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- PDB-4xfz: Structure of the native full-length HIV-1 capsid protein in compl... -

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Basic information

Entry
Database: PDB / ID: 4xfz
TitleStructure of the native full-length HIV-1 capsid protein in complex with PF-3450074 (PF74)
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / capsid protein / PF-3450074 / PF74 / complex / antiviral
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 / structural molecule activity / virion membrane / RNA binding / zinc ion 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) / 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
Chem-1B0 / IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsGres, A.T. / Kirby, K.A. / Sarafianos, S.G.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI076119 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI099284 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100890 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI112417 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103368 United States
CitationJournal: Science / Year: 2015
Title: STRUCTURAL VIROLOGY. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability.
Authors: Gres, A.T. / Kirby, K.A. / KewalRamani, V.N. / Tanner, J.J. / Pornillos, O. / Sarafianos, S.G.
History
DepositionDec 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references / Refinement description / Structure summary
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: HIV-1 capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,88810
Polymers25,6301
Non-polymers1,2589
Water50428
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)161,33060
Polymers153,7836
Non-polymers7,54754
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 area22260 Å2
ΔGint-227 kcal/mol
Surface area59820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.181, 92.181, 56.976
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: x-y, x, z; -y, x-y, z; -x, -y, z; -x+y, -x, z and y, -x+y, z.

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Components

#1: Protein HIV-1 capsid protein / Pr55Gag


Mass: 25630.426 Da / Num. of mol.: 1
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 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12493
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / 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.: 28 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00012 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00012 Å / Relative weight: 1
ReflectionResolution: 2.7→46.38 Å / Num. obs: 7709 / % possible obs: 99.5 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.025 / Net I/σ(I): 24.4 / Num. measured all: 85991
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.7-2.8310.71.6821.8104209750.7140.53596.5
8.94-46.389.90.03274.222522280.9990.01199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å46.38 Å
Translation2.7 Å46.38 Å

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHASER2.5.2phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFX

4xfx


Resolution: 2.7→45 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2242 / WRfactor Rwork: 0.1923 / FOM work R set: 0.7651 / SU B: 28.292 / SU ML: 0.312 / SU R Cruickshank DPI: 1.1668 / SU Rfree: 0.3206 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 1.167 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 354 4.6 %RANDOM
Rwork0.2102 7347 --
obs0.2115 7347 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.45 Å2 / Biso mean: 88.088 Å2 / Biso min: 46.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0.51 Å20 Å2
2---1.02 Å2-0 Å2
3---3.31 Å2
Refinement stepCycle: final / Resolution: 2.7→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 40 28 1731
Biso mean--63.18 63.77 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191737
X-RAY DIFFRACTIONr_bond_other_d0.0030.021666
X-RAY DIFFRACTIONr_angle_refined_deg1.451.982362
X-RAY DIFFRACTIONr_angle_other_deg0.9173.0043840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7265211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90924.79573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58315294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6681510
X-RAY DIFFRACTIONr_chiral_restr0.070.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
X-RAY DIFFRACTIONr_mcbond_it2.6034.338850
X-RAY DIFFRACTIONr_mcbond_other2.5754.333849
X-RAY DIFFRACTIONr_mcangle_it4.1146.4991059
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 25 -
Rwork0.311 519 -
all-544 -
obs--95.61 %
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)
10.45971.1947-2.46963.1109-6.424113.3061-0.0257-0.09190.1042-1.02640.1970.26962.27890.4463-0.17131.16180.0963-0.12540.88990.03031.0078-4.3673-13.548613.6662
21.0736-4.7449-2.342323.347316.414136.6920.09740.07110.2008-0.86-0.16490.0892-1.25610.49060.06750.0633-0.0514-0.08560.27320.04820.6776-1.1688-13.0375-3.2508
310.5645-2.1078-9.53876.0057-1.00210.18660.24360.1983-0.0444-0.2545-0.31880.0994-0.22720.0090.07520.2207-0.0691-0.04790.16120.08110.47835.908-19.8556-1.2061
44.568-0.62153.3263.1051-4.488627.4125-0.1757-0.74290.56370.462-0.0911-0.3177-0.60050.09880.26690.1052-0.00960.00080.1798-0.0290.3826-5.9312-21.39823.4437
57.24341.30855.02645.4287-8.005526.07830.151-0.3865-0.2489-0.0595-0.1599-0.10990.9963-0.20490.00890.1460.01620.05720.1338-0.04750.263-3.8466-32.7483-2.6199
66.06970.0926-1.128110.0752-3.39282.5206-0.1220.01230.23220.34540.09710.03990.81950.27620.0250.77430.09050.02020.4350.00310.3704-0.7406-39.818412.0539
717.2435-4.6513-4.50758.23252.01931.2772-0.0074-1.7879-0.78580.8983-0.21070.55460.06370.43850.21810.83010.01590.01590.87060.04680.6473-6.7282-39.319723.4483
810.9322-6.5033-10.4553.98237.424926.4025-0.2233-0.67910.16890.33440.3523-0.09870.597-0.3463-0.12890.9502-0.09050.10470.5371-0.00140.5889-8.4593-31.773124.0399
91.5836-0.10492.27910.17240.15537.2893-0.3296-0.80350.54820.20580.32260.0685-0.9031-0.26990.0070.69480.16470.06990.8592-0.21680.6148-8.1485-26.100116.3558
101.21156.27579.106841.33139.018776.04360.13770.1801-0.09281.4771.10380.04270.33710.952-1.24150.67110.025-0.03291.12560.11480.82840.9084-25.940525.6496
1114.5357-2.89092.25815.4088-12.471930.26930.1642-1.42951.87280.10780.0149-0.1239-0.20360.8326-0.17910.4564-0.01620.06360.516-0.1390.47931.124-26.67311.871
1210.11060.1669-15.87036.3125-2.913726.9973-0.435-0.5699-0.3620.6341-0.0883-0.4150.72951.03340.52330.2102-0.0045-0.070.2070.00590.40524.4265-30.40131.4727
1324.7648.7041-18.476416.5123-12.240216.244-0.02411.6973-0.63050.5671-0.29260.0577-0.2528-0.94690.31670.4488-0.00440.09750.6659-0.03320.39547.3401-31.7234-10.8782
1414.534815.6791-11.067818.4657-8.903314.4583-0.6661.0684-0.0435-0.61411.1442-0.29680.7242-0.5556-0.47820.42160.163-0.01510.54650.04750.321922.1955-31.4154-18.9554
156.63244.9446-5.879411.0908-2.155713.47060.01170.91180.6351-0.89710.0962-0.2427-0.4060.1807-0.10790.28610.08840.0070.41140.14250.366424.4185-23.2244-16.1739
1610.9524-9.8132.013523.5631-9.28374.1726-0.2962-0.6568-0.29660.1340.29840.36940.11970.0982-0.00220.56590.08450.00840.28960.01460.280118.0193-32.7287-3.9578
179.45849.9059-11.33710.3793-11.878213.5947-0.1907-0.453-0.6604-0.1333-0.5573-0.71750.15270.58290.7480.28310.1472-0.05010.4791-0.00590.450127.2398-34.2544-8.3994
1842.2907-4.466710.76490.4892-0.9275.4297-0.36741.7499-1.0932-0.0365-0.14980.1692-0.57531.69620.51731.0026-0.0390.1891.03420.0290.899432.9549-28.8674-21.4917
1924.384513.79691.820911.52028.394315.9484-0.23850.2718-1.27570.20270.716-1.2897-0.12031.2331-0.47750.86230.1103-0.20570.7422-0.06840.904839.3401-28.8964-15.4459
2011.39781.3929-4.00764.51560.945325.3046-0.33441.03560.5568-1.07480.1098-0.3895-0.24221.15490.22460.2762-0.00720.00290.4347-0.06210.498935.6404-21.3443-11.4063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 29
3X-RAY DIFFRACTION3A30 - 46
4X-RAY DIFFRACTION4A47 - 61
5X-RAY DIFFRACTION5A62 - 75
6X-RAY DIFFRACTION6A76 - 82
7X-RAY DIFFRACTION7A83 - 91
8X-RAY DIFFRACTION8A92 - 101
9X-RAY DIFFRACTION9A102 - 119
10X-RAY DIFFRACTION10A120 - 124
11X-RAY DIFFRACTION11A125 - 131
12X-RAY DIFFRACTION12A132 - 142
13X-RAY DIFFRACTION13A143 - 147
14X-RAY DIFFRACTION14A148 - 157
15X-RAY DIFFRACTION15A158 - 171
16X-RAY DIFFRACTION16A172 - 180
17X-RAY DIFFRACTION17A181 - 192
18X-RAY DIFFRACTION18A193 - 198
19X-RAY DIFFRACTION19A199 - 206
20X-RAY DIFFRACTION20A207 - 221

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