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- PDB-4ipy: HIV capsid C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4ipy
TitleHIV capsid C-terminal domain
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / CAPSID / CORE PROTEIN
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain ...Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsLampel, A. / Yaniv, O. / Berger, O. / Bachrach, E. / Gazit, E. / Frolow, F.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: A triclinic crystal structure of the carboxy-terminal domain of HIV-1 capsid protein with four molecules in the asymmetric unit reveals a novel packing interface.
Authors: Lampel, A. / Yaniv, O. / Berger, O. / Bacharach, E. / Gazit, E. / Frolow, F.
History
DepositionJan 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7115
Polymers38,6484
Non-polymers621
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7242
Polymers9,6621
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)9,6621
Polymers9,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)9,6621
Polymers9,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)9,6621
Polymers9,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.141, 43.578, 55.189
Angle α, β, γ (deg.)74.02, 74.21, 69.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Capsid protein p24 / CA


Mass: 9662.116 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 278-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: NEW YORK-5 ISOLATE / Gene: gag-pol / Plasmid: WISP97-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12497
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: reservoir contained 0.2 M magnesium formate dihydrate (pH 7.0) and 20% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725 Å
DetectorDate: Sep 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 1.64→19.7 Å / Num. all: 40722 / Num. obs: 40722 / % possible obs: 95.32 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 11.58 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 22.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: dev_1261)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A8O

1a8o


Resolution: 1.64→19.7 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1949 5.05 %resolution shells
Rwork0.1758 ---
obs0.1779 38622 95.29 %-
all-40722 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 4 346 2920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062695
X-RAY DIFFRACTIONf_angle_d1.0743642
X-RAY DIFFRACTIONf_dihedral_angle_d12.9931049
X-RAY DIFFRACTIONf_chiral_restr0.064404
X-RAY DIFFRACTIONf_plane_restr0.006480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.6810.25591120.19762049X-RAY DIFFRACTION73
1.681-1.72640.23631440.19212529X-RAY DIFFRACTION93
1.7264-1.77720.24681460.19082610X-RAY DIFFRACTION96
1.7772-1.83450.23951530.19792622X-RAY DIFFRACTION96
1.8345-1.90.24361190.19232684X-RAY DIFFRACTION96
1.9-1.9760.25261480.19072632X-RAY DIFFRACTION97
1.976-2.06590.24121210.17562700X-RAY DIFFRACTION97
2.0659-2.17470.19371370.1752691X-RAY DIFFRACTION97
2.1747-2.31070.20781470.16962650X-RAY DIFFRACTION97
2.3107-2.48880.23171350.18252714X-RAY DIFFRACTION98
2.4888-2.73870.24141390.18422696X-RAY DIFFRACTION98
2.7387-3.13370.23131600.18872680X-RAY DIFFRACTION99
3.1337-3.94310.20171450.16122719X-RAY DIFFRACTION99
3.9431-19.70.1721430.15142697X-RAY DIFFRACTION98
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)
11.8027-0.75531.64574.9326-0.46221.51510.00170.1347-0.0955-0.2669-0.0446-0.2430.20140.11690.12780.16790.02050.01240.0805-0.01580.08092.9725-3.5761-7.8276
24.24791.8609-0.52364.49390.11132.3935-0.1004-0.1257-0.04760.1810.0046-0.35440.11340.26380.09670.0740.0097-0.0180.1236-0.00620.07677.0679-0.0749-1.1805
32.66810.36040.24895.0656-0.77342.7820.0187-0.19950.21170.1587-0.0255-0.0392-0.23040.12660.00310.084-0.00810.00330.1108-0.00960.062-0.91467.4161-2.5822
42.3841.0373-0.69838.2694.72836.3538-0.0062-0.0375-0.0443-0.10060.02130.44370.176-0.77740.06390.1342-0.03220.0070.2860.03490.1423-7.7689-3.53414.4962
52.70010.9575-0.00843.99872.77063.24550.0264-0.3363-0.13760.22520.059-0.48330.37430.0707-0.08130.15580.01550.00060.17510.04110.0990.0082-6.22018.2239
63.04253.93620.68195.32751.51988.86240.08590.08210.2791-0.38290.16821.6206-0.1514-1.1294-0.27170.40180.0037-0.0210.35050.17750.5572-6.6961-19.98267.2237
71.52562.84210.43055.6148-0.25453.61320.09970.14790.4994-0.43590.05490.6606-0.6168-0.82550.08520.23470.08940.03020.18560.02320.169-7.6031-8.5542-30.5092
80.89460.4085-0.22551.77720.70920.77770.0026-0.10920.14240.140.02930.0469-0.10440.0083-0.13650.17760.0608-0.02350.054-0.05680.118-6.0478-8.2097-16.9813
91.4417-0.33540.35711.6050.3671.22190.03350.00020.01670.01330.00180.32990.1415-0.4257-0.00330.0592-0.0200.12080.00160.1332-9.5858-16.5588-21.8392
101.7576-0.0812-0.65263.85061.40854.2920.07850.2112-0.152-0.2190.029-0.09050.24120.0048-0.06250.11210.0166-0.00450.0792-0.01830.1276-0.6787-17.8378-28.9794
111.351-0.883-0.56976.10260.66021.9449-0.1315-0.08910.1745-0.19280.242-0.208-0.19010.248-0.08660.0891-0.0021-0.01920.0793-0.02660.14835.1611-17.0422-15.6217
122.16942.78851.53965.62864.32623.78830.0322-0.0787-0.19180.23850.00120.23840.4163-0.27950.20890.1118-0.0342-0.01110.15570.10120.2687-2.4338-22.9043-14.2124
135.89264.74381.63245.00012.47391.59390.1404-0.34240.3240.17-0.2370.29960.2191-0.18580.07940.1913-0.00730.07870.13560.02030.1833-12.6612-19.3047-11.0249
141.9523-0.30580.87782.75911.20652.80250.02980.0606-0.1524-0.16730.01870.29790.0905-0.0813-0.02310.0593-0.0063-0.01230.04180.00970.17-12.90126.3382-17.9839
152.35171.04850.01212.6177-0.12391.7999-0.16870.20420.0816-0.15050.24770.1063-0.01850.0034-0.04850.0644-0.0306-0.00740.11930.02320.1544-4.497812.3483-18.6491
164.625-4.5891-0.41344.72730.44810.05110.32260.9644-0.3764-0.7183-0.57690.0840.0756-0.20160.34770.5420.1099-0.02940.406-0.03560.3095-18.386612.8502-29.2312
171.07330.8255-2.20072.8416-2.00064.55520.0556-0.3028-0.02870.1654-0.1951-0.2009-0.1490.54510.12930.2198-0.1330.00620.38270.1270.1048.1509-7.6305-28.3191
183.9059-1.5627-1.88976.3211-1.3556.08340.1294-0.35760.18690.40110.12980.3015-0.4438-0.0143-0.29160.16-0.09020.04480.2515-0.04930.10195.96014.3282-34.2163
192.2734-1.113-0.10711.59950.38930.3334-0.0067-0.18740.14-0.03320.0435-0.1637-0.02850.21580.11670.0848-0.0399-0.00540.2990.04950.101211.5612-3.7419-38.2405
201.6494-1.5469-0.14187.461.96621.5668-0.0108-0.1799-0.18250.0496-0.058-0.17820.0050.32850.0890.104-0.01030.0170.29290.07930.13554.399-11.6576-36.9664
214.4248-0.43262.87976.89633.79938.37140.0204-0.37860.05930.4360.02720.4478-0.0298-0.2108-0.07040.1222-0.01960.04530.2038-0.01720.1346-3.95841.1872-41.5521
223.8002-0.01050.09955.93111.59482.15320.10110.30160.099-0.25830.0538-0.4206-0.24780.3619-0.10040.108-0.04180.00190.26340.04120.11563.7465-0.4086-48.2035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 147 through 160 )
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 174 )
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 210 )
5X-RAY DIFFRACTION5chain 'A' and (resid 211 through 223 )
6X-RAY DIFFRACTION6chain 'A' and (resid 224 through 231 )
7X-RAY DIFFRACTION7chain 'B' and (resid 147 through 152 )
8X-RAY DIFFRACTION8chain 'B' and (resid 153 through 160 )
9X-RAY DIFFRACTION9chain 'B' and (resid 161 through 174 )
10X-RAY DIFFRACTION10chain 'B' and (resid 175 through 195 )
11X-RAY DIFFRACTION11chain 'B' and (resid 196 through 210 )
12X-RAY DIFFRACTION12chain 'B' and (resid 211 through 217 )
13X-RAY DIFFRACTION13chain 'B' and (resid 218 through 231 )
14X-RAY DIFFRACTION14chain 'C' and (resid 147 through 174 )
15X-RAY DIFFRACTION15chain 'C' and (resid 175 through 217 )
16X-RAY DIFFRACTION16chain 'C' and (resid 218 through 231 )
17X-RAY DIFFRACTION17chain 'D' and (resid 148 through 152 )
18X-RAY DIFFRACTION18chain 'D' and (resid 153 through 160 )
19X-RAY DIFFRACTION19chain 'D' and (resid 161 through 174 )
20X-RAY DIFFRACTION20chain 'D' and (resid 175 through 195 )
21X-RAY DIFFRACTION21chain 'D' and (resid 196 through 205 )
22X-RAY DIFFRACTION22chain 'D' and (resid 206 through 221 )

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