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- PDB-6axt: Structure of the T58S/T107I/P122A mutant of the HIV-1 capsid protein -

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Basic information

Entry
Database: PDB / ID: 6axt
TitleStructure of the T58S/T107I/P122A mutant of the HIV-1 capsid protein
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / T58S/T107I/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: 2.4 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: 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

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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)26,95716
Polymers25,6021
Non-polymers1,35515
Water73941
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)161,74496
Polymers153,6146
Non-polymers8,12990
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 area29720 Å2
ΔGint-471 kcal/mol
Surface area58760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.407, 92.407, 57.509
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: 25602.416 Da / Num. of mol.: 1 / Fragment: UNP residues 133-363 / Mutation: T58S, T107I, 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.: 9 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.77 Å3/Da / Density % sol: 55.57 % / Mosaicity: 0.21 °
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: APS / Beamline: 23-ID-B / Wavelength: 1.03376 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03376 Å / Relative weight: 1
ReflectionResolution: 2.4→46.7 Å / Num. obs: 10448 / % possible obs: 94.1 % / Redundancy: 8.3 % / Biso Wilson estimate: 60.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.026 / Rrim(I) all: 0.075 / Net I/σ(I): 17.7 / Num. measured all: 86620 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.498.11.31310990.490.491.40695.2
8.98-46.77.60.0422050.9980.0160.04688.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.4 Å46.7 Å
Translation2.4 Å46.7 Å

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
Blu-Icedata collection
PHENIX1.11.1-2575_1692refinement
PDB_EXTRACT3.22data extraction
Aimless0.5.17data reduction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 2.4→46.7 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.55
RfactorNum. reflection% reflection
Rfree0.2433 500 4.79 %
Rwork0.2237 --
obs0.2247 10446 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.51 Å2 / Biso mean: 79.5318 Å2 / Biso min: 37.8 Å2
Refinement stepCycle: final / Resolution: 2.4→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 15 41 1746
Biso mean--92.03 67.19 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021732
X-RAY DIFFRACTIONf_angle_d0.4742354
X-RAY DIFFRACTIONf_chiral_restr0.038264
X-RAY DIFFRACTIONf_plane_restr0.004305
X-RAY DIFFRACTIONf_dihedral_angle_d9.1931066
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 (%)
2.4003-2.64190.32961310.30112505263696
2.6419-3.02410.31361040.29112519262395
3.0241-3.80980.25081240.24332465258994
3.8098-46.70990.21941410.18982457259892
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)
10.12860.29660.08250.1409-0.3105-0.00771.9205-0.7484-0.79532.33071.212.1615-0.8441-0.46470.0071.40030.09680.02110.89260.08690.9478-1.5768-12.369615.2179
20.5819-0.77650.2860.25790.58441.0173-0.1660.72470.8323-0.0214-0.0268-0.285-0.75330.0146-0.00010.5363-0.0047-0.03560.74920.11850.85852.8479-17.0688-3.4882
31.2666-0.4759-0.32622.262-0.00581.9868-0.22560.06860.17070.464-0.1787-0.16730.4836-0.04680.00010.4866-0.020.06730.42180.04090.4868-3.5287-29.54933.2584
4-0.16510.2833-0.417-0.08540.02691.760.002-0.3633-0.47820.5642-0.12540.1524-0.6407-0.152501.0798-0.07080.00040.67570.01390.6014-6.7039-29.426320.5225
51.4047-0.4302-0.99520.9511.67931.9562-0.19340.5552-0.3343-0.1698-0.10410.05290.0079-0.4557-0.00010.50680.0447-0.00360.58780.14420.574814.3696-28.0746-8.953
60.02290.3111-0.09011.0978-0.06150.25420.346-0.36211.20630.4299-0.0709-0.24560.76690.7160.00040.62760.1569-0.01940.71750.08510.717524.349-34.6305-6.9274
70.96380.0422-1.47791.1527-0.22240.7817-0.30220.02370.2965-0.5845-0.0636-0.21450.41461.7209-0.00120.63650.18240.06991.0360.11670.650235.7375-25.3444-15.0095
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 44 )A17 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 83 )A45 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 125 )A84 - 125
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 174 )A126 - 174
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 192 )A175 - 192
7X-RAY DIFFRACTION7chain 'A' and (resid 193 through 221 )A193 - 221

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