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- PDB-6axv: Structure of the T58S/T107I/P122A mutant of the HIV-1 capsid prot... -

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Basic information

Entry
Database: PDB / ID: 6axv
TitleStructure of the T58S/T107I/P122A mutant of the HIV-1 capsid protein in complex with PF-3450074 (PF74)
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / T58S/T107I/P122A mutant / PF-3450074 (PF74) complex
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
Chem-1B0 / IODIDE ION / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.77 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 30, 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)26,98216
Polymers25,6021
Non-polymers1,37915
Water37821
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)161,88996
Polymers153,6146
Non-polymers8,27590
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 area27220 Å2
ΔGint-660 kcal/mol
Surface area60240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.998, 92.998, 57.631
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 / 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.: 5 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-1B0 / N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE


Mass: 425.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.81 Å3/Da / Density % sol: 56.23 % / Mosaicity: 0.24 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, Sodium cacosylate, 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 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.77→46.5 Å / Num. obs: 7089 / % possible obs: 95.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 63.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.034 / Rrim(I) all: 0.11 / Net I/σ(I): 19.1 / Num. measured all: 72267 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.77-2.927.80.9329210.7140.3410.99586.5
8.75-46.510.30.0352530.9980.0120.03798.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.43 Å46.5 Å
Translation5.43 Å46.5 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: 2.77→46.499 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.43
RfactorNum. reflection% reflection
Rfree0.2785 460 6.58 %
Rwork0.2279 --
obs0.2312 6994 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.28 Å2 / Biso mean: 67.3506 Å2 / Biso min: 26.87 Å2
Refinement stepCycle: final / Resolution: 2.77→46.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 46 21 1740
Biso mean--47.08 44.52 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031750
X-RAY DIFFRACTIONf_angle_d0.5732380
X-RAY DIFFRACTIONf_chiral_restr0.04263
X-RAY DIFFRACTIONf_plane_restr0.005307
X-RAY DIFFRACTIONf_dihedral_angle_d14.7861058
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7685-3.1690.31891470.30012140228794
3.169-3.99230.34781450.27792060220590
3.9923-46.50550.23351680.187523342502100
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)
10.4209-0.84120.66130.98010.05421.0285-0.0040.1454-0.2108-0.0149-0.2588-0.1251-0.59110.66980.00020.4561-0.1408-0.02360.49580.15430.80651.097-16.05620.7348
20.8774-0.6375-0.46261.03660.41312.3892-0.05520.03810.11490.1418-0.0639-0.23040.48330.55010.00010.33240.02210.02090.34880.06120.3886-3.5804-29.55553.4774
3-0.20980.1771-0.44440.0352-0.17860.3102-0.0775-0.27710.03640.0762-0.08990.10530.03680.2523-0.00020.7411-0.02340.11380.68080.08780.5205-8.0468-34.353322.729
43.4586-0.0371-0.42493.6111-3.3071.4609-0.6989-1.1039-0.35070.7731-0.0048-0.1177-0.1831.3494-0.0640.27570.0173-0.08680.643-0.04210.377-1.0897-27.472110.0738
50.95470.42231.11560.23230.11641.02240.24630.63240.2299-0.76210.05840.4240.2058-0.6408-0.04560.58370.0550.04860.4650.16510.365922.2034-26.8695-16.0339
60.17260.45020.00763.1893-0.45410.5580.1125-0.21140.2727-1.23240.50260.0760.778-0.28470.08940.18590.18330.10140.55580.2240.45124.7006-34.935-6.6279
71.25731.3093-0.71451.5119-0.02710.3665-0.2619-0.29870.3378-0.49570.4278-0.42690.34110.57330.01410.53370.20610.17260.8027-0.00720.626235.9633-25.4337-14.6518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )A1 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 83 )A44 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 104 )A84 - 104
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 145 )A105 - 145
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 174 )A146 - 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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