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- PDB-6axs: Structure of the V11I/T58A/P122A mutant of the HIV-1 capsid protein -

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Basic information

Entry
Database: PDB / ID: 6axs
TitleStructure of the V11I/T58A/P122A mutant of the HIV-1 capsid protein
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / V11I/T58A/P122A mutant
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding ...viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / ATP binding / membrane
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) ...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) / 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 / 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: 2.402 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: To be published
Title: Identification of a novel element in HIV-1 capsid critical for assembly and maturation
Authors: Novikova, M. / Gres, A.T. / Kirby, K.A. / Sarafianos, S.G. / Freed, E.O.
History
DepositionSep 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)27,07017
Polymers25,5881
Non-polymers1,48216
Water1,27971
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)162,421102
Polymers153,5306
Non-polymers8,89196
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 area28160 Å2
ΔGint-505 kcal/mol
Surface area60290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.475, 92.475, 57.675
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: 25588.389 Da / Num. of mol.: 1 / Fragment: UNP residues 133-363 / Mutation: V11I, T58A, 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


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.79 % / Mosaicity: 0.29 °
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: ALS / Beamline: 4.2.2 / Wavelength: 1.000032 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000032 Å / Relative weight: 1
ReflectionResolution: 2.4→36.076 Å / Num. obs: 10917 / % possible obs: 98.2 % / Redundancy: 10.5 % / Biso Wilson estimate: 48.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.025 / Rrim(I) all: 0.082 / Net I/σ(I): 20.7 / Num. measured all: 114114 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.498.80.78111400.8150.270.82998.1
8.99-57.689.90.042190.9970.0140.04294.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.36 Å36.08 Å
Translation5.36 Å36.08 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: pdbid 4XFX

4xfx


Resolution: 2.402→36.076 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.59
RfactorNum. reflection% reflection
Rfree0.2659 629 5.77 %
Rwork0.2284 --
obs0.2306 10897 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.72 Å2 / Biso mean: 61.0166 Å2 / Biso min: 27.21 Å2
Refinement stepCycle: final / Resolution: 2.402→36.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 16 71 1768
Biso mean--70.37 51.1 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041719
X-RAY DIFFRACTIONf_angle_d0.6332336
X-RAY DIFFRACTIONf_chiral_restr0.042262
X-RAY DIFFRACTIONf_plane_restr0.004303
X-RAY DIFFRACTIONf_dihedral_angle_d13.711054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4019-2.64360.34381520.28342594274699
2.6436-3.02590.34661530.288326042757100
3.0259-3.81170.28271540.24272416257093
3.8117-36.07970.22451700.19552654282499
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)
10.2343-0.09640.09490.21290.10670.11280.0279-0.05730.4212-0.097-0.0144-0.1483-0.65540.42770.00020.3962-0.033-0.03780.38430.12240.69321.6199-15.86551.6231
20.4086-0.2086-0.37760.1727-0.00190.6377-0.26070.1541-0.03120.3448-0.0670.05160.26680.0722-0.00250.4510.01980.03130.28640.05920.3771-3.5972-30.63015.3942
30.91990.2276-0.48420.59720.33620.0836-0.00630.0224-0.10580.1369-0.1716-0.0301-0.0903-0.0533-0.00010.43030.0452-0.01890.37750.09490.31866.0565-28.04393.1561
40.01390.0186-0.04660.0705-0.08040.10890.1846-0.3781-0.01680.7144-0.0425-0.59-0.6758-0.02930.00050.49170.1188-0.01480.41180.11330.477924.0251-35.1835-5.0799
50.16050.0048-0.19220.14050.04320.2919-0.31310.2507-0.0906-0.09870.1618-0.16940.55311.243600.48730.16050.11460.70570.11640.474535.2059-26.148-14.5111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 44 )A1 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 87 )A45 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 175 )A88 - 175
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 189 )A176 - 189
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 221 )A190 - 221

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