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

ID or keywords:

Entry

Database: PDB / ID: 3p05

Title

X-ray structure of pentameric HIV-1 CA

Components

HIV-1 CA

Keywords

VIRAL PROTEIN / capsid protein

Function / homology

Function and homology information

viral budding via host ESCRT complex / HIV-1 retropepsin / 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 ...
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 / Reverse transcriptase thumb ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Pornillos, O.

Citation

Journal: Nature / Year: 2011
Title: Atomic-level modelling of the HIV capsid.
Authors: Pornillos, O. / Ganser-Pornillos, B.K. / Yeager, M.

History

Deposition	Sep 27, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 12, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3p05.cif.gz	204.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3p05.ent.gz	164.6 KB	Display	PDB format
PDBx/mmJSON format	3p05.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3p05_validation.pdf.gz	471.4 KB	Display	wwPDB validaton report
Full document	3p05_full_validation.pdf.gz	488.5 KB	Display
Data in XML	3p05_validation.xml.gz	36.3 KB	Display
Data in CIF	3p05_validation.cif.gz	49.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p0/3p05 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/3p05	HTTPS FTP

-
Related structure data

Related structure data	3p0aC 3h47S 2dik 3gv2 3h4e S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3p0a-2 3p0a-3 3p0a-1 3p0a-4 1c7y-1 6y5x-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (6) #87 - Mar 2007 Zinc Fingers similarity (2)

Deposited unit

A: HIV-1 CA

B: HIV-1 CA

C: HIV-1 CA

D: HIV-1 CA

E: HIV-1 CA

hetero molecules

129 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

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 number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3
4
5
6
7
8

#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

#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

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.54 %
Crystal grow	Temperature: 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

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 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 shell	Resolution: 2.5→2.54 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / R_sym value: 0.53 / % possible all: 94.9

-
Processing

Software

Name	Version	Classification
MOLREP		phasing
PHENIX	(phenix.refine: 1.6.1_357)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2662	2083	5.07 %	THIN SHELL
R_work	0.2304	-	-	-
obs	0.2322	41121	97.42 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.679 Å² / k_sol: 0.34 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.2214 Å²	-0 Å²	-0.6062 Å²
2-	-	-2.7843 Å²	-0 Å²
3-	-	-	-0.4371 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→32.577 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7908	0	10	0	7918

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	8079
X-RAY DIFFRACTION	f_angle_d	1.473	10986
X-RAY DIFFRACTION	f_dihedral_angle_d	13.798	2999
X-RAY DIFFRACTION	f_chiral_restr	0.092	1260
X-RAY DIFFRACTION	f_plane_restr	0.008	1426

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	747	X-RAY DIFFRACTION	POSITIONAL
1	2	B	747	X-RAY DIFFRACTION	POSITIONAL	0.125
1	3	C	740	X-RAY DIFFRACTION	POSITIONAL	0.116
1	4	D	747	X-RAY DIFFRACTION	POSITIONAL	0.091
1	5	E	747	X-RAY DIFFRACTION	POSITIONAL	0.105
2	1	B	54	X-RAY DIFFRACTION	POSITIONAL
2	2	C	54	X-RAY DIFFRACTION	POSITIONAL	0.133
2	3	D	44	X-RAY DIFFRACTION	POSITIONAL	0.109
3	1	A	80	X-RAY DIFFRACTION	POSITIONAL
3	2	B	80	X-RAY DIFFRACTION	POSITIONAL	0.071
3	3	C	80	X-RAY DIFFRACTION	POSITIONAL	0.051
3	4	D	80	X-RAY DIFFRACTION	POSITIONAL	0.065
3	5	E	80	X-RAY DIFFRACTION	POSITIONAL	0.056
4	1	A	139	X-RAY DIFFRACTION	POSITIONAL
4	2	B	139	X-RAY DIFFRACTION	POSITIONAL	0.075
4	3	C	139	X-RAY DIFFRACTION	POSITIONAL	0.075
4	4	D	139	X-RAY DIFFRACTION	POSITIONAL	0.073
4	5	E	131	X-RAY DIFFRACTION	POSITIONAL	0.077
5	1	E	96	X-RAY DIFFRACTION	POSITIONAL
5	2	A	96	X-RAY DIFFRACTION	POSITIONAL	0.08
5	3	B	96	X-RAY DIFFRACTION	POSITIONAL	0.075
5	4	C	96	X-RAY DIFFRACTION	POSITIONAL	0.078
5	5	D	96	X-RAY DIFFRACTION	POSITIONAL	0.078
6	1	A	299	X-RAY DIFFRACTION	POSITIONAL
6	2	B	299	X-RAY DIFFRACTION	POSITIONAL	0.088
6	3	C	298	X-RAY DIFFRACTION	POSITIONAL	0.08
6	4	D	299	X-RAY DIFFRACTION	POSITIONAL	0.086
6	5	E	298	X-RAY DIFFRACTION	POSITIONAL	0.083
7	1	A	100	X-RAY DIFFRACTION	POSITIONAL
7	2	B	100	X-RAY DIFFRACTION	POSITIONAL	0.124
7	3	C	100	X-RAY DIFFRACTION	POSITIONAL	0.062
7	4	D	100	X-RAY DIFFRACTION	POSITIONAL	0.077
7	5	E	100	X-RAY DIFFRACTION	POSITIONAL	0.079
8	1	A	58	X-RAY DIFFRACTION	POSITIONAL
8	2	C	58	X-RAY DIFFRACTION	POSITIONAL	0.092
8	3	D	58	X-RAY DIFFRACTION	POSITIONAL	0.065
8	4	E	58	X-RAY DIFFRACTION	POSITIONAL	0.078

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 (%)
2.5-2.5584	0.298	140	0.2728	2417	X-RAY DIFFRACTION	89
2.5584-2.6223	0.3289	138	0.2773	2501	X-RAY DIFFRACTION	96
2.6223-2.6932	0.3526	139	0.2821	2553	X-RAY DIFFRACTION	96
2.6932-2.7724	0.318	138	0.2789	2554	X-RAY DIFFRACTION	97
2.7724-2.8619	0.3189	139	0.2744	2578	X-RAY DIFFRACTION	97
2.8619-2.9641	0.2794	138	0.2691	2581	X-RAY DIFFRACTION	97
2.9641-3.0827	0.3524	138	0.2614	2621	X-RAY DIFFRACTION	98
3.0827-3.2229	0.3011	139	0.2561	2608	X-RAY DIFFRACTION	98
3.2229-3.3926	0.2594	139	0.2422	2624	X-RAY DIFFRACTION	99
3.3926-3.6049	0.2593	139	0.2186	2649	X-RAY DIFFRACTION	99
3.6049-3.8828	0.2649	139	0.2202	2654	X-RAY DIFFRACTION	99
3.8828-4.2728	0.2185	139	0.2066	2668	X-RAY DIFFRACTION	99
4.2728-4.8893	0.2437	139	0.193	2671	X-RAY DIFFRACTION	99
4.8893-6.1532	0.2798	139	0.2238	2660	X-RAY DIFFRACTION	99
6.1532-32.5797	0.2107	140	0.1941	2699	X-RAY DIFFRACTION	99

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi