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- PDB-7qdf: Hexameric HIV-1 (M-group) CA R120 mutant -

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Basic information

Entry
Database: PDB / ID: 7qdf
TitleHexameric HIV-1 (M-group) CA R120 mutant
ComponentsGag polyproteinGroup-specific antigen
KeywordsVIRAL PROTEIN / HIV-1 CAPSID PROTEIN / HEXAMER / R120 MUTANT
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / 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 ...Gag protein p6 / Gag protein p6 / 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.
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsGovasli, M.A.L. / Pinotsis, N. / McAlpine-Scott, S.
Funding support Australia, United Kingdom, European Union, 6items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP180101384 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1158338 Australia
Wellcome Trust214344/Z/18/Z United Kingdom
Wellcome Trust108183 United Kingdom
Wellcome Trust220863 United Kingdom
European Research Council (ERC)339223European Union
CitationJournal: Nat Microbiol / Year: 2022
Title: Evasion of cGAS and TRIM5 defines pandemic HIV.
Authors: Zuliani-Alvarez, L. / Govasli, M.L. / Rasaiyaah, J. / Monit, C. / Perry, S.O. / Sumner, R.P. / McAlpine-Scott, S. / Dickson, C. / Rifat Faysal, K.M. / Hilditch, L. / Miles, R.J. / Bibollet- ...Authors: Zuliani-Alvarez, L. / Govasli, M.L. / Rasaiyaah, J. / Monit, C. / Perry, S.O. / Sumner, R.P. / McAlpine-Scott, S. / Dickson, C. / Rifat Faysal, K.M. / Hilditch, L. / Miles, R.J. / Bibollet-Ruche, F. / Hahn, B.H. / Boecking, T. / Pinotsis, N. / James, L.C. / Jacques, D.A. / Towers, G.J.
History
DepositionNov 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2979
Polymers25,7881
Non-polymers5098
Water25214
1
AAA: Gag polyprotein
hetero molecules
x 6


  • defined by author&software
  • Evidence: electron microscopy
  • 158 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)157,78154
Polymers154,7266
Non-polymers3,05548
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 area23930 Å2
ΔGint-469 kcal/mol
Surface area63850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.360, 92.360, 57.440
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 Gag polyprotein / Group-specific antigen / Pr55Gag


Mass: 25787.621 Da / Num. of mol.: 1 / Mutation: R120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Strain: isolate NY5 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P12493
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


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


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


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.23 % / Description: hexagonal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9.5% PEG 3350 (v/v), 310 mM NaI, 100 mM Sodium Cacodylate. Crystals grew in 1 uL protein (3 mg/mL) + 1 uL crystallant. Cryoprotected in 20% (v/v) Glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.9178
pseudo-merohedral22-K, -H, -L20.0822
ReflectionResolution: 2.304→79.98 Å / Num. obs: 12346 / % possible obs: 98.4 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rrim(I) all: 0.071 / Net I/σ(I): 10.76
Reflection shellResolution: 2.304→2.44 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1951 / CC1/2: 0.503

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 2.304→46.656 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 16.695 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.054 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2775 578 4.708 %
Rwork0.2423 11698 -
all0.244 --
obs-12276 98.397 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 93.332 Å2
Baniso -1Baniso -2Baniso -3
1--5.699 Å2-0 Å2-0 Å2
2---5.699 Å2-0 Å2
3---11.398 Å2
Refinement stepCycle: LAST / Resolution: 2.304→46.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 11 14 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121791
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.6462437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.435227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95923.06888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.02315310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0621511
X-RAY DIFFRACTIONr_chiral_restr0.1410.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021357
X-RAY DIFFRACTIONr_nbd_refined0.3010.2883
X-RAY DIFFRACTIONr_nbtor_refined0.3310.21252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.250
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4050.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4490.24
X-RAY DIFFRACTIONr_mcbond_it6.1477.436902
X-RAY DIFFRACTIONr_mcangle_it8.90311.121131
X-RAY DIFFRACTIONr_scbond_it6.8137.472889
X-RAY DIFFRACTIONr_scangle_it9.55811.111306
X-RAY DIFFRACTIONr_lrange_it14.589135.5787519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.304-2.3640.408340.321875X-RAY DIFFRACTION99.2358
2.364-2.4290.377410.291835X-RAY DIFFRACTION99.5454
2.429-2.4990.315410.309838X-RAY DIFFRACTION99.8864
2.499-2.5760.301420.329786X-RAY DIFFRACTION99.3998
2.576-2.660.313430.342762X-RAY DIFFRACTION99.8759
2.66-2.7530.359370.336756X-RAY DIFFRACTION99.7484
2.753-2.8560.357210.309733X-RAY DIFFRACTION99.3412
2.856-2.9730.375340.306696X-RAY DIFFRACTION99.5907
2.973-3.1040.346340.294671X-RAY DIFFRACTION98.878
3.104-3.2550.416260.305637X-RAY DIFFRACTION98.5141
3.255-3.430.282300.286608X-RAY DIFFRACTION98.7616
3.43-3.6370.293280.269572X-RAY DIFFRACTION98.3606
3.637-3.8860.285280.235537X-RAY DIFFRACTION98.2609
3.886-4.1950.328230.219500X-RAY DIFFRACTION97.0315
4.195-4.5920.224260.185451X-RAY DIFFRACTION97.1487
4.592-5.1280.192230.221411X-RAY DIFFRACTION97.0917
5.128-5.9090.329230.228360X-RAY DIFFRACTION96.7172
5.909-7.2080.169240.208305X-RAY DIFFRACTION94.2693
7.208-10.0750.196120.173232X-RAY DIFFRACTION91.3858
10.075-46.6560.33380.214133X-RAY DIFFRACTION83.9286
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)
10.8419-0.84551.71463.0242-2.74894.02140.01880.12480.2241-0.168-0.24930.46860.07880.33170.23050.037-0.0176-0.06460.0716-0.00560.503111.9824-8.1146-3.0845
21.8459-1.0512-0.23641.2063-0.37043.01110.12090.2046-0.1234-0.1121-0.3480.18070.10110.20170.22710.07330.0162-0.00260.123-0.02390.205527.7638-11.3065-8.5127
31.09042.48142.18886.95146.69116.6754-0.27390.2966-0.1917-0.6434-0.03740.0816-0.4617-0.35090.31120.3513-0.04830.10140.5787-0.21930.387822.5353-6.9005-19.7465
41.7891.5924-1.55791.651-1.5552.4388-0.0114-0.1787-0.0995-0.0072-0.0506-0.06660.27310.25880.0620.20660.06090.05310.11-0.01520.186114.2172-32.71279.1639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 36
2X-RAY DIFFRACTION2ALLAAA37 - 110
3X-RAY DIFFRACTION3ALLAAA111 - 121
4X-RAY DIFFRACTION4ALLAAA122 - 222

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