PDB-5j7u: Faustovirus major capsid protein

ID or keywords:

Entry

Database: PDB / ID: 5j7u

Title

Faustovirus major capsid protein

Components

major capsid protein
unknown

Keywords

VIRAL PROTEIN / virus / capsid / double jelly-roll

Function / homology

Group II dsDNA virus coat/capsid protein / Putative major capsid protein p72

Function and homology information

Biological species

Faustovirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.44 Å

Authors

Klose, T. / Rossmann, M.G.

Citation

Journal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structure of faustovirus, a large dsDNA virus.
Authors: Thomas Klose / Dorine G Reteno / Samia Benamar / Adam Hollerbach / Philippe Colson / Bernard La Scola / Michael G Rossmann /

Abstract: Many viruses protect their genome with a combination of a protein shell with or without a membrane layer. Here we describe the structure of faustovirus, the first DNA virus (to our knowledge) that ...

History

Deposition	Apr 6, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 18, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 1, 2016	Group: Database references
Revision 1.2	Jun 15, 2016	Group: Database references
Revision 1.3	Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5j7u.cif.gz	2.8 MB	Display	PDBx/mmCIF format
PDB format	pdb5j7u.ent.gz	2.4 MB	Display	PDB format
PDBx/mmJSON format	5j7u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5j7u_validation.pdf.gz	568 KB	Display	wwPDB validaton report
Full document	5j7u_full_validation.pdf.gz	623.9 KB	Display
Data in XML	5j7u_validation.xml.gz	258.8 KB	Display
Data in CIF	5j7u_validation.cif.gz	356.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j7/5j7u ftp://data.pdbj.org/pub/pdb/validation_reports/j7/5j7u	HTTPS FTP

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Related structure data

Related structure data	8144C 8145C 5j7oSC 5j7vC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5j7o-2 5j7o-1 5j7v-d 6lcn-d 4cof-d 6bm0-d 6d8g-d 5a8w-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search

Related structure data

8144C

8145C

5j7oSC

5j7vC

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#132 - Dec 2010 Adenovirus similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (2)

Deposited unit

A: major capsid protein

B: major capsid protein

C: major capsid protein

D: major capsid protein

E: major capsid protein

F: major capsid protein

M: unknown

N: unknown

O: unknown

P: unknown

Q: unknown

R: unknown

G: major capsid protein

H: major capsid protein

I: major capsid protein

J: major capsid protein

K: major capsid protein

L: major capsid protein

S: unknown

T: unknown

U: unknown

V: unknown

W: unknown

X: unknown

883 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: major capsid protein

B: major capsid protein

C: major capsid protein

M: unknown

N: unknown

O: unknown

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

2

D: major capsid protein

E: major capsid protein

F: major capsid protein

P: unknown

Q: unknown

R: unknown

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

3

G: major capsid protein

H: major capsid protein

I: major capsid protein

S: unknown

T: unknown

U: unknown

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

4

J: major capsid protein

K: major capsid protein

L: major capsid protein

V: unknown

W: unknown

X: unknown

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

Unit cell

Length a, b, c (Å)	86.380, 390.830, 130.140
Angle α, β, γ (deg.)	90.00, 91.66, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	major capsid protein Mass: 71781.891 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Faustovirus / References: UniProt: A0A0H3TLP8*PLUS
#2: Protein/peptide	unknown Mass: 1805.216 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Faustovirus
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2031 / 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: 2.5 Å³/Da / Density % sol: 50.75 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6 M ammonium sulfate, 10% dioxane

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2014
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03318 Å / Relative weight: 1
Reflection	Resolution: 2.44→78.17 Å / Num. obs: 317565 / % possible obs: 99.8 % / Redundancy: 4.9 % / R_merge(I) obs: 0.23 / Net I/σ(I): 8
Reflection shell	Resolution: 2.44→2.5 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER	2.5.6	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 5J7O

5j7o

Resolution: 2.44→72.919 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.61

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.252	15703	4.96 %	Random selection
R_work	0.2047	301641	-	-
obs	0.207	316888	99.62 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.44→72.919 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	59004	0	0	2031	61035

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	60387
X-RAY DIFFRACTION	f_angle_d	0.606	82532
X-RAY DIFFRACTION	f_dihedral_angle_d	16.044	21353
X-RAY DIFFRACTION	f_chiral_restr	0.044	9543
X-RAY DIFFRACTION	f_plane_restr	0.004	10667

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 (%)
2.44-2.4677	0.3695	495	0.3344	10149	X-RAY DIFFRACTION	99
2.4677-2.4968	0.3842	498	0.3099	9838	X-RAY DIFFRACTION	99
2.4968-2.5272	0.3542	541	0.3021	10043	X-RAY DIFFRACTION	100
2.5272-2.5592	0.3425	514	0.3006	10049	X-RAY DIFFRACTION	100
2.5592-2.5929	0.3397	558	0.2919	9964	X-RAY DIFFRACTION	100
2.5929-2.6284	0.3314	565	0.2855	9927	X-RAY DIFFRACTION	99
2.6284-2.666	0.3153	557	0.2735	9969	X-RAY DIFFRACTION	99
2.666-2.7058	0.3213	536	0.264	10074	X-RAY DIFFRACTION	99
2.7058-2.748	0.3158	497	0.2585	9971	X-RAY DIFFRACTION	100
2.748-2.7931	0.3178	528	0.2576	10095	X-RAY DIFFRACTION	100
2.7931-2.8413	0.3062	495	0.2494	10031	X-RAY DIFFRACTION	100
2.8413-2.8929	0.3025	526	0.2495	10114	X-RAY DIFFRACTION	100
2.8929-2.9486	0.3024	492	0.2351	10018	X-RAY DIFFRACTION	100
2.9486-3.0088	0.2861	518	0.2267	10080	X-RAY DIFFRACTION	100
3.0088-3.0742	0.2866	526	0.2244	10096	X-RAY DIFFRACTION	100
3.0742-3.1457	0.2987	550	0.222	9982	X-RAY DIFFRACTION	100
3.1457-3.2244	0.2697	516	0.2172	10112	X-RAY DIFFRACTION	100
3.2244-3.3115	0.2675	464	0.2101	10103	X-RAY DIFFRACTION	100
3.3115-3.409	0.2583	518	0.2076	10044	X-RAY DIFFRACTION	100
3.409-3.519	0.2353	508	0.1952	10138	X-RAY DIFFRACTION	100
3.519-3.6448	0.2385	554	0.1868	10005	X-RAY DIFFRACTION	100
3.6448-3.7907	0.2114	568	0.181	10034	X-RAY DIFFRACTION	100
3.7907-3.9632	0.2312	517	0.1793	10123	X-RAY DIFFRACTION	100
3.9632-4.1722	0.2232	521	0.1694	10042	X-RAY DIFFRACTION	100
4.1722-4.4335	0.2048	545	0.1533	10013	X-RAY DIFFRACTION	100
4.4335-4.7758	0.2113	530	0.1502	10148	X-RAY DIFFRACTION	100
4.7758-5.2563	0.1887	571	0.1619	9973	X-RAY DIFFRACTION	100
5.2563-6.0165	0.2144	446	0.176	10161	X-RAY DIFFRACTION	100
6.0165-7.5789	0.2443	524	0.1945	10140	X-RAY DIFFRACTION	100
7.5789-72.9516	0.1928	525	0.1817	9749	X-RAY DIFFRACTION	96

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	0.2441	0.0422	-0.084	0.2449	-0.1038	0.3764	0.01	-0.0223	0.0227	-0.0163	-0.0035	0.0685	0.0087	-0.0946	-0.0084	0.2275	-0.0063	-0.0145	0.2626	-0.02	0.2504	-21.3316	-44.0149	132.9628
2	0.2498	0.1624	-0.0922	0.4926	-0.1264	0.2625	0.0011	0.0269	-0.0443	-0.1033	-0.0064	-0.0543	0.056	-0.0152	0.0064	0.2462	-0.0073	-0.0049	0.258	-0.0185	0.2399	-5.5423	-57.8982	122.9579
3	0.3543	0.0124	0.0103	0.3078	-0.0588	0.3437	0.0259	-0.0703	-0.0591	0.0412	-0.0138	-0.0223	0.0405	0.0329	-0.0122	0.2328	-0.0142	-0.0153	0.2939	-0.0047	0.2445	-6.0577	-56.1586	145.7644
4	0.3269	0.2057	-0.0083	0.4474	-0.0192	0.3883	0.0086	-0.0548	0.0889	-0.011	0.0149	0.081	-0.0251	-0.0427	-0.0222	0.2711	-0.0022	0.0191	0.34	-0.0284	0.3167	-3.6303	-136.2022	128.7406
5	0.3318	0.0584	0.0558	0.3225	0.0167	0.2595	0.0176	-0.1567	0.0759	0.0556	-0.0238	0.0427	-0.0257	-0.0683	0.0072	0.3096	-0.0158	0.0397	0.4058	-0.0313	0.3172	0.625	-137.5496	151.4869
6	0.331	0.0642	0.0456	0.4363	-0.0253	0.4615	0.0016	-0.0476	0.0017	0.0176	0.0119	-0.0454	0.0008	0.0732	-0.0111	0.2717	-0.0028	0.0018	0.3173	-0.0294	0.2809	13.8209	-149.8524	136.9704
7	1.6514	-0.7909	0.3514	2.7896	-0.0765	3.04	0.0686	0.0007	0.1167	0.094	0.101	-0.1168	-0.2136	0.1945	-0.1653	0.6021	-0.2675	0.1445	0.6581	0.0768	0.742	-29.6352	-94.7216	149.89
8	4.4696	-1.7562	-0.6395	2.0066	2.0157	2.473	-0.1355	0.1504	-0.0557	0.0368	-0.0809	0.1496	0.0979	-0.1913	0.2019	0.5474	-0.1597	-0.0224	0.5278	0.0423	0.5744	-52.9789	-76.241	139.5343
9	4.1037	1.423	1.4716	3.2394	-0.6838	4.2139	-0.2034	-0.0599	-0.3085	-0.0528	0.1417	-0.1023	0.2235	-0.0866	0.0673	0.4851	-0.0243	-0.0088	0.4158	0.081	0.6709	-34.9762	-92.1915	118.7705
10	2.7661	1.3575	2.0293	0.7051	0.8202	2.2329	-0.2573	-0.0544	0.0357	0.0746	0.1459	-0.2182	0.2676	-0.1718	0.0998	0.8232	-0.1277	0.0329	0.6241	0.0243	0.5036	46.4435	-117.5617	138.7936
11	6.1024	1.6336	-0.5327	3.9255	1.2882	3.3186	-0.0718	0.3321	0.651	-0.1449	0.1083	0.6174	-0.3265	0.1408	-0.0309	0.4756	-0.0068	0.1	0.4065	0.0973	0.6824	25.8261	-102.3046	120.1834
12	0.1755	-0.0207	-0.2966	0.0022	0.0353	0.5008	0.0101	-0.0382	-0.1775	0.0179	0.0454	0.0554	0.1249	-0.1159	-0.0349	0.5227	0.014	-0.1465	1.0016	-0.0669	0.8465	24.9645	-98.7242	150.7838
13	0.3113	0.2088	-0.0657	0.6131	0.0802	0.4371	0.1046	-0.0886	0.0088	0.1964	-0.1398	0.0546	0.0056	-0.1321	0.0337	0.3286	-0.0416	0.0024	0.2966	-0.007	0.2339	20.3136	-41.6475	198.0668
14	0.3055	0.2409	0.0223	0.8106	0.0522	0.4663	0.0524	-0.0435	-0.1117	0.0873	-0.0754	-0.144	0.0373	-0.0203	0.0242	0.245	-0.01	-0.0289	0.2569	0.0221	0.2577	36.078	-55.4112	188.0189
15	0.3081	0.2193	0.0541	0.5985	0.0368	0.3012	0.1451	-0.1842	-0.0869	0.3102	-0.1626	-0.1182	0.0693	0.0083	0.0182	0.4798	-0.1066	-0.0778	0.389	0.0308	0.3313	35.5704	-53.7796	210.8277
16	0.3888	0.2406	-0.0267	0.5891	-0.0822	0.5338	0.0776	-0.0118	0.1079	0.008	-0.0484	0.108	-0.0457	0.0371	-0.0275	0.2556	-0.0324	0.0215	0.265	-0.0276	0.2802	37.5799	-133.7719	193.6913
17	0.4152	0.2576	-0.1795	0.5096	-0.1201	0.3978	0.1628	-0.2026	0.1056	0.1591	-0.1395	0.0302	-0.0605	0.1055	-0.0271	0.3691	-0.1174	0.0365	0.3998	-0.0497	0.3198	41.7397	-135.2842	216.5479
18	0.4026	0.2701	-0.055	0.6599	-0.0839	0.4531	0.0927	-0.0882	-0.0424	0.0353	-0.1196	-0.0981	0.0138	0.1691	0.0321	0.2874	-0.0268	-0.0025	0.3507	0.0088	0.2505	54.9544	-147.4748	201.7198
19	1.2518	-0.345	-0.5628	4.2191	0.2016	1.9659	-0.0055	-0.0749	-0.0202	-0.0387	0.2211	-0.0395	-0.1598	0.2244	-0.2167	0.849	-0.326	0.0824	0.7824	0.0701	0.5801	11.7096	-92.4122	214.7581
20	2.1575	-0.0583	-1.0486	0.3907	1.0938	3.4308	-0.0495	-0.1114	-0.2111	0.1765	0.1104	0.4745	0.2137	-0.2813	-0.0695	0.4795	-0.2359	0.0578	0.5696	0.0578	0.4916	-11.5482	-73.7022	204.4204
21	6.1673	-1.3428	-3.4871	4.5491	-2.7031	4.7877	-0.4712	0.6933	-0.7808	-0.0733	-0.0283	-0.0006	0.3514	-0.6796	0.4819	0.5902	-0.1563	-0.0514	0.4901	-0.1499	0.5997	6.3361	-89.6974	183.6441
22	2.2746	-0.4803	0.0168	2.354	-1.2451	2.2583	-0.213	-0.0059	0.0387	-0.2702	-0.049	-0.3944	-0.0787	0.1085	0.239	0.8293	-0.4042	0.0632	0.6644	0.0271	0.5467	87.6025	-115.1657	203.6054
23	2.908	-0.0219	-0.6032	2.0139	0.2466	1.0168	-0.202	0.0889	0.1794	-0.2507	-0.0456	0.3427	-0.1202	-0.0007	0.2371	0.8978	-0.1087	0.3258	0.3632	-0.1491	0.8455	66.8605	-99.7694	185.1733
24	3.5164	-0.4512	-0.1518	6.2714	1.0409	2.2782	-0.1097	-0.4191	-0.3339	0.1995	0.0055	0.2592	0.3854	-0.3282	0.0688	0.506	-0.1643	-0.0149	0.7363	0.0342	0.5094	66.5005	-96.5301	215.6785

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 12 through 620)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 6 through 621)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 5 through 620)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 12 through 620)
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 4 through 619)
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 11 through 620)
7	X-RAY DIFFRACTION	7	(chain 'M' and resid 991 through 1011)
8	X-RAY DIFFRACTION	8	(chain 'N' and resid 991 through 1011)
9	X-RAY DIFFRACTION	9	(chain 'O' and resid 991 through 1011)
10	X-RAY DIFFRACTION	10	(chain 'P' and resid 991 through 1011)
11	X-RAY DIFFRACTION	11	(chain 'Q' and resid 991 through 1011)
12	X-RAY DIFFRACTION	12	(chain 'R' and resid 991 through 1009)
13	X-RAY DIFFRACTION	13	(chain 'G' and resid 11 through 621)
14	X-RAY DIFFRACTION	14	(chain 'H' and resid 6 through 620)
15	X-RAY DIFFRACTION	15	(chain 'I' and resid 5 through 620)
16	X-RAY DIFFRACTION	16	(chain 'J' and resid 11 through 620)
17	X-RAY DIFFRACTION	17	(chain 'K' and resid 6 through 619)
18	X-RAY DIFFRACTION	18	(chain 'L' and resid 11 through 620)
19	X-RAY DIFFRACTION	19	(chain 'S' and resid 991 through 1011)
20	X-RAY DIFFRACTION	20	(chain 'T' and resid 991 through 1011)
21	X-RAY DIFFRACTION	21	(chain 'U' and resid 991 through 1011)
22	X-RAY DIFFRACTION	22	(chain 'V' and resid 991 through 1011)
23	X-RAY DIFFRACTION	23	(chain 'W' and resid 991 through 1011)
24	X-RAY DIFFRACTION	24	(chain 'X' and resid 991 through 1009)

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Yorodumi