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- PDB-4xfy: Structure of the native full-length dehydrated HIV-1 capsid protein -

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Basic information

Entry
Database: PDB / ID: 4xfy
TitleStructure of the native full-length dehydrated HIV-1 capsid protein
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / capsid protein / native / HIV-1 / dehydrated
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
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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)25,9404
Polymers25,6301
Non-polymers3093
Water1086
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)155,63824
Polymers153,7836
Non-polymers1,85518
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 area20470 Å2
ΔGint-212 kcal/mol
Surface area60860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.137, 87.137, 55.881
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting 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: Mar 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00012 Å / Relative weight: 1
ReflectionResolution: 2.79→55.88 Å / Num. obs: 6091 / % possible obs: 99.7 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.034 / Net I/σ(I): 19.8 / Num. measured all: 65579
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
2.79-2.969.81.2691.893679600.7040.42598.2
8.38-55.8810.20.02767.1252824710.00999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.55 Å44.91 Å
Translation5.55 Å44.91 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: 3H47

3h47


Resolution: 2.8→45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2304 / WRfactor Rwork: 0.1824 / FOM work R set: 0.8066 / SU B: 33.964 / SU ML: 0.321 / SU R Cruickshank DPI: 0.3211 / SU Rfree: 0.3859 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 277 4.6 %RANDOM
Rwork0.2081 5801 --
obs0.2099 5801 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.04 Å2 / Biso mean: 75.734 Å2 / Biso min: 37.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.53 Å20 Å2
2--1.07 Å2-0 Å2
3----3.46 Å2
Refinement stepCycle: final / Resolution: 2.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 18 6 1709
Biso mean--71.02 51.31 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191739
X-RAY DIFFRACTIONr_bond_other_d0.0020.021680
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9632356
X-RAY DIFFRACTIONr_angle_other_deg0.7643.0043879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8285214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00124.86574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17815299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5551510
X-RAY DIFFRACTIONr_chiral_restr0.0470.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
X-RAY DIFFRACTIONr_mcbond_it2.5714.986862
X-RAY DIFFRACTIONr_mcbond_other2.5694.984861
X-RAY DIFFRACTIONr_mcangle_it4.2477.4731074
LS refinement shellResolution: 2.797→2.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 16 -
Rwork0.395 409 -
all-425 -
obs--97.7 %
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)
11.4699-2.8682-1.87427.01334.59533.0127-0.194-0.24670.32120.5370.09220.12370.34190.07770.10180.26-0.0659-0.10860.441-0.11820.6099-0.4903-14.369621.2484
20.72030.28892.46540.13351.01038.4649-0.0939-0.0060.02880.01420.0489-0.0289-0.25630.03890.0450.26850.0948-0.05240.2035-0.09060.3213-4.6611-10.680810.8812
31.7855-2.5891-1.06374.55332.99786.6081-0.08130.2320.05120.07590.02370.0191-0.2477-0.00050.05760.1746-0.0168-0.00750.2892-0.00450.3263-0.5686-14.8954-2.8548
41.2527-1.5042-0.4581.8590.54270.16980.1140.17460.2128-0.1554-0.0649-0.2415-0.0425-0.0893-0.04910.169-0.0355-0.03130.4073-0.05340.46315.7464-20.6960.5188
54.5123-0.38660.77662.67173.03123.7712-0.2155-0.05280.01530.0236-0.04220.205-0.0408-0.0620.25760.2454-0.0085-0.04820.18690.05370.3117-5.2068-22.26463.976
65.6639-3.62131.01567.3605-0.7790.2044-0.19850.1209-0.0061-0.00940.1618-0.1333-0.0196-0.04810.03670.2049-0.02980.0030.2836-0.03060.2324-4.9936-32.499-0.6228
70.5757-0.6497-0.7471.4465-0.71598.2727-0.36480.1680.0820.16750.011-0.36921.0851-0.52240.35380.466-0.03880.06370.2412-0.00150.2269-2.2439-39.911412.9744
817.782-10.0181-3.928715.693817.486224.10741.09790.56580.04870.3064-1.23990.01491.1466-1.54650.1420.4792-0.11030.11240.1363-0.10120.3454-14.5743-37.606827.559
97.8338-0.9716-6.64874.96595.0679.37540.11510.01670.0928-0.0448-0.10520.0948-0.1675-0.0593-0.00990.2982-0.0248-0.0060.1831-0.0150.2261-9.6671-32.263124.4435
100.5583-1.2282-0.0998.75180.7992.5337-0.1956-0.0470.22790.39730.3470.14910.3513-0.1303-0.15140.2398-0.0131-0.01040.2143-0.00690.2471-10.4611-28.095416.0564
114.047-3.23850.08075.53351.77911.1619-0.2576-0.49010.22830.35920.1748-0.10120.117-0.14830.08280.36140.03830.0260.3773-0.00190.1571-2.0924-25.786221.9648
125.0565-0.287-5.20913.8613.77148.5124-0.238-0.2851-0.398-0.0912-0.0303-0.16250.12910.26780.26830.20310.022-0.10320.28210.05360.30372.549-29.42666.9549
134.81640.3205-1.93970.06090.798522.9856-0.3630.1757-0.3596-0.00430.0098-0.01720.6706-0.41340.35320.216-0.00160.00890.222-0.02610.22484.7067-32.2032-5.6549
1418.0468-5.6995-5.43582.44452.683.0808-0.00350.0934-0.32690.2336-0.13060.12050.3458-0.2040.1340.2245-0.0372-0.02790.1963-0.02930.284115.3967-31.8418-14.9845
158.99635.2919-5.785415.1046-5.75199.6318-0.1160.52880.5335-0.53170.49140.56750.5192-0.4027-0.37540.1983-0.07720.02440.2659-0.0160.173925.0578-24.9662-23.2358
167.07984.7293-4.62723.7599-3.38923.1725-0.3606-0.01590.1159-0.42590.39560.00830.3248-0.1928-0.03490.2028-0.07880.02030.2959-0.09210.337320.4868-24.2639-11.6728
1710.71352.30499.37681.03520.690511.49580.16440.10180.2234-0.1838-0.08960.16010.69930.3031-0.07480.1440.05690.03770.25450.00620.252419.4733-32.3822-0.8275
186.9705-1.7451-0.5832.0817-2.10313.1611-0.6161-0.5651-1.17730.15640.0113-0.1253-0.06790.2780.60480.4528-0.05850.24650.2488-0.08920.553127.908-32.4626-11.4819
193.6194-0.92352.29221.19810.549716.8405-0.3690.1299-0.0791-0.1539-0.1452-0.15350.7370.07210.51410.22560.06010.0910.1719-0.00850.261336.778-28.9998-14.8625
202.7238-0.36383.55990.0763-0.15818.5048-0.293-0.10150.14080.04850.0613-0.0342-0.17310.42510.23170.13960.02910.02640.2249-0.03050.310533.4477-21.3781-9.7149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 11
2X-RAY DIFFRACTION2A12 - 18
3X-RAY DIFFRACTION3A19 - 31
4X-RAY DIFFRACTION4A32 - 44
5X-RAY DIFFRACTION5A45 - 65
6X-RAY DIFFRACTION6A66 - 72
7X-RAY DIFFRACTION7A73 - 85
8X-RAY DIFFRACTION8A86 - 93
9X-RAY DIFFRACTION9A94 - 100
10X-RAY DIFFRACTION10A101 - 113
11X-RAY DIFFRACTION11A114 - 129
12X-RAY DIFFRACTION12A130 - 139
13X-RAY DIFFRACTION13A140 - 145
14X-RAY DIFFRACTION14A146 - 153
15X-RAY DIFFRACTION15A154 - 159
16X-RAY DIFFRACTION16A160 - 175
17X-RAY DIFFRACTION17A176 - 182
18X-RAY DIFFRACTION18A183 - 196
19X-RAY DIFFRACTION19A197 - 208
20X-RAY DIFFRACTION20A209 - 220

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