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- PDB-6b2j: E45A mutant of HIV-1 capsid protein (other crystal form) -

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Basic information

Entry
Database: PDB / ID: 6b2j
TitleE45A mutant of HIV-1 capsid protein (other crystal form)
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / E45A 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 / SAD / Resolution: 2.21 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: Nat Commun / Year: 2023
Title: Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization.
Authors: Gres, A.T. / Kirby, K.A. / McFadden, W.M. / Du, H. / Liu, D. / Xu, C. / Bryer, A.J. / Perilla, J.R. / Shi, J. / Aiken, C. / Fu, X. / Zhang, P. / Francis, A.C. / Melikyan, G.B. / Sarafianos, S.G.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
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 / _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: HIV-1 capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,98315
Polymers25,5721
Non-polymers1,41114
Water1,76598
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)161,89990
Polymers153,4346
Non-polymers8,46584
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 area29740 Å2
ΔGint-400 kcal/mol
Surface area60560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.493, 92.493, 57.748
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: 25572.391 Da / Num. of mol.: 1 / Fragment: UNP residues 133-363 / Mutation: E45A
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 / Iodide


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.79 Å3/Da / Density % sol: 55.89 % / Mosaicity: 0.13 °
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: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.21→47 Å / Num. obs: 14252 / % possible obs: 99.9 % / Redundancy: 11.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.027 / Rrim(I) all: 0.089 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.21-2.2810.71.3212180.6280.4171.38599.2
9.11-46.8410.10.0472230.9990.0160.0599.6

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Processing

Software
NameVersionClassification
Aimless0.5.24data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
Aimless0.5.24data reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.21→47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 14.842 / SU ML: 0.18 / SU R Cruickshank DPI: 0.2497 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.185
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 693 4.9 %RANDOM
Rwork0.2023 ---
obs0.2033 13556 99.95 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 137.83 Å2 / Biso mean: 63.319 Å2 / Biso min: 38.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0.29 Å2-0 Å2
2---0.58 Å20 Å2
3---1.88 Å2
Refinement stepCycle: final / Resolution: 2.21→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 14 98 1833
Biso mean--82.78 62.81 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191775
X-RAY DIFFRACTIONr_bond_other_d0.0010.021716
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9582419
X-RAY DIFFRACTIONr_angle_other_deg0.85133962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2825226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9232576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68715309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2311510
X-RAY DIFFRACTIONr_chiral_restr0.0540.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212009
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
X-RAY DIFFRACTIONr_sphericity_free51.76752
X-RAY DIFFRACTIONr_sphericity_bonded53.232512
LS refinement shellResolution: 2.21→2.267 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 54 -
Rwork0.278 987 -
all-1041 -
obs--99.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1125-0.14880.81270.2764-1.23346.3237-0.0926-0.03010.07370.0795-0.1490.0327-0.35350.0320.24170.6106-0.00080.00460.6303-0.17320.54871.6086-10.553615.3375
23.836-0.79171.99570.6315-1.84375.64090.6097-0.87710.07340.2534-0.12840.0982-0.52710.6933-0.48130.9094-0.0356-0.01910.6662-0.11020.4177-3.7374-12.53599.3643
32.0074-2.1999-1.87177.81573.216110.48420.06470.12020.1989-0.2246-0.06480.0229-0.217-0.20210.00020.0603-0.0079-0.02240.11560.01230.2025-1.386-13.2048-8.1581
45.8971-2.0872-3.10946.20591.18423.5914-0.1250.32350.1738-0.1742-0.0866-0.3383-0.28120.13980.21160.107-0.0394-0.02430.08760.04480.22465.7633-20.1238-6.1902
52.5191-1.76992.43684.5262-0.64754.7282-0.0347-0.00590.05890.11460.00210.1583-0.01410.14410.03260.0378-0.00470.06160.06050.03720.1615-5.0762-26.3845-4.8065
612.30071.75045.59446.168-5.615310.5523-0.0044-0.5179-0.60060.2337-0.1486-0.2610.47480.10870.1530.5290.15960.11010.12450.11120.233-1.6716-39.87818.2746
713.1584-2.4717-3.43236.41942.700611.3078-0.0425-0.1789-0.2020.2777-0.2238-0.42780.05820.2350.26630.37010.02910.01480.33820.0810.228-9.5753-33.07322.7719
87.412-1.9709-1.32186.7639-0.17396.9994-0.0442-1.054-0.03360.93640.0542-0.0841-0.3866-0.1649-0.01010.36820.09920.04610.26880.06950.1075-4.8374-26.758112.9319
93.2109-0.1873-4.59162.1604-0.187411.3256-0.08040.052-0.136-0.00390.0847-0.01040.29490.318-0.00440.06370.0141-0.00370.08850.01370.1854.5406-30.3715-5.5195
109.99612.55-5.02878.6938-1.83878.9576-0.25430.61960.0471-0.62760.4041-0.16310.3313-0.199-0.14980.19190.0706-0.03810.15910.00590.06924.5829-27.3862-24.2968
119.48712.573-8.57732.11520.030911.7547-0.26740.20760.1717-0.06690.19810.23560.36940.05440.06940.18190.0427-0.11820.06420.03350.158920.4364-26.0369-16.826
129.792-1.823-3.14756.1474-0.79191.34160.08820.2405-0.00090.313-0.06930.0271-0.1084-0.0811-0.01880.1880.0401-0.00080.1910.01920.156521.4405-35.4346-7.562
1313.4455-0.587-4.8084.00691.07945.9380.0020.114-0.5641-0.00480.3393-0.13380.21030.42-0.34130.23980.094-0.05620.2596-0.02320.206331.5411-31.469-20.4655
1412.2807-11.2692-9.640216.209710.24857.9029-0.54440.2295-0.39570.39190.3050.11440.404-0.06190.23930.26970.0597-0.07890.3805-0.00250.259338.5323-29.1093-15.3551
152.13460.1517-1.80315.81930.251215.1666-0.0570.20620.1842-0.2370.0966-0.1456-0.23930.2587-0.03960.11240.0338-0.00830.2306-0.00020.20634.7565-20.3541-17.6553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2A10 - 16
3X-RAY DIFFRACTION3A17 - 29
4X-RAY DIFFRACTION4A30 - 47
5X-RAY DIFFRACTION5A48 - 73
6X-RAY DIFFRACTION6A74 - 86
7X-RAY DIFFRACTION7A87 - 98
8X-RAY DIFFRACTION8A99 - 129
9X-RAY DIFFRACTION9A130 - 147
10X-RAY DIFFRACTION10A148 - 162
11X-RAY DIFFRACTION11A163 - 175
12X-RAY DIFFRACTION12A176 - 184
13X-RAY DIFFRACTION13A185 - 201
14X-RAY DIFFRACTION14A202 - 210
15X-RAY DIFFRACTION15A211 - 221

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