01130.5709-7.739-34.188522.9608
61.52620.6103-0.12242.8932-2.37981.3553-0.29130.01230.25250.6671-0.2541-0.4091-0.35150.104300.50260.0545-0.0810.4936-0.00630.481-0.6324-27.492510.3116
7-0.0875-0.2719-0.1843-0.16180.11520.60260.09731.03330.2611-0.20410.32070.14320.2964-0.678-00.84270.00190.09690.77950.07390.589121.8761-29.4359-19.6125
80.3577-0.19410.25410.06570.31450.63140.06380.20070.2252-0.418-0.52690.19070.2205-0.0354-00.69690.06470.09040.4580.09780.506221.7736-25.3484-12.6665
90.16940.95580.28551.11480.04230.3693-0.37170.1059-0.12060.29150.3738-0.42810.3064-0.1963-00.84310.28360.13950.68320.09610.688225.2801-34.6658-6.4998
100.61430.2553-0.79030.3725-0.04650.3362-0.57830.17910.1222-0.5802-0.03510.2033-0.03030.9225-00.71760.23030.08210.87990.12970.629235.9302-25.5467-14.5583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 43 )A17 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 62 )A44 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 83 )A63 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 104 )A84 - 104
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 145 )A105 - 145
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 160 )A146 - 160
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 175 )A161 - 175
9X-RAY DIFFRACTION9chain 'A' and (resid 176 through 192 )A176 - 192
10X-RAY DIFFRACTION10chain 'A' and (resid 193 through 221 )A193 - 221

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