PDB-3h4e: X-ray Structure of Hexameric HIV-1 CA

ID or keywords:

Entry

Database: PDB / ID: 3h4e

Title

X-ray Structure of Hexameric HIV-1 CA

Components

Capsid protein p24

Keywords

VIRAL PROTEIN /

capsid protein /

hexamer / engineered disulfide bonds

Function / homology

Function and homology information

HIV-1 retropepsin /

: /

retroviral ribonuclease H /

exoribonuclease H /

: /

exoribonuclease H activity / host multivesicular body / DNA integration /

RNA-directed DNA polymerase / viral genome integration into host DNA ...
Similarity search - Function

Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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. ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus type 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.704 Å

Authors

Pornillos, O.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2009
Title: X-ray structures of the hexameric building block of the HIV capsid.
Authors: Pornillos, O. / Ganser-Pornillos, B.K. / Kelly, B.N. / Hua, Y. / Whitby, F.G. / Stout, C.D. / Sundquist, W.I. / Hill, C.P. / Yeager, M.

History

Deposition	Apr 19, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 23, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 13, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3h4e.cif.gz	467.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3h4e.ent.gz	387.6 KB	Display	PDB format
PDBx/mmJSON format	3h4e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h4/3h4e ftp://data.pdbj.org/pub/pdb/validation_reports/h4/3h4e	HTTPS FTP

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Related structure data

Related structure data	3gv2C 3h47SC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6bht-2 4u0d-1 5tsx-1 6erm-1 5tsx-2 6r8c-1 4u0d-2 5hgm-1 5hgl-d 4xrq-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (2)

Deposited unit

A: Capsid protein p24

B: Capsid protein p24

C: Capsid protein p24

D: Capsid protein p24

E: Capsid protein p24

F: Capsid protein p24

G: Capsid protein p24

H: Capsid protein p24

I: Capsid protein p24

J: Capsid protein p24

K: Capsid protein p24

L: Capsid protein p24

306 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Capsid protein p24

B: Capsid protein p24

C: Capsid protein p24

D: Capsid protein p24

E: Capsid protein p24

F: Capsid protein p24

defined by author&software
153 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Capsid protein p24

H: Capsid protein p24

I: Capsid protein p24

J: Capsid protein p24

K: Capsid protein p24

L: Capsid protein p24

defined by author&software
153 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	136.062, 136.657, 208.454
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID
1	1	1	chain E resseq 1:3 or resseq 11-12 or (resseq 13...	E
2	1	1	chain B resseq 1:3 or resseq 11-12 or (resseq 13...	B
3	1	1	chain C resseq 1:3 or resseq 11-12 or (resseq 13...	C
4	1	1	chain D resseq 1:3 or resseq 11-12 or (resseq 13...	D
5	1	1	chain A resseq 1:3 or resseq 11-12 or (resseq 13...	A
6	1	1	chain F resseq 1:3 or resseq 11-12 or (resseq 13...	F
7	1	1	chain G resseq 1:3 or resseq 11-12 or (resseq 13...	G
8	1	1	chain H resseq 1:3 or resseq 11-12 or (resseq 13...	H
9	1	1	chain I resseq 1:3 or resseq 11-12 or (resseq 13...	I
10	1	1	chain J resseq 1:3 or resseq 11-12 or (resseq 13...	J
11	1	1	chain K resseq 1:3 or resseq 11-12 or (resseq 13...	K
12	1	1	chain L resseq 1:3 or resseq 11-12 or (resseq 13...	L
1	1	2	chain A resseq 116:125	A
2	1	2	chain B resseq 116:125	B
3	1	2	chain C resseq 116:125	C
4	1	2	chain D resseq 116:125	D
5	1	2	chain E resseq 116:125	E
6	1	2	chain F resseq 116:125	F
7	1	2	chain G resseq 116:125	G
8	1	2	chain H resseq 116:125	H
9	1	2	chain I resseq 116:125	I
10	1	2	chain J resseq 116:125	J
11	1	2	chain K resseq 116:125	K
12	1	2	chain L resseq 116:125	L
1	1	3	chain E resseq 149:153 or (resseq 154 and backbone) or...	E
2	1	3	chain A resseq 149:153 or (resseq 154 and backbone) or...	A
3	1	3	chain B resseq 149:153 or (resseq 154 and backbone) or...	B
4	1	3	chain C resseq 149:153 or (resseq 154 and backbone) or...	C
5	1	3	chain D resseq 149:153 or (resseq 154 and backbone) or...	D
6	1	3	chain F resseq 149:153 or (resseq 154 and backbone) or...	F
7	1	3	chain G resseq 149:153 or (resseq 154 and backbone) or...	G
8	1	3	chain H resseq 149:153 or (resseq 154 and backbone) or...	H
9	1	3	chain I resseq 149:153 or (resseq 154 and backbone) or...	I
10	1	3	chain J resseq 149:153 or (resseq 154 and backbone) or...	J
11	1	3	chain K resseq 149:153 or (resseq 154 and backbone) or...	K
12	1	3	chain L resseq 149:153 or (resseq 154 and backbone) or...	L
1	1	4	chain E resseq 190:191 or (resseq 192 and backbone) or...	E
2	1	4	chain F resseq 190:191 or (resseq 192 and backbone) or...	F
3	1	4	chain G resseq 190:191 or (resseq 192 and backbone) or...	G
4	1	4	chain H resseq 190:191 or (resseq 192 and backbone) or...	H
5	1	4	chain I resseq 190:191 or (resseq 192 and backbone) or...	I
6	1	4	chain J resseq 190:191 or (resseq 192 and backbone) or...	J
7	1	4	chain K resseq 190:191 or (resseq 192 and backbone) or...	K
8	1	4	chain L resseq 190:191 or (resseq 192 and backbone) or...	L
9	1	4	chain A resseq 190:191 or (resseq 192 and backbone) or...	A
10	1	4	chain B resseq 190:191 or (resseq 192 and backbone) or...	B
11	1	4	chain C resseq 190:191 or (resseq 192 and backbone) or...	C
12	1	4	chain D resseq 190:191 or (resseq 192 and backbone) or...	D
1	1	5	chain E resseq 206:218 or (resseq 219 and backbone)	E
2	1	5	chain A resseq 206:218 or (resseq 219 and backbone)	A
3	1	5	chain B resseq 206:218 or (resseq 219 and backbone)	B
4	1	5	chain C resseq 206:218 or (resseq 219 and backbone)	C
5	1	5	chain D resseq 206:218 or (resseq 219 and backbone)	D
6	1	5	chain F resseq 206:218 or (resseq 219 and backbone)	F
7	1	5	chain G resseq 206:218 or (resseq 219 and backbone)	G
8	1	5	chain H resseq 206:218 or (resseq 219 and backbone)	H
9	1	5	chain I resseq 206:218 or (resseq 219 and backbone)	I
10	1	5	chain J resseq 206:218 or (resseq 219 and backbone)	J
11	1	5	chain K resseq 206:218 or (resseq 219 and backbone)	K
12	1	5	chain L resseq 206:218 or (resseq 219 and backbone)	L
1	1	6	chain C (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	C
2	1	6	chain A (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	A
3	1	6	chain B (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	B
4	1	6	chain D (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	D
5	1	6	chain E (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	E
6	1	6	chain F (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	F
7	1	6	chain G (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	G
8	1	6	chain H (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	H
9	1	6	chain I (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	I
10	1	6	chain J (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	J
11	1	6	chain K (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	K
12	1	6	chain L (resseq 4 and backbone) or resseq 5 or (resseq 6:10 and backbone)	L
1	1	7	chain C resseq 175:189	C
2	1	7	chain J resseq 175:189	J
1	1	8	chain B resseq 175:189	B
2	1	8	chain I resseq 175:189	I
1	1	9	chain D resseq 175:189	D
2	1	9	chain K resseq 175:189	K
1	1	10	chain L resseq 175:181 or (resseq 182 and backbone) or resseq 183:189	L
2	1	10	chain A resseq 175:181 or (resseq 182 and backbone) or resseq 183:189	A
3	1	10	chain E resseq 175:181 or (resseq 182 and backbone) or resseq 183:189	E
4	1	10	chain F resseq 175:181 or (resseq 182 and backbone) or resseq 183:189	F
5	1	10	chain G resseq 175:181 or (resseq 182 and backbone) or resseq 183:189	G
6	1	10	chain H resseq 175:181 or (resseq 182 and backbone) or resseq 183:189	H

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	Capsid protein p24 / / CA Mass: 25461.271 Da / Num. of mol.: 12 / Fragment: UNP residues 133-363 / Mutation: A14C,E45C,W184A,M185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) Strain: NL4-3 / Gene: CA, gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12497

#1: Protein

Capsid protein p24 /

/ CA

Mass: 25461.271 Da / Num. of mol.: 12 / Fragment: UNP residues 133-363 / Mutation: A14C,E45C,W184A,M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Strain: NL4-3 / Gene: CA, gag-pol / Plasmid: pET11a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12497

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.17 Å³/Da / Density % sol: 61.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10-12% PEG 8,000, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9773 Å
Detector	Date: Jun 27, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9773 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 102201

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Processing

Software

Name	Version	Classification
MOLREP		phasing
PHENIX	(phenix.refine)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H47

3h47

Resolution: 2.704→34.742 Å / SU ML: 0.39 / σ(F): 1.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2632	2565	2.51 %	Thin shell
R_work	0.2385	-	-	-
obs	0.2391	102181	95.87 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 35.268 Å² / k_sol: 0.301 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.704→34.742 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19082	0	0	0	19082

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	E	825	X-RAY DIFFRACTION	POSITIONAL
1	2	B	825	X-RAY DIFFRACTION	POSITIONAL	0.11
1	3	C	837	X-RAY DIFFRACTION	POSITIONAL	0.101
1	4	D	837	X-RAY DIFFRACTION	POSITIONAL	0.117
1	5	A	837	X-RAY DIFFRACTION	POSITIONAL	0.12
1	6	F	837	X-RAY DIFFRACTION	POSITIONAL	0.109
1	7	G	837	X-RAY DIFFRACTION	POSITIONAL	0.104
1	8	H	837	X-RAY DIFFRACTION	POSITIONAL	0.094
1	9	I	837	X-RAY DIFFRACTION	POSITIONAL	0.112
1	10	J	837	X-RAY DIFFRACTION	POSITIONAL	0.11
1	11	K	837	X-RAY DIFFRACTION	POSITIONAL	0.111
1	12	L	837	X-RAY DIFFRACTION	POSITIONAL	0.095
2	1	A	77	X-RAY DIFFRACTION	POSITIONAL
2	2	B	77	X-RAY DIFFRACTION	POSITIONAL	0.099
2	3	C	77	X-RAY DIFFRACTION	POSITIONAL	0.077
2	4	D	77	X-RAY DIFFRACTION	POSITIONAL	0.094
2	5	E	77	X-RAY DIFFRACTION	POSITIONAL	0.103
2	6	F	77	X-RAY DIFFRACTION	POSITIONAL	0.072
2	7	G	77	X-RAY DIFFRACTION	POSITIONAL	0.092
2	8	H	77	X-RAY DIFFRACTION	POSITIONAL	0.072
2	9	I	77	X-RAY DIFFRACTION	POSITIONAL	0.081
2	10	J	77	X-RAY DIFFRACTION	POSITIONAL	0.086
2	11	K	77	X-RAY DIFFRACTION	POSITIONAL	0.091
2	12	L	77	X-RAY DIFFRACTION	POSITIONAL	0.083
3	1	E	208	X-RAY DIFFRACTION	POSITIONAL
3	2	A	208	X-RAY DIFFRACTION	POSITIONAL	0.077
3	3	B	208	X-RAY DIFFRACTION	POSITIONAL	0.112
3	4	C	208	X-RAY DIFFRACTION	POSITIONAL	0.09
3	5	D	205	X-RAY DIFFRACTION	POSITIONAL	0.094
3	6	F	208	X-RAY DIFFRACTION	POSITIONAL	0.071
3	7	G	208	X-RAY DIFFRACTION	POSITIONAL	0.086
3	8	H	208	X-RAY DIFFRACTION	POSITIONAL	0.089
3	9	I	208	X-RAY DIFFRACTION	POSITIONAL	0.112
3	10	J	208	X-RAY DIFFRACTION	POSITIONAL	0.098
3	11	K	208	X-RAY DIFFRACTION	POSITIONAL	0.101
3	12	L	208	X-RAY DIFFRACTION	POSITIONAL	0.068
4	1	E	96	X-RAY DIFFRACTION	POSITIONAL
4	2	F	96	X-RAY DIFFRACTION	POSITIONAL	0.075
4	3	G	94	X-RAY DIFFRACTION	POSITIONAL	0.078
4	4	H	95	X-RAY DIFFRACTION	POSITIONAL	0.08
4	5	I	98	X-RAY DIFFRACTION	POSITIONAL	0.085
4	6	J	96	X-RAY DIFFRACTION	POSITIONAL	0.099
4	7	K	90	X-RAY DIFFRACTION	POSITIONAL	0.102
4	8	L	98	X-RAY DIFFRACTION	POSITIONAL	0.073
4	9	A	95	X-RAY DIFFRACTION	POSITIONAL	0.084
4	10	B	98	X-RAY DIFFRACTION	POSITIONAL	0.081
4	11	C	96	X-RAY DIFFRACTION	POSITIONAL	0.104
4	12	D	87	X-RAY DIFFRACTION	POSITIONAL	0.078
5	1	E	89	X-RAY DIFFRACTION	POSITIONAL
5	2	A	89	X-RAY DIFFRACTION	POSITIONAL	0.064
5	3	B	91	X-RAY DIFFRACTION	POSITIONAL	0.075
5	4	C	91	X-RAY DIFFRACTION	POSITIONAL	0.067
5	5	D	91	X-RAY DIFFRACTION	POSITIONAL	0.069
5	6	F	91	X-RAY DIFFRACTION	POSITIONAL	0.061
5	7	G	91	X-RAY DIFFRACTION	POSITIONAL	0.068
5	8	H	91	X-RAY DIFFRACTION	POSITIONAL	0.068
5	9	I	91	X-RAY DIFFRACTION	POSITIONAL	0.084
5	10	J	87	X-RAY DIFFRACTION	POSITIONAL	0.068
5	11	K	91	X-RAY DIFFRACTION	POSITIONAL	0.074
5	12	L	91	X-RAY DIFFRACTION	POSITIONAL	0.06
6	1	C	32	X-RAY DIFFRACTION	POSITIONAL
6	2	A	32	X-RAY DIFFRACTION	POSITIONAL	0.098
6	3	B	32	X-RAY DIFFRACTION	POSITIONAL	0.127
6	4	D	32	X-RAY DIFFRACTION	POSITIONAL	0.146
6	5	E	32	X-RAY DIFFRACTION	POSITIONAL	0.072
6	6	F	32	X-RAY DIFFRACTION	POSITIONAL	0.149
6	7	G	32	X-RAY DIFFRACTION	POSITIONAL	0.07
6	8	H	32	X-RAY DIFFRACTION	POSITIONAL	0.1
6	9	I	32	X-RAY DIFFRACTION	POSITIONAL	0.09
6	10	J	32	X-RAY DIFFRACTION	POSITIONAL	0.132
6	11	K	32	X-RAY DIFFRACTION	POSITIONAL	0.068
6	12	L	32	X-RAY DIFFRACTION	POSITIONAL	0.104
7	1	C	102	X-RAY DIFFRACTION	POSITIONAL
7	2	J	102	X-RAY DIFFRACTION	POSITIONAL	0.08
8	1	B	42	X-RAY DIFFRACTION	POSITIONAL
8	2	I	42	X-RAY DIFFRACTION	POSITIONAL	0.071
9	1	D	28	X-RAY DIFFRACTION	POSITIONAL
9	2	K	28	X-RAY DIFFRACTION	POSITIONAL	0.071
10	1	L	87	X-RAY DIFFRACTION	POSITIONAL
10	2	A	87	X-RAY DIFFRACTION	POSITIONAL	0.076
10	3	E	96	X-RAY DIFFRACTION	POSITIONAL	0.067
10	4	F	96	X-RAY DIFFRACTION	POSITIONAL	0.074
10	5	G	87	X-RAY DIFFRACTION	POSITIONAL	0.078
10	6	H	28	X-RAY DIFFRACTION	POSITIONAL	0.086

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.704-2.7561	0.3342	171	0.313	4871	X-RAY DIFFRACTION	86
2.7561-2.8124	0.3217	171	0.2846	5485	X-RAY DIFFRACTION	97
2.8124-2.8735		0	0.2801	5726	X-RAY DIFFRACTION	98
2.8735-2.9403	0.319	171	0.2759	5519	X-RAY DIFFRACTION	98
2.9403-3.0138	0.3211	171	0.2682	5584	X-RAY DIFFRACTION	98
3.0138-3.0952	0.3013	171	0.2677	5534	X-RAY DIFFRACTION	97
3.0952-3.1862	0.3188	171	0.2689	5566	X-RAY DIFFRACTION	98
3.1862-3.289	0.3281	171	0.2725	5516	X-RAY DIFFRACTION	97
3.289-3.4065		0	0.2653	5725	X-RAY DIFFRACTION	97
3.4065-3.5427	0.2749	171	0.2524	5538	X-RAY DIFFRACTION	97
3.5427-3.7038	0.2872	171	0.2372	5564	X-RAY DIFFRACTION	97
3.7038-3.8988	0.272	171	0.2313	5554	X-RAY DIFFRACTION	97
3.8988-4.1427	0.2351	171	0.216	5538	X-RAY DIFFRACTION	96
4.1427-4.462	0.2103	171	0.1968	5522	X-RAY DIFFRACTION	96
4.462-4.9099		0	0.1802	5719	X-RAY DIFFRACTION	96
4.9099-5.6178	0.2231	171	0.2086	5530	X-RAY DIFFRACTION	95
5.6178-7.068	0.2691	171	0.2298	5543	X-RAY DIFFRACTION	95
7.068-34.7452	0.1598	171	0.1837	5582	X-RAY DIFFRACTION	92

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