PDB-2xgu: Structure of the N-terminal domain of capsid protein from Rabbit ...

ID or keywords:

Entry

Database: PDB / ID: 2xgu

Title

Structure of the N-terminal domain of capsid protein from Rabbit Endogenous Lentivirus (RELIK)

Components

RELIK CAPSID N-TERMINAL DOMAIN

Keywords

VIRAL PROTEIN / RETROVIRAL CAPSID

Function / homology

Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Orthogonal Bundle / Mainly Alpha / ACETATE ION

Function and homology information

Biological species

ORYCTOLAGUS CUNICULUS (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.502 Å

Authors

Goldstone, D.C. / Taylor, I.A. / Robertson, L.E. / Haire, L.F. / Stoye, J.P.

Citation

Journal: Cell Host Microbe / Year: 2010
Title: Structural and Functional Analysis of Prehistoric Lentiviruses Uncovers an Ancient Molecular Interface.
Authors: Goldstone, D.C. / Yap, M.W. / Robertson, L.E. / Haire, L.F. / Taylor, W.R. / Katzourakis, A. / Stoye, J.P. / Taylor, I.A.

History

Deposition	Jun 7, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 22, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2xgu.cif.gz	126.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2xgu.ent.gz	101 KB	Display	PDB format
PDBx/mmJSON format	2xgu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2xgu_validation.pdf.gz	449.5 KB	Display	wwPDB validaton report
Full document	2xgu_full_validation.pdf.gz	453.7 KB	Display
Data in XML	2xgu_validation.xml.gz	16.1 KB	Display
Data in CIF	2xgu_validation.cif.gz	23.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xg/2xgu ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xgu	HTTPS FTP

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Related structure data

Related structure data	2xgvC 2xgyC C: citing same article (ref.)
Similar structure data	1ckn-1 2b3d-d 6mev-4 5r5s-d 7a49-1 6sna-4 4gps-d 3dse-d 5v8u-2 2noi-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: RELIK CAPSID N-TERMINAL DOMAIN

B: RELIK CAPSID N-TERMINAL DOMAIN

hetero molecules

33.1 kDa, 2 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)	87.000, 38.680, 84.717
Angle α, β, γ (deg.)	90.00, 114.87, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-2028- HOH
2	1	A-2126- HOH
3	1	B-2108- HOH

#1: Protein	RELIK CAPSID N-TERMINAL DOMAIN Mass: 16511.818 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ORYCTOLAGUS CUNICULUS (rabbit) / Description: SYNTHESISED RECONSTRUCTED GENE / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.94 Å³/Da / Density % sol: 33.5 % / Description: NONE
Crystal grow	pH: 4.6 / Details: 16-26% PEG3350, 0.1M NA-ACETATE PH 4.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9805
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9805 Å / Relative weight: 1
Reflection	Resolution: 1.5→35 Å / Num. obs: 40134 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / B_iso Wilson estimate: 20.1 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 37
Reflection shell	Resolution: 1.5→1.55 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
DENZO		data reduction
SCALING		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.502→29.659 Å / SU ML: 0.19 / σ(F): 0.03 / Phase error: 23.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2182	1954	5.1 %
R_work	0.1951	-	-
obs	0.1963	38047	92.48 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 65.111 Å² / k_sol: 0.396 e/Å³

Displacement parameters

B_iso mean: 26.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.3514 Å²	-0 Å²	-1.9097 Å²
2-	-	-1.6398 Å²	-0 Å²
3-	-	-	2.9912 Å²

Refinement step

Cycle: LAST / Resolution: 1.502→29.659 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2099	0	4	308	2411

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2241
X-RAY DIFFRACTION	f_angle_d	0.966	3073
X-RAY DIFFRACTION	f_dihedral_angle_d	13.86	833
X-RAY DIFFRACTION	f_chiral_restr	0.058	351
X-RAY DIFFRACTION	f_plane_restr	0.005	400

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 (%)
1.502-1.5396	0.286	119	0.2429	2307	X-RAY DIFFRACTION	82
1.5396-1.5812	0.2441	122	0.2167	2399	X-RAY DIFFRACTION	87
1.5812-1.6278	0.238	143	0.2026	2414	X-RAY DIFFRACTION	88
1.6278-1.6803	0.2385	137	0.2078	2464	X-RAY DIFFRACTION	90
1.6803-1.7403	0.2706	126	0.1985	2545	X-RAY DIFFRACTION	92
1.7403-1.81	0.2123	146	0.1879	2579	X-RAY DIFFRACTION	93
1.81-1.8924	0.2052	149	0.1777	2596	X-RAY DIFFRACTION	94
1.8924-1.9921	0.2182	143	0.1823	2625	X-RAY DIFFRACTION	95
1.9921-2.1169	0.2324	153	0.1787	2698	X-RAY DIFFRACTION	97
2.1169-2.2803	0.1769	135	0.172	2743	X-RAY DIFFRACTION	97
2.2803-2.5097	0.2116	153	0.1819	2723	X-RAY DIFFRACTION	98
2.5097-2.8726	0.2025	134	0.1802	2751	X-RAY DIFFRACTION	98
2.8726-3.6181	0.2096	151	0.1827	2672	X-RAY DIFFRACTION	95
3.6181-29.6647	0.2002	143	0.2026	2577	X-RAY DIFFRACTION	89

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.8439	-0.6419	-0.603	0.5121	0.3625	0.7859	0.2783	0.3753	0.0915	-0.149	-0.1771	-0.2567	0.1067	0.0322	-0.0698	0.1507	0.0379	0.042	0.2197	-0.0203	0.159	16.4155	31.1013	-5.3829
2	1.4051	0.0788	-0.0685	0.8573	-0.3079	0.5914	0.1524	-0.2397	-0.3389	0.0226	-0.0064	0.317	0.2159	-0.0546	-0.1061	0.1869	-0.0336	-0.0197	0.1579	0.0343	0.1504	2.3103	24.2105	11.2001
3	0.8771	0.5493	0.5699	0.774	0.0368	0.5726	0.0644	-0.0606	0.0348	0.0646	-0.0151	0.0543	0.2103	-0.0739	-0.0288	0.1218	-0.0019	0.0191	0.1321	-0.008	0.0924	5.5368	32.3333	9.5348
4	1.8178	-0.3971	0.763	1.1682	-0.4698	1.8578	-0.3641	-0.0953	0.3957	0.5243	0.3847	0.2581	-0.4024	-0.2219	-0.0616	0.1905	0.0532	0.0415	0.122	0.0021	0.1634	5.7149	48.7907	14.8189
5	2.949	-0.864	-0.6825	1.6114	0.432	1.8993	-0.2539	1.2153	0.3224	-0.107	-0.079	0.3053	-0.2848	-0.0614	0.351	0.2064	-0.0518	-0.0228	0.4226	0.1166	0.3388	15.4142	58.6192	1.5014
6	2.0064	1.2379	0.413	1.1731	0.2084	0.3641	-0.1955	0.3877	0.658	-0.2925	0.0618	0.2351	-0.2699	0.1886	0.0514	0.1377	-0.0155	-0.0024	0.2001	0.0702	0.1936	9.5968	46.3728	-0.3405
7	0.7804	0.1964	0.3194	0.3588	-0.2362	0.4519	0.031	0.0412	0.1068	0.0531	-0.0198	0.0176	-0.1025	0.0651	-0.0235	0.1461	-0.0174	0.0235	0.1223	-0.0119	0.1285	11.6727	40.0264	11.4198
8	1.4343	-1.0691	0.8061	1.7236	0.9015	3.0509	-0.091	0.0333	-0.5513	0.0196	-0.071	0.7171	0.1374	0.3482	-0.0022	0.3661	-0.0058	0.1116	0.22	0.07	0.3507	1.9761	24.2727	27.2052
9	0.4675	0.2499	0.0364	0.1391	0.0122	0.0073	0.2473	-0.1369	0.1691	0.2172	-0.0717	-0.01	-0.0791	0.1231	-0.1143	0.1642	-0.0343	0.0439	0.2452	-0.0011	0.2103	8.5227	33.3362	44.2207
10	1.0541	1.1255	0.1323	1.2925	0.2776	0.7952	0.0657	0.0349	-0.1911	0.0477	0.0483	-0.1256	0.3471	-0.0009	-0.0882	0.1615	0.0265	-0.0268	0.1191	-0.0247	0.1268	19.9415	28.208	26.8423
11	0.7565	-0.2383	-0.2083	0.8848	0.3715	0.7021	0.1104	0.1187	0.2107	0.0701	-0.1212	-0.2218	0.0153	-0.0539	0.0098	0.1077	0.0019	0.0181	0.144	-0.0001	0.1371	20.9409	36.7606	33.9772
12	1.1741	-0.4363	-0.841	1.3109	0.4528	0.6623	0.192	0.3893	0.0362	-0.4813	-0.1303	-0.4237	-0.2033	0.3865	-0.0769	0.1515	-0.026	0.0804	0.2345	-0.0211	0.2001	27.1625	41.1859	21.4609
13	0.6363	1.0619	0.0057	2.7476	0.8579	1.4166	-0.2718	0.0044	0.2871	-0.3786	0.2366	0.6946	-0.2202	0.0832	0.0534	0.2113	-0.0199	0.0281	0.1343	-0.0279	0.2546	16.7059	55.3631	25.6724
14	0.5865	0.2609	0.7175	0.1632	0.4233	1.1067	0.3347	-1.3787	0.4187	0.1821	0.1543	-0.4364	0.0127	-0.2816	-0.3532	0.1379	-0.0268	0.0975	0.4458	-0.2044	0.5282	8.3232	58.8697	38.0998
15	0.7226	-0.4098	-0.3571	1.0928	-0.4449	0.6676	-0.0091	-0.0694	0.1816	-0.009	-0.0145	0.0253	-0.2246	-0.0396	-0.0069	0.1416	-0.0071	0.0298	0.1555	-0.0553	0.1651	14.3694	46.2698	35.8233
16	0.3376	0.1072	0.4106	0.9671	0.1412	0.4989	-0.0297	0.203	0.1524	-0.2233	0.0264	0.0396	-0.219	0.1744	0.0383	0.1352	-0.002	0.0141	0.151	-0.0204	0.0999	18.9824	38.4482	17.5808

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:14)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 15:33)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 34:68)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 69:83)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 84:94)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 95:116)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 117:135)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 136:143)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 1:13)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 14:45)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 46:60)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 64:72)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 73:87)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 88:97)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 98:127)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 128:138)

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