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- PDB-9rpc: HIV-1 capsid (M-group) - native -

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Basic information

Entry
Database: PDB / ID: 9rpc
TitleHIV-1 capsid (M-group) - native
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / Hexameric HIV-1 (M-group)
Function / homology
Function and homology information


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
Similarity search - Function
: / 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 ...: / 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 knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.969 Å
AuthorsGovasli, M.A.L. / Pinotsis, N. / Towers, G. / Selwood, D. / Jacques, D.A.
Funding support United Kingdom, European Union, Australia, 4items
OrganizationGrant numberCountry
Wellcome Trust220863 United Kingdom
Wellcome Trust214344 United Kingdom
European Research Council (ERC)339223European Union
National Health and Medical Research Council (NHMRC, Australia)GNT2013215 Australia
CitationJournal: To Be Published
Title: Cofactor-mimicking HIV-1 capsid inhibitors, and their escape mutants, drive innate immune sensing
Authors: Govasli, M.A.L. / Pinotsis, N. / Towers, G. / Selwood, D. / Jacques, D.A.
History
DepositionJun 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,17510
Polymers25,6301
Non-polymers5459
Water1,17165
1
A: Gag polyprotein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)157,05160
Polymers153,7836
Non-polymers3,26854
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 area25600 Å2
ΔGint-544 kcal/mol
Surface area63040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.46, 92.46, 57.76
Angle α, β, γ (deg.)90, 90, 120
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Gag polyprotein


Mass: 25630.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6DRA0
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / 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: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 55.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9.5-11% PEG 3350 (v/v), 250-350 mM NaI, 100 mM Sodium Cacodylate [pH 6.5]. Crystals grew in 1 uL protein (3 mg/mL) + 1 uL crystallant. Cryoprotected in 20% (v/v) Glycerol.
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.97→80.07 Å / Num. obs: 18549 / % possible obs: 92.4 % / Redundancy: 19.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.2
Reflection shellResolution: 1.97→2 Å / Num. unique obs: 1004 / CC1/2: 0.396

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
autoPROC1.0.5 (20200319)data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.969→80.07 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.188 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.278 997 -RANDOM
Rwork0.2329 ---
obs0.2352 18541 92.3 %-
Displacement parametersBiso mean: 59.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.1243 Å20 Å20 Å2
2---2.1243 Å20 Å2
3---4.2486 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 1.969→80.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 12 65 1802
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081811HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.972464HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d636SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes308HARMONIC5
X-RAY DIFFRACTIONt_it1811HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion241SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1527SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion17.23
LS refinement shellResolution: 1.97→1.98 Å
RfactorNum. reflection% reflection
Rfree0.1731 20 -
Rwork0.1936 --
obs0.1925 379 99.46 %
Refinement TLS params.

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)
12.79150.72810.12971.10840.66110-0.24710.0850.2340.0850.0120.06740.2340.06740.235-0.157-0.0295-0.0323-0.02640.08960.2725-14.9146-8.3053-3.3112
20.34580.25890.58960.91361.45138.3155-0.24520.04370.15950.0437-0.2025-0.10190.1595-0.10190.4477-0.1058-0.04280.05470.0819-0.0622-0.0057-25.4924-18.0215-12.5004
31.4137-1.3352-1.20763.69890.81132.0626-0.07810.3456-0.07770.34560.0391-0.5591-0.0777-0.55910.039-0.1349-0.01810.01250.211-0.0854-0.0551-37.81238.673413.4532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|62}
2X-RAY DIFFRACTION2{ A|63 - A|142}
3X-RAY DIFFRACTION3{ A|143 - A|221}

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