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- PDB-3p05: X-ray structure of pentameric HIV-1 CA -

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Basic information

Entry
Database: PDB / ID: 3p05
TitleX-ray structure of pentameric HIV-1 CA
ComponentsHIV-1 CA
KeywordsVIRAL PROTEIN / capsid protein
Function / homology
Function and homology information


viral budding via host ESCRT complex / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase ...viral budding via host ESCRT complex / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / 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 / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / 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 / Reverse transcriptase connection / Reverse transcriptase connection 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 / 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 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPornillos, O.
CitationJournal: Nature / Year: 2011
Title: Atomic-level modelling of the HIV capsid.
Authors: Pornillos, O. / Ganser-Pornillos, B.K. / Yeager, M.
History
DepositionSep 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 16, 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: HIV-1 CA
B: HIV-1 CA
C: HIV-1 CA
D: HIV-1 CA
E: HIV-1 CA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,65015
Polymers127,3815
Non-polymers1,26910
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-90 kcal/mol
Surface area46750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.723, 130.308, 81.831
Angle α, β, γ (deg.)90.00, 97.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
12
22
32
13
23
33
43
53
14
24
34
44
54
15
25
35
45
55
16
26
36
46
56
17
27
37
47
57
18
28
38
48

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A resseq 1:2 or resseq 12:20 or (resseq 21:22...
211chain B resseq 1:2 or resseq 12:20 or (resseq 21:22...
311chain C resseq 1:2 or resseq 12:20 or (resseq 21:22...
411chain D resseq 1:2 or resseq 12:20 or (resseq 21:22...
511chain E resseq 1:2 or resseq 12:20 or (resseq 21:22...
112chain B resseq 3:11
212chain C resseq 3:11
312chain D resseq 3:11
113chain A resseq 116:125
213chain B resseq 116:125
313chain C resseq 116:125
413chain D resseq 116:125
513chain E resseq 116:125
114chain A resid 96:99 or (resid 100 and backbone) or...
214chain B resid 96:99 or (resid 100 and backbone) or...
314chain C resid 96:99 or (resid 100 and backbone) or...
414chain D resid 96:99 or (resid 100 and backbone) or...
514chain E resid 96:99 or (resid 100 and backbone) or...
115chain E resid 206:219
215chain A resid 206:219
315chain B resid 206:219
415chain C resid 206:219
515chain D resid 206:219
116chain A resseq 154:174 or resseq 190:205
216chain B resseq 154:174 or resseq 190:205
316chain C resseq 154:174 or resseq 190:191 or (resseq 192 and backbone) or resseq 193:205
416chain D resseq 154:174 or resseq 190:205
516chain E resseq 154:174 or resseq 190:191 or (resseq 192 and backbone) or resseq 193:205
117chain A resseq 175:189
217chain B resseq 175:189
317chain C resseq 175:189
417chain D resseq 175:189
517chain E resseq 175:189
118chain A resseq 146:153
218chain C resseq 146:153
318chain D resseq 146:153
418chain E resseq 146:153

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

#1: Protein
HIV-1 CA


Mass: 25476.283 Da / Num. of mol.: 5 / Fragment: UNP residues 133-363 / Mutation: N21C, A22C, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: CA, gag / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72497, UniProt: P12497*PLUS
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 27-30% PEG 4000, 100 mM Tris, 0.2 M sodium iodide, pH 8-9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 8-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 43086 / Num. obs: 41160 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.53 / % possible all: 94.9

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H47

3h47


Resolution: 2.5→32.577 Å / SU ML: 0.37 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 2083 5.07 %THIN SHELL
Rwork0.2304 ---
obs0.2322 41121 97.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.679 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2214 Å2-0 Å2-0.6062 Å2
2---2.7843 Å2-0 Å2
3----0.4371 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7908 0 10 0 7918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158079
X-RAY DIFFRACTIONf_angle_d1.47310986
X-RAY DIFFRACTIONf_dihedral_angle_d13.7982999
X-RAY DIFFRACTIONf_chiral_restr0.0921260
X-RAY DIFFRACTIONf_plane_restr0.0081426
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A747X-RAY DIFFRACTIONPOSITIONAL
12B747X-RAY DIFFRACTIONPOSITIONAL0.125
13C740X-RAY DIFFRACTIONPOSITIONAL0.116
14D747X-RAY DIFFRACTIONPOSITIONAL0.091
15E747X-RAY DIFFRACTIONPOSITIONAL0.105
21B54X-RAY DIFFRACTIONPOSITIONAL
22C54X-RAY DIFFRACTIONPOSITIONAL0.133
23D44X-RAY DIFFRACTIONPOSITIONAL0.109
31A80X-RAY DIFFRACTIONPOSITIONAL
32B80X-RAY DIFFRACTIONPOSITIONAL0.071
33C80X-RAY DIFFRACTIONPOSITIONAL0.051
34D80X-RAY DIFFRACTIONPOSITIONAL0.065
35E80X-RAY DIFFRACTIONPOSITIONAL0.056
41A139X-RAY DIFFRACTIONPOSITIONAL
42B139X-RAY DIFFRACTIONPOSITIONAL0.075
43C139X-RAY DIFFRACTIONPOSITIONAL0.075
44D139X-RAY DIFFRACTIONPOSITIONAL0.073
45E131X-RAY DIFFRACTIONPOSITIONAL0.077
51E96X-RAY DIFFRACTIONPOSITIONAL
52A96X-RAY DIFFRACTIONPOSITIONAL0.08
53B96X-RAY DIFFRACTIONPOSITIONAL0.075
54C96X-RAY DIFFRACTIONPOSITIONAL0.078
55D96X-RAY DIFFRACTIONPOSITIONAL0.078
61A299X-RAY DIFFRACTIONPOSITIONAL
62B299X-RAY DIFFRACTIONPOSITIONAL0.088
63C298X-RAY DIFFRACTIONPOSITIONAL0.08
64D299X-RAY DIFFRACTIONPOSITIONAL0.086
65E298X-RAY DIFFRACTIONPOSITIONAL0.083
71A100X-RAY DIFFRACTIONPOSITIONAL
72B100X-RAY DIFFRACTIONPOSITIONAL0.124
73C100X-RAY DIFFRACTIONPOSITIONAL0.062
74D100X-RAY DIFFRACTIONPOSITIONAL0.077
75E100X-RAY DIFFRACTIONPOSITIONAL0.079
81A58X-RAY DIFFRACTIONPOSITIONAL
82C58X-RAY DIFFRACTIONPOSITIONAL0.092
83D58X-RAY DIFFRACTIONPOSITIONAL0.065
84E58X-RAY DIFFRACTIONPOSITIONAL0.078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55840.2981400.27282417X-RAY DIFFRACTION89
2.5584-2.62230.32891380.27732501X-RAY DIFFRACTION96
2.6223-2.69320.35261390.28212553X-RAY DIFFRACTION96
2.6932-2.77240.3181380.27892554X-RAY DIFFRACTION97
2.7724-2.86190.31891390.27442578X-RAY DIFFRACTION97
2.8619-2.96410.27941380.26912581X-RAY DIFFRACTION97
2.9641-3.08270.35241380.26142621X-RAY DIFFRACTION98
3.0827-3.22290.30111390.25612608X-RAY DIFFRACTION98
3.2229-3.39260.25941390.24222624X-RAY DIFFRACTION99
3.3926-3.60490.25931390.21862649X-RAY DIFFRACTION99
3.6049-3.88280.26491390.22022654X-RAY DIFFRACTION99
3.8828-4.27280.21851390.20662668X-RAY DIFFRACTION99
4.2728-4.88930.24371390.1932671X-RAY DIFFRACTION99
4.8893-6.15320.27981390.22382660X-RAY DIFFRACTION99
6.1532-32.57970.21071400.19412699X-RAY DIFFRACTION99

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