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- PDB-5w4q: Structure of the R18A/E28A mutant of the HIV-1 capsid protein -

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Basic information

Entry
Database: PDB / ID: 5w4q
TitleStructure of the R18A/E28A mutant of the HIV-1 capsid protein
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / capsid protein
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: 2.285 Å
AuthorsGres, A.T. / Kirby, K.A. / Sarafianos, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103368 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120860 United States
CitationJournal: MBio / Year: 2019
Title: Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket.
Authors: Craveur, P. / Gres, A.T. / Kirby, K.A. / Liu, D. / Hammond, J.A. / Deng, Y. / Forli, S. / Goodsell, D.S. / Williamson, J.R. / Sarafianos, S.G. / Olson, A.J.
History
DepositionJun 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

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Assembly

Deposited unit
A: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,62315
Polymers25,4861
Non-polymers1,13614
Water1,67593
1
A: Capsid protein p24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)159,73790
Polymers152,9186
Non-polymers6,81984
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 area26470 Å2
ΔGint-528 kcal/mol
Surface area61860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.055, 92.055, 58.253
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 Capsid protein p24 /


Mass: 25486.273 Da / Num. of mol.: 1 / Fragment: residues 133-363 / Mutation: R18A, E28A
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.: 7 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.8 Å3/Da / Density % sol: 56 % / Mosaicity: 0.12 °
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: APS / Beamline: 23-ID-B / Wavelength: 1.033203 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033203 Å / Relative weight: 1
ReflectionResolution: 2.28→47.034 Å / Num. obs: 12728 / % possible obs: 98.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 52.57 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.035 / Rrim(I) all: 0.083 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.28-2.365.60.93697712460.5790.4281.02698.1
8.85-47.035.30.0390.9950.020.04499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.43 Å47.03 Å
Translation5.43 Å47.03 Å

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASER2.7.17phasing
PHENIX(1.11.1-2575_1692)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4XFX

4xfx


Resolution: 2.285→47.03 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.96
RfactorNum. reflection% reflection
Rfree0.2452 713 5.6 %
Rwork0.2057 --
obs0.208 12722 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.48 Å2 / Biso mean: 61.2915 Å2 / Biso min: 26.83 Å2
Refinement stepCycle: final / Resolution: 2.285→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 14 93 1786
Biso mean--71.58 59.01 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031727
X-RAY DIFFRACTIONf_angle_d0.5642354
X-RAY DIFFRACTIONf_chiral_restr0.04267
X-RAY DIFFRACTIONf_plane_restr0.004305
X-RAY DIFFRACTIONf_dihedral_angle_d14.4581060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2854-2.46180.39611510.355823972548100
2.4618-2.70950.30721610.250924052566100
2.7095-3.10160.24911230.225624262549100
3.1016-3.90730.26461140.19632317243194
3.9073-47.04440.21081640.180224642628100
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)
13.2258-0.473-0.60430.0890.08670.11370.5628-1.3020.05131.30450.2875-0.4649-0.47760.66760.07130.812-0.0755-0.14630.7720.09170.6979-2.0368-12.406315.7203
2-0.002-0.0056-0.00390.1425-0.04020.2004-0.07940.10710.5455-0.3354-0.2499-0.51570.20030.2229-0.00430.3165-0.01630.04170.32830.02420.59812.8266-17.3178-3.6249
30.0376-0.0660.02170.14170.01440.0455-0.13850.13590.2324-0.02020.13090.0052-0.28540.15060.00010.4052-0.0099-0.03280.2884-0.0150.4195-4.3324-20.92063.3507
40.221-0.0359-0.16020.10720.01820.1139-0.25360.0457-0.12460.11550.06590.09870.4656-0.02560.00020.5259-0.00060.06680.28450.0650.3314-2.9844-35.92213.753
50.09320.0675-0.18010.0463-0.07120.23840.1199-0.49750.15620.7874-0.30720.0026-0.15360.1500.8111-0.0130.04670.549-0.06190.4359-6.6324-29.310321.0331
60.0749-0.0274-0.07870.3975-0.08990.0977-0.27080.01120.03330.1349-0.21-0.66030.36630.307-0.00970.32840.04810.04030.38350.05250.46453.5721-29.871.9304
70.0415-0.00170.02840.03540.04970.08450.04750.1835-0.1058-0.2421-0.13190.15140.4611-0.2383-0.00020.55130.04980.01650.57470.02450.355221.6168-29.1706-20.0025
80.0668-0.01430.06080.01970.01620.10110.04710.26730.4042-0.3522-0.07730.31310.10860.02030.00070.49720.06440.05160.36490.05590.399621.5124-25.1692-12.9586
90.00030.0040.00380.008-0.00740.0060.0193-0.1443-0.00340.24940.1317-0.34450.08750.02720.10230.51380.70960.20680.46010.19420.508325.0311-34.5705-6.9849
100.1574-0.0159-0.07310.06840.00960.0231-0.43520.07630.09230.00120.135-0.1739-0.03090.3687-0.00020.49310.15010.00710.69830.00270.488635.5864-25.6136-14.9697
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 43 )A17 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 62 )A44 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 83 )A63 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 125 )A84 - 125
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 145 )A126 - 145
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 160 )A146 - 160
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 175 )A161 - 175
9X-RAY DIFFRACTION9chain 'A' and (resid 176 through 192 )A176 - 192
10X-RAY DIFFRACTION10chain 'A' and (resid 193 through 221 )A193 - 221

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