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

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Basic information

Entry
Database: PDB / ID: 4xfx
TitleStructure of the native full-length HIV-1 capsid protein
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / capsid protein / native
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / 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) ...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) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.43 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 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)26,59010
Polymers25,6301
Non-polymers9599
Water1,35175
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)159,53860
Polymers153,7836
Non-polymers5,75554
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 area23640 Å2
ΔGint-215 kcal/mol
Surface area60330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.328, 92.328, 57.340
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.: 7 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 55.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaI, MMT

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 28, 2013
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→80 Å / Num. obs: 10588 / % possible obs: 99.7 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.026 / Rrim(I) all: 0.077 / Χ2: 0.957 / Net I/av σ(I): 29.943 / Net I/σ(I): 9.2 / Num. measured all: 115799
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.43-2.4710.15220.6940.3990.857100
2.47-2.5210.95140.7910.3420.85100
2.52-2.5710.95290.8190.3070.9061000.971
2.57-2.6211.15340.8190.2550.8851000.8130.853
2.62-2.67115120.8580.2290.8871000.7260.762
2.67-2.74115340.8960.1820.931000.580.609
2.74-2.81115250.9290.1540.9091000.4880.512
2.81-2.88115480.9490.1310.9581000.4170.437
2.88-2.9711.15130.9770.0960.9551000.3050.32
2.97-3.0611.15280.9830.0810.9561000.2570.27
3.06-3.1711.15360.9870.0610.9831000.1940.203
3.17-3.3115270.9920.0470.9721000.150.158
3.3-3.4511.25240.9960.0371.0011000.120.126
3.45-3.6311.25310.9980.0261.0261000.0840.088
3.63-3.8611.15360.9980.021.0371000.0650.068
3.86-4.1611.25250.9990.0140.9091000.0460.048
4.16-4.5711.25400.9980.0130.91000.040.042
4.57-5.2311.15330.9990.0110.8461000.0350.037
5.23-6.59115410.9960.0110.7991000.0350.037
6.59-809.85360.9990.0081.63394.70.0240.025

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.43→19 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2193 / WRfactor Rwork: 0.1951 / FOM work R set: 0.7629 / SU B: 18.716 / SU ML: 0.244 / SU R Cruickshank DPI: 0.4689 / SU Rfree: 0.2695 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.469 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 475 4.7 %RANDOM
Rwork0.2215 9555 --
obs0.2229 9555 94.44 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 118.64 Å2 / Biso mean: 47.815 Å2 / Biso min: 12.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å2-0 Å2
3----1.05 Å2
Refinement stepCycle: final / Resolution: 2.43→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 9 75 1764
Biso mean--56.25 36.09 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191719
X-RAY DIFFRACTIONr_bond_other_d0.0010.021654
X-RAY DIFFRACTIONr_angle_refined_deg0.8051.9572337
X-RAY DIFFRACTIONr_angle_other_deg0.67933815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4975214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33524.79573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.615295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6251510
X-RAY DIFFRACTIONr_chiral_restr0.0450.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_mcbond_it3.7583.677862
X-RAY DIFFRACTIONr_mcbond_other3.7573.672861
X-RAY DIFFRACTIONr_mcangle_it5.7995.4891074
LS refinement shellResolution: 2.432→2.494 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 19 -
Rwork0.287 479 -
all-498 -
obs--64.18 %
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)
13.38922.6133-3.11212.2663-2.44622.86640.1987-0.24480.5207-0.09410.15730.4236-0.03610.1858-0.3560.1874-0.0767-0.0030.2475-0.01890.0819-1.4285-12.836616.4152
20.9112-0.9791-1.32791.18321.47983.1596-0.019-0.00430.0513-0.0448-0.056-0.0042-0.0857-0.02380.0750.0635-0.0003-0.00940.0712-0.00830.1355-2.1017-12.8882-1.2661
31.5277-1.20030.23481.1350.41951.95750.06480.06670.0987-0.065-0.0958-0.0914-0.0476-0.1270.0310.0512-0.01570.00750.05640.03140.15666.0927-19.945-3.5351
40.53640.08971.01191.36060.92174.5702-0.0299-0.00090.08870.1039-0.05820.01190.0032-0.0750.08810.06770.003-0.00380.05590.0030.1231-4.3062-21.19263.3149
50.163-0.34410.7271.0897-1.01594.06020.0050.00980.00140.0334-0.04480.00370.1698-0.04230.03980.1016-0.00270.03670.07120.01160.1036-3.3692-34.35971.9021
60.0373-0.2842-0.03653.46280.40650.04850.0122-0.0298-0.04570.2023-0.0840.12090.0294-0.00710.07180.1370.04550.03430.16610.07630.1177-5.5594-39.95421.7963
75.1952-5.13290.40775.7163-0.10030.1739-0.1685-0.14310.25590.17120.177-0.2771-0.00170.0138-0.00840.1133-0.03960.03770.0824-0.00690.0558-9.0613-29.210728.4009
81.08210.3913-1.44954.03991.01372.5489-0.00540.0944-0.22650.1987-0.2940.03580.005-0.23970.29940.15010.0450.01950.07760.00390.0735-8.1507-30.295714.6635
91.07560.4637-1.28490.2074-0.57581.59940.04230.010.10010.05170.03370.0276-0.1562-0.0799-0.0760.23070.0906-0.02180.0955-0.06350.0905-6.6953-22.917419.0624
107.80891.01324.71740.13920.6342.91310.0139-0.4465-0.4687-0.00390.1463-0.0702-0.0332-0.118-0.16020.17610.0838-0.01850.4036-0.03760.04030.864-24.905425.0671
113.23110.7071-2.35020.57670.41123.7609-0.1169-0.16820.0497-0.0577-0.00250.0729-0.04730.25430.11940.12310.0112-0.04730.0730.04060.10882.6008-28.20259.2735
125.8146-0.8508-2.10630.28511.534610.12980.05130.0255-0.0515-0.0106-0.04760.0067-0.0191-0.1172-0.00370.0760.0020.0150.07660.00810.10034.8161-30.6957-3.3574
137.5928-1.5503-3.80390.31890.75932.0412-0.07540.1948-0.17470.0096-0.00690.03960.1463-0.17240.08230.125-0.02440.01350.0750.00330.095113.3525-32.9088-13.1353
142.94820.6848-1.0160.62640.35991.1379-0.06560.09-0.0201-0.06690.1051-0.0214-0.03050.026-0.03950.1084-0.00130.0030.09940.01790.074826.0535-24.0944-19.1822
155.10621.8509-0.11531.4386-1.32482.1562-0.17840.1160.0909-0.30790.00770.00420.36430.24490.17070.14880.03760.00920.08180.05120.104217.5905-27.3181-9.0033
167.3391-1.0556-2.23863.7793-0.18840.7550.05460.2825-0.0140.1972-0.05220.1541-0.0401-0.0774-0.00240.1260.03460.00210.09650.0230.054221.4905-35.6795-2.7282
171.76973.0302-2.20155.1981-3.77722.7453-0.0183-0.1251-0.0362-0.1951-0.0983-0.04020.14920.14050.11660.11120.048-0.00570.12510.04570.135827.5014-33.519-9.5222
185.19490.5280.88580.77610.98381.2571-0.12690.0709-0.09770.0050.06420.07390.00170.11030.06270.08390.04490.02530.1061-0.02130.084233.175-30.8103-19.3301
191.4680.10323.09650.00850.21966.5370.13860.0574-0.2250.00530.1627-0.0055-0.02910.1296-0.30130.11420.05670.0170.1160.03720.145739.1981-29.1281-13.2988
201.24280.76930.35510.55050.91656.7395-0.04860.02130.1153-0.03160.07120.05980.0720.2634-0.02270.04860.0310.0160.11990.01090.094134.9696-21.2829-11.5617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 13
2X-RAY DIFFRACTION2A14 - 28
3X-RAY DIFFRACTION3A29 - 44
4X-RAY DIFFRACTION4A45 - 62
5X-RAY DIFFRACTION5A63 - 81
6X-RAY DIFFRACTION6A82 - 91
7X-RAY DIFFRACTION7A92 - 97
8X-RAY DIFFRACTION8A98 - 111
9X-RAY DIFFRACTION9A112 - 118
10X-RAY DIFFRACTION10A119 - 124
11X-RAY DIFFRACTION11A125 - 136
12X-RAY DIFFRACTION12A137 - 142
13X-RAY DIFFRACTION13A143 - 153
14X-RAY DIFFRACTION14A154 - 168
15X-RAY DIFFRACTION15A169 - 175
16X-RAY DIFFRACTION16A176 - 184
17X-RAY DIFFRACTION17A185 - 190
18X-RAY DIFFRACTION18A191 - 200
19X-RAY DIFFRACTION19A201 - 207
20X-RAY DIFFRACTION20A208 - 221

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