PDB-4fp9: Human MTERF4-NSUN4 protein complex

ID or keywords:

Entry

Database: PDB / ID: 4fp9

Title

Human MTERF4-NSUN4 protein complex

Components

mTERF domain-containing protein 2
methyltransferase NSUN4

Keywords

TRANSFERASE / Modification enzyme

Function / homology

Function and homology information

rRNA modification in the mitochondrion / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / rRNA methyltransferase activity / mitochondrial transcription / mitochondrial ribosome assembly / protein targeting to mitochondrion / camera-type eye development / mitochondrial large ribosomal subunit / rRNA methylation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 2.9 Å

Authors

Spahr, H. / Hallberg, B.M.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the human MTERF4-NSUN4 protein complex that regulates mitochondrial ribosome biogenesis.
Authors: Spahr, H. / Habermann, B. / Gustafsson, C.M. / Larsson, N.G. / Hallberg, B.M.

History

Deposition	Jun 21, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 26, 2012	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Download

PDBx/mmCIF format	4fp9.cif.gz	940.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4fp9.ent.gz	790.2 KB	Display	PDB format
PDBx/mmJSON format	4fp9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4fp9_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	4fp9_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4fp9_validation.xml.gz	73.8 KB	Display
Data in CIF	4fp9_validation.cif.gz	100.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fp/4fp9 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/4fp9	HTTPS FTP

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Related structure data

Similar structure data	4frw-d 7nd6-d 20107 9142 6red-d 8898 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: methyltransferase NSUN4

B: mTERF domain-containing protein 2

C: methyltransferase NSUN4

D: methyltransferase NSUN4

E: mTERF domain-containing protein 2

F: methyltransferase NSUN4

G: mTERF domain-containing protein 2

H: mTERF domain-containing protein 2

hetero molecules

319 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: methyltransferase NSUN4

B: mTERF domain-containing protein 2

hetero molecules

defined by software
79.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: methyltransferase NSUN4

E: mTERF domain-containing protein 2

hetero molecules

defined by software
79.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: methyltransferase NSUN4

G: mTERF domain-containing protein 2

hetero molecules

defined by software
79.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

F: methyltransferase NSUN4

H: mTERF domain-containing protein 2

hetero molecules

defined by software
79.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.760, 82.270, 507.570
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	methyltransferase NSUN4 / NOL1/NOP2/Sun domain family member 4 Mass: 40410.195 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NSUN4 / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: Q96CB9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein	mTERF domain-containing protein 2 Mass: 38717.246 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPC096, MTERFD2 / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q7Z6M4
#3: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.65 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion / pH: 5.5 Details: 100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD

Radiation

Scattering type: x-ray

Radiation wavelength

Relative weight: 1

Reflection

Resolution: 2.9→50 Å / Num. all: 74674 / Num. obs: 74514 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / B_iso Wilson estimate: 64.931 Å² / R_merge(I) obs: 0.105 / Net I/σ(I): 11.58

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2.9-3		0.977	1.76	32259	7096	99.9
3-3.1		0.734	2.31	28685	6185	100
3.1-3.2		0.581	2.87	25268	5481	99.9
3.2-3.3		0.417	3.85	22044	4857	99.9
3.3-3.4		0.291	5.15	18920	4254	99.8
3.4-3.6		0.219	6.62	31211	7230	99.8
3.6-3.8		0.161	8.92	26395	5795	99.8
3.8-4		0.128	10.85	21430	4651	99.8
4-6		0.074	17.51	90135	20128	99.8
6-10		0.039	26.98	29225	6828	99.8
10-20		0.022	45.9	6867	1754	99.5
20-30		0.022	47.7	675	190	100
30-40		0.018	52.18	178	54	96.4
	40	0.02	45.94	31	11	27.5

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
BUSTER-TNT	BUSTER 2.10.0	refinement
PDB_EXTRACT	3.11	data extraction
SHARP		phasing
BUSTER	2.10.0	refinement

Refinement

Method to determine structure:

MIR / Resolution: 2.9→40 Å / Cor.coef. F_o:F_c: 0.8659 / Cor.coef. F_o:F_c free: 0.8408 / Occupancy max: 1 / Occupancy min: 0.69 / Cross valid method: THROUGHOUT / σ(F): 0

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2461	3754	5.04 %	RANDOM
R_work	0.2286	-	-	-
obs	0.2295	74501	99.82 %	-

Displacement parameters

B_iso max: 292.32 Å² / B_iso mean: 73.4798 Å² / B_iso min: 3 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-18.2896 Å²	0 Å²	0 Å²
2-	-	-2.2444 Å²	0 Å²
3-	-	-	20.534 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18569	0	148	0	18717

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	10654	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	470	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	5505	HARMONIC	5
X-RAY DIFFRACTION	t_it	38036	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	2419	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	40322	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	38036	HARMONIC	2	0.008
X-RAY DIFFRACTION	t_angle_deg	68885	HARMONIC	2	0.9
X-RAY DIFFRACTION	t_omega_torsion				3
X-RAY DIFFRACTION	t_other_torsion				3.09

LS refinement shell

Resolution: 2.9→2.98 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2692	243	4.5 %
R_work	0.2688	5152	-
all	0.2688	5395	-
obs	-	-	99.82 %

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	0.1269	0.1326	-0.4369	0	-0.2267	0.1814	-0.0072	0.0482	-0.0269	-0.0494	-0.0038	-0.0294	-0.015	0.023	0.011	0.0466	0.0413	0.1637	0.0439	0.1133	-0.058	128.76	82.3333	25.7641
2	0.0423	-0.305	-0.3626	0.0552	0.0429	0.0189	-0.0883	-0.1812	0.0669	-0.1525	0.1207	-0.0114	0.0642	-0.0307	-0.0324	0.1425	0.1467	0.0007	-0.0722	-0.1149	-0.0383	116.533	74.7914	33.0938
3	0.8501	-0.3043	-0.6911	0.0982	2.3766	2.0289	0.0019	0.0933	-0.0534	0.0253	0.0778	0.0981	-0.1015	-0.0741	-0.0797	-0.0279	0.1465	-0.0053	0.0954	-0.051	-0.0578	91.3218	86.685	40.4094
4	0	-0.6923	-0.4058	0.0969	-0.1882	0.0547	-0.1701	0.0534	-0.023	0.0174	-0.2118	0.1623	-0.0337	0.1078	0.3819	0.0731	-0.0142	-0.0505	-0.0437	-0.0827	-0.0057	98.2799	74.0951	44.229
5	0.0642	-3.4975	3.0979	0	-0.4141	0	-0.092	0.1659	0.2668	0.0007	0.0851	0.0994	-0.0154	0.0294	0.007	0.117	0.216	0.0542	-0.082	0.0672	-0.0444	97.9649	96.076	40.6313
6	0	0.0375	0.1266	0	0.2177	0	0.1333	-0.0246	0.0776	-0.0471	0.0392	0.0557	0.0909	0.0859	-0.1724	0.112	0.0789	0.0225	-0.0748	-0.0342	-0.0112	110.313	85.7653	51.2313
7	3.3688	0.0415	2.4625	0	-0.6383	0	0.0833	-0.0994	0.2596	-0.0494	-0.0899	0.003	-0.2089	0.062	0.0066	0.1457	0.2018	-0.0252	-0.2285	-0.0662	0.0629	106.242	96.6984	52.8501
8	0	-0.0761	0.1004	0	0.1095	0.3313	0.0513	-0.1132	0.1471	-0.1259	0.131	0.0615	0.1466	0.0843	-0.1823	-0.0464	0.1529	0.013	0.0413	-0.0903	0.0255	120.192	84.0007	54.9261
9	2.6655	0.2516	-0.2845	0	-4.4089	2.1313	0.0234	-0.1567	0.0504	-0.1303	0.0514	-0.0859	-0.0779	0.2312	-0.0747	0.0823	0.0032	-0.0103	0.0541	-0.0163	-0.1309	131.068	83.5135	35.41
10	0	-0.0789	0.0559	0	0.3399	0.0084	-0.2548	-0.124	0.2027	-0.1145	0.0342	0.0237	0.1989	0.0361	0.2206	0.1505	0.1318	0.0617	-0.0811	-0.0427	-0.0492	118.115	70.3634	50.2773
11	0.7307	-0.4168	3.8065	2.2124	1.1617	1.4911	0.0264	0.2543	0.1551	0.3111	0.0716	0.0047	0.1324	-0.0491	-0.098	0.2702	-0.2556	0.0373	-0.0336	-0.0793	-0.2335	97.5184	58.5459	-36.5241
12	0	3.9547	3.9677	0.8458	0.4652	0.6545	0.0104	-0.2362	0.0388	0.131	0.0485	0.1495	0.1567	-0.3236	-0.0589	-0.0855	-0.304	-0.0835	-0.053	-0.0602	-0.2708	93.9417	60.3161	-25.1741
13	0	0.3663	0.1572	0.0023	-0.8752	0.2734	0.19	-0.06	0.5936	-0.0295	-0.1948	-0.046	0.6335	-0.0204	0.0047	0.1732	-0.2594	-0.0269	0.0752	-0.0144	-0.2271	105.278	69.2371	-24.2928
14	0	-1.0243	1.4726	1.1676	-0.259	0	0.0231	-0.186	-0.1865	-0.2232	-0.0813	-0.0357	-0.25	-0.1195	0.0582	0.122	-0.1833	-0.074	0.0407	-0.0228	-0.1714	111.861	76.3439	-14.4225
15	0	-0.1736	0.2382	0	-0.7056	2.0627	-0.0822	-0.0016	0.0907	0.0053	-0.0184	0.2952	0.0592	0.2978	0.1006	0.0614	-0.1293	-0.0619	0.1224	-0.1292	-0.1981	117.8	77.9943	-6.1684
16	0.1537	-1.4568	3.1253	0.0586	0.0279	1.217	-0.0152	-0.0118	0.0385	-0.0347	-0.0698	0.0976	-0.0526	0.0933	0.085	0.1146	0.0709	-0.2526	0.1448	-0.1292	-0.2477	122.926	79.3557	7.1026
17	0	-1.3484	0.2638	0.0201	0.0997	0.5557	0.0547	0.186	0.2148	0.1854	0.0666	-0.0048	0.1478	0.0117	-0.1213	0.2047	0.0483	-0.0718	0.0853	-0.1155	-0.2674	118.253	72.4058	8.5288
18	0	0.5749	0.1232	0	0.2301	0	-0.0015	-0.001	0.0221	0.0084	-0.0027	-0.0176	-0.0158	-0.004	0.0042	0.007	0.1564	-0.0476	0.0834	0.0438	-0.0305	136.339	75.9645	10.9389
19	0	2.286	0.6891	0.5249	1.515	0.248	-0.0285	0.1151	0.053	0.009	-0.1514	0.0486	0.2983	0.1426	0.1799	0.3169	0.1714	-0.0415	-0.0372	-0.2012	-0.2682	117.89	64.2824	10.8618
20	0	0.1483	-0.7013	1.484	0.0638	0.0141	-0.0513	0.3789	0.3354	0.2423	-0.0931	0.0092	0.3445	-0.159	0.1445	0.2985	0.051	-0.0262	0.0254	-0.0932	-0.2785	107.764	74.8314	19.7094
21	0.6893	1.047	1.7671	0.7377	0.4314	0	0.0051	-0.1159	0.0661	0.024	-0.0313	-0.0333	-0.0183	0.042	0.0262	0.1013	0.0272	-0.2732	0.1634	-0.2808	-0.2265	133.087	121.092	97.875
22	0	-0.4018	-0.2826	0.0726	-0.0243	0.1513	0.0772	-0.1488	-0.0237	-0.1752	-0.0222	-0.0451	0.0008	-0.0415	-0.0551	0.0229	0.1042	-0.0925	0.0672	-0.0688	-0.0605	124.434	108.683	92.3353
23	0.6005	-3.8859	0.4113	1.2807	-1.4786	1.5967	-0.0269	0.0159	-0.2425	-0.0709	0.0773	-0.2197	0.0768	0.0292	-0.0504	0.2504	0.2868	-0.0872	-0.3101	0.0246	0.0741	135.068	83.4109	83.1155
24	0.5142	-0.2851	0.2315	0.0913	0.9871	0.3241	-0.2071	0.2588	0.027	0.2867	-0.0104	-0.0566	0.2608	-0.0413	0.2175	0.1575	-0.0024	-0.1547	-0.1153	-0.0112	-0.0309	121.874	90.1727	81.8826
25	0.0007	-3.1851	0.5294	0	-1.1426	0.2227	-0.0066	0.0155	-0.0416	-0.0088	-0.0308	-0.1122	0.038	-0.0171	0.0375	-0.2458	0.2544	-0.2303	0.1414	-0.042	0.104	144.085	89.9233	81.4711
26	0.0072	0.0561	0.3238	0	0.381	0.1865	-0.1456	0.1016	-0.1464	0.0601	0.3728	-0.0348	-0.1101	-0.0167	-0.2273	-0.0289	-0.0378	0.0112	0.0444	-0.1077	0.007	131.693	102.199	72.4231
27	1.5912	-1.0562	1.6824	0.5196	-2.6104	0.0446	-0.0287	0.0743	0.0314	-0.2132	0.0725	-0.1094	-0.006	0.0688	-0.0437	-0.4095	-0.0311	-0.0078	0.2297	-0.1236	0.1945	142.12	98.1587	68.5793
28	0.0158	-0.2587	0.2238	0	-0.2988	0.1355	-0.1144	-0.0528	-0.0518	-0.0915	0.2569	-0.1988	-0.0846	-0.1984	-0.1425	0.0958	-0.0328	0.0374	-0.112	-0.0789	0.0236	128.974	111.831	68.9294
29	0	0.3721	5.7423	3.5979	1.5286	1.0169	0.0355	0.0389	0.1249	-0.069	0.1439	0.0309	-0.2445	0.3102	-0.1794	0.1167	-0.0439	-0.1041	-0.0048	-0.0151	-0.1109	132.311	123.236	88.1164
30	0	-0.0855	0.1061	0	0.0739	0.2091	-0.0267	-0.0378	0.0668	-0.0341	-0.1264	-0.1775	0.0598	-0.155	0.1531	0.0804	0.0337	-0.0667	0.0182	-0.0721	-0.0807	116.649	109.818	76.3698
31	0.3418	0.4626	-0.9045	0	-1.147	0.2012	-0.0214	0.059	0.0056	-0.0813	-0.0035	-0.0497	-0.0738	0.028	0.0249	-0.028	0.0276	0.1611	0.0152	0.0138	0.0622	102.137	119.727	37.7484
32	0	-0.8937	0.0966	0.1804	0.3431	0.5224	-0.046	-0.1357	0.0802	-0.1237	0.0811	-0.1801	0.0968	-0.2246	-0.0351	-0.0157	0.1311	-0.0182	-0.0778	-0.0591	0.103	87.9774	114.401	43.3703
33	2.3409	0.4031	0.0068	0	1.4019	1.486	0.0318	-0.0536	0.0157	-0.0868	0.0247	0.1577	-0.0429	-0.1056	-0.0565	-0.0871	0.1265	-0.0305	0.1881	-0.0577	-0.096	62.2396	126.949	39.395
34	0	0.295	0.4163	0	0.4463	0.1472	0.1608	0.039	-0.0596	0.0414	-0.4018	0.2038	-0.0335	0.0385	0.241	-0.0013	-0.0518	0.0032	0.0503	-0.0706	-0.0344	68.2445	117.018	46.6022
35	0	-3.7383	1.913	0	-0.866	1.6469	-0.0067	0.0534	0.1564	-0.0857	0.0249	0.0039	0.0886	-0.066	-0.0182	0.1276	0.304	-0.0156	-0.0678	-0.0704	-0.0051	69.191	136.017	37.9157
36	0.2051	0.023	0.1644	0	0.1972	0	0.1056	-0.0511	0.1424	-0.0576	-0.0852	-0.1512	0.1308	-0.1344	-0.0204	-0.0003	0.0348	0.0097	-0.0026	-0.0044	0.0175	77.4758	130.243	54.8186
37	0.7802	-0.7489	3.1991	0	-0.3457	0.0009	-0.0466	-0.0967	0.1212	-0.1482	-0.0713	0.0256	-0.0133	-0.1079	0.1179	0.1576	0.0959	-0.1413	-0.2019	-0.0137	0.029	73.3422	140.779	52.0293
38	0	0.1709	-0.2726	0	-0.0554	0	0.073	0.0895	0.0654	0.0864	-0.0909	-0.0974	0.0593	-0.1015	0.0179	0.0264	0.1087	-0.086	-0.0304	-0.074	0.0223	85.7916	129.967	61.5488
39	0.354	-0.7674	-1.0334	0	-1.3621	2.1284	-0.0037	-0.0974	0.1395	0.0329	0.0846	-0.2149	-0.1854	0.0912	-0.0809	-0.074	-0.0727	-0.001	0.0937	0.0851	0.0048	101.651	124.14	46.8131
40	0.4001	-0.64	0.1987	0.0077	0.1447	0	-0.0807	0.0309	0.0174	0.0692	0.0922	-0.0955	0.0338	-0.1309	-0.0114	0.1076	-0.0053	-0.0311	-0.0924	0.0252	-0.0022	84.4217	115.507	60.7531
41	1.1241	-1.0874	-3.4307	0	-4.3231	3.2772	0.031	-0.0059	-0.1239	0.1374	-0.0642	-0.0719	-0.14	-0.2972	0.0332	0.1615	-0.304	-0.131	0.0145	0.0965	-0.1547	122.349	88.044	163.18
42	0.5012	3.1973	-0.1324	0	0.368	0	-0.0259	0.0333	-0.0417	-0.0819	0.0584	-0.0815	0.2698	-0.1709	-0.0325	0.3889	-0.304	-0.2604	-0.0623	0.2427	-0.3012	121.849	84.885	151.697
43	0.1604	0.5843	2.0205	0	-0.3415	0.5052	0.009	-0.2232	-0.0075	-0.1918	0.2738	-0.3914	0.014	-0.3914	-0.2829	0.1422	-0.1882	-0.1467	0.0508	0.1203	-0.1803	130.212	96.5587	149.413
44	2.0763	-1.6032	1.3243	0	-3.7876	1.193	-0.0323	-0.1353	0.0862	-0.1174	0.2314	0.2643	0.125	0.3373	-0.1991	0.2068	-0.1528	-0.0992	0.0546	0.108	-0.2849	134.951	103.462	138.607
45	0	-0.221	1.0163	0	0.6734	0.2233	0.0692	-0.0822	-0.2793	-0.0688	0.0079	0.0407	-0.3111	0.0868	-0.0771	0.3944	-0.0518	-0.17	-0.115	0.0309	-0.2568	134.872	109.778	130.343
46	0.0854	-0.9004	-0.0121	0.4175	-2.278	0.7475	-0.0251	-0.0229	-0.0788	-0.0982	-0.0647	-0.0674	-0.0865	0.0836	0.0897	0.2145	-0.0787	-0.1908	0.0981	0.1911	-0.3179	133.612	115.201	117.183
47	0	-1.7172	0.9513	0.561	0.61	0.6113	0.0917	0.1326	-0.0336	0.0861	0.0573	-0.1279	-0.0532	-0.1112	-0.149	0.2359	0.0934	-0.1948	0.0032	0.0655	-0.2489	126.598	110.441	117.016
48	0	0.5076	-0.0188	0	-0.088	0	0.002	0.0215	0.0073	-0.027	-0.002	-0.0163	0.0204	0.0316	0	0.0216	0.0468	-0.091	-0.0095	-0.0466	0.0345	129.495	128.555	114.133
49	0	1.4647	-0.0838	0.5494	-0.5461	0.703	-0.0156	-0.2037	0.0104	-0.051	-0.0971	-0.1041	-0.0481	-0.2537	0.1127	0.2316	0.0886	-0.0205	0.1032	0.0542	-0.3009	118.194	110.044	116.219
50	2.276	1.1698	-0.9446	0	2.3704	0	0.0099	0.0141	0.1327	0.1149	0.216	-0.0533	0.3446	-0.039	-0.226	0.3944	0.1679	-0.1841	-0.1122	0.0086	-0.2692	126.99	100.039	105.52
51	0	-0.1742	0.2999	0.2254	0.5455	0.2624	0.0034	-0.055	0.0044	-0.0117	-0.0215	-0.0023	-0.0155	-0.0003	0.0181	0.3138	0.1294	-0.0767	-0.0929	-0.2917	-0.1818	89.4086	93.6455	96.9623
52	0.7648	-0.2197	0.3618	0.0557	0.4686	0.0749	0.2117	-0.0888	-0.0595	0.1442	-0.2327	-0.3117	-0.0573	-0.3143	0.021	0.3657	0.2737	0.1397	-0.0472	-0.1663	-0.3093	81.7235	80.2815	92.1812
53	1.0697	-0.9205	0.4265	0.2484	1.3408	0.8985	0.0002	0.1167	-0.1251	0.0926	0.1352	0.1201	0.0257	0.1056	-0.1354	0.3822	0.0791	0.0748	-0.0452	-0.0834	-0.3402	92.9112	53.6122	91.4233
54	0	-0.2803	0.36	0.1362	-0.2515	0	-0.0167	0.1476	-0.1361	0.1795	-0.0089	0.1587	-0.0912	0.1153	0.0256	0.1425	0.0804	0.0796	-0.0307	-0.0152	-0.0874	80.8125	59.9852	85.561
55	0	-3.7392	0.6166	0	-3.4761	1.3354	0.0266	0.0852	0.0466	0.1701	-0.0038	0.0185	-0.0865	0.1351	-0.0228	0.2428	0.2952	-0.0931	-0.1161	-0.0493	-0.1266	102.624	59.6224	90.9667
56	0.0813	0.1115	0.0904	0	-0.1114	0.0359	0.0448	-0.031	-0.0171	-0.0317	0.0915	-0.1578	-0.0251	-0.1491	-0.1363	0.0337	0.111	0.0055	-0.0288	-0.069	0.0242	93.3028	69.645	76.5766
57	0	-2.3221	2.445	1.7588	-1.0853	0.117	0.0194	-0.0546	-0.1498	-0.108	0.0598	-0.1965	-0.1557	0.0916	-0.0791	-0.0495	0.1524	-0.0634	0.0462	-0.0529	0.0134	104.026	64.8843	76.4134
58	0	-0.2629	0.8545	0	-0.3476	0	-0.0101	0.1729	0.0703	0.1145	0.1811	-0.1145	0.0355	-0.1668	-0.1709	0.1055	0.1983	0.0151	-0.1349	-0.0607	0.0359	92.0391	78.4708	70.6018
59	0	0.8828	0.9718	0.5467	2.5299	0.4451	0.0029	0.0218	0.4039	-0.0422	0.0661	-0.0578	-0.0861	0.2874	-0.069	0.4802	0.1997	-0.0153	-0.3652	-0.2705	-0.0929	91.3552	93.4378	87.0687
60	0.0929	-0.4579	-0.2206	0.1168	-0.1476	0	-0.0098	0.1395	0.105	0.1589	-0.1569	0.0134	0.1162	-0.0059	0.1667	0.0111	0.2025	0.0536	0.0095	-0.0793	0.0049	78.1578	77.9171	74.921
61	0	-0.2172	0.4431	0.4896	0.2138	0	-0.0093	-0.0462	-0.0025	-0.0155	0.0128	0.0635	0.0266	0.0315	-0.0034	0.0008	-0.0294	-0.0181	-0.0551	-0.1501	0.0533	84.9914	77.7974	-22.0177
62	0	0.1877	0.2644	0	2.0744	0	0.0097	0.0613	0.0845	-0.0627	-0.0219	-0.0063	-0.0641	-0.0119	0.0122	-0.0966	-0.0994	-0.0493	0.0623	-0.2227	0.0124	79.3776	83.1592	-12.813
63	0	5.6961	-0.9648	0	3.4754	0	-0.014	0.1474	-0.1525	-0.1274	0.0968	0.153	0.1227	-0.1556	-0.0828	0.1295	0.1329	-0.005	0.2406	-0.1604	-0.3685	90.8037	92.4638	-11.3527
64	0	0.485	-4.2844	0	4.8011	2.1308	0.0734	0.0409	0.0208	0.0043	-0.0332	-0.0024	-0.0621	0.0096	-0.0402	0.1035	0.2848	0.1999	0.2545	0.1864	-0.4033	95.1307	101.615	-2.0059
65	0	-1.473	-1.0495	0	-0.0007	3.0303	-0.0376	0.084	0.1555	-0.1866	0.0874	0.1208	0.0086	0.1416	-0.0498	0.0776	0.304	0.1762	0.3106	-0.0913	-0.4015	99.2175	105.34	6.7087
66	0	-0.2423	-0.4934	1.1853	-0.7499	0.7994	-0.0176	-0.0323	0.0435	-0.0061	0.0229	-0.0515	-0.0959	0.0731	-0.0054	0.1116	0.1537	0.304	0.1897	0.0891	-0.2596	101.203	110.505	19.8945
67	0.4002	-2.1379	-0.4668	0.0608	0.5965	1.222	0.1359	-0.0355	0.0675	0.0128	-0.1916	-0.2672	0.0155	-0.2264	0.0558	0.1707	0.2709	0.0094	0.0382	-0.1093	-0.1978	95.9399	104.241	22.0365
68	0.0001	0.1581	-0.2256	0	0.1334	0.0039	0.0038	0.0048	-0.0078	-0.0042	-0.0033	-0.003	-0.0274	-0.0115	-0.0005	0.077	0.0345	-0.0518	0.0551	0.024	-0.043	113.131	109.069	27.9948
69	1.6004	0.107	0.5926	0	2.8637	1.7893	0.0294	-0.095	0.0236	-0.3162	-0.2342	0.0904	0.0455	0.1881	0.2048	0.1125	0.2777	-0.1486	-0.0482	-0.2463	-0.0919	94.5555	97.2321	26.7177
70	0	0.5065	-0.3875	0.031	0.3383	0	0.1891	0.2401	-0.1489	0.0441	-0.0017	0.0785	-0.0536	-0.0721	-0.1874	0.1542	0.2136	-0.0575	0.0324	-0.1199	-0.1842	83.1346	109.62	28.9238
71	0.3561	0.1449	-0.0777	0.4792	0.9788	0	0.0189	0.0257	-0.0357	0.0563	-0.0029	0.0452	-0.0228	-0.0291	-0.016	0.09	0.0175	0.0928	-0.01	-0.2222	-0.0949	68.2125	77.2074	164.687
72	5.1387	4.1393	-2.0956	9.3324	1.8349	11.7168	0.0055	0.0121	0.062	0.0732	0.0059	0.1257	-0.0422	-0.0669	-0.0114	0.6079	-0.0645	0.0884	0.6079	-0.0218	0.5632	69.3538	72.127	154.596
73	0	1.718	-4.1427	0	2.2265	2.519	0.0224	-0.1359	-0.1129	-0.0374	0.1726	-0.0268	-0.081	0.1188	-0.195	0.1908	0.0892	0.1245	0.1883	-0.2983	-0.3878	78.0111	83.1397	150.68
74	0.0048	0.4205	0.2171	0.0002	1.1311	1.7142	0.0103	-0.0721	-0.0226	-0.0106	0.0991	-0.0508	0.0207	-0.0746	-0.1093	0.4038	0.192	0.1049	-0.0864	-0.3023	-0.3078	83.9741	87.3165	139.077
75	0.4327	0.8748	3.2199	0.0058	3.5774	3.3814	0.0017	-0.213	-0.0767	-0.082	-0.0902	-0.2318	-0.0251	-0.1347	0.0884	0.5587	0.2686	0.2323	-0.1598	-0.2939	-0.4315	84.89	91.2604	129.651
76	0.8176	0.6391	-0.9831	0	-0.5902	1.1923	0.0145	0.0414	0.0453	0.021	-0.0366	-0.0463	-0.0937	0.0738	0.022	0.3956	0.1734	0.2409	-0.1133	-0.1787	-0.2541	85.8573	92.9147	115.545
77	0	-2.336	0.8412	1.2189	1.1416	1.399	0.0189	0.0327	0.0422	0.0403	-0.0558	-0.0753	0.0303	0.012	0.0369	0.5146	0.2497	0.304	0.072	-0.2977	-0.5889	78.8883	88.0869	115.473
78	0.1355	0.0774	-0.0843	0.0123	-0.1963	0	0.0039	-0.0042	-0.0137	0.0042	0.0081	0.0062	0.0193	-0.0029	-0.012	0.0858	0.0391	0.0107	-0.0553	0.0154	0.0859	82.6979	104.889	108.561
79	0	-0.4109	-5.5008	0	2.1562	0.6729	-0.0679	0.0804	0.064	0.1449	-0.0202	0.1372	0.0165	-0.1563	0.0881	0.278	0.3034	0.304	0.1257	-0.304	-0.3872	70.7189	87.2754	113.327
80	0.5325	-1.4499	1.2424	0	-0.1575	0.5102	-0.009	0.0097	-0.0554	0.2888	-0.0732	0.015	-0.063	-0.0432	0.0822	0.4072	0.1847	0.2433	0.0275	-0.208	-0.3996	81.0927	75.0481	107.304

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|39 - A\|42 }	A	39 - 42
2	X-RAY DIFFRACTION	2	{ A\|43 - A\|81 }	A	43 - 81
3	X-RAY DIFFRACTION	3	{ A\|82 - A\|94 }	A	82 - 94
4	X-RAY DIFFRACTION	4	{ A\|95 - A\|142 }	A	95 - 142
5	X-RAY DIFFRACTION	5	{ A\|143 - A\|150 }	A	143 - 150
6	X-RAY DIFFRACTION	6	{ A\|151 - A\|214 }	A	151 - 214
7	X-RAY DIFFRACTION	7	{ A\|215 - A\|229 }	A	215 - 229
8	X-RAY DIFFRACTION	8	{ A\|230 - A\|264 }	A	230 - 264
9	X-RAY DIFFRACTION	9	{ A\|265 - A\|282 }	A	265 - 282
10	X-RAY DIFFRACTION	10	{ A\|283 - A\|384 }	A	283 - 384
11	X-RAY DIFFRACTION	11	{ B\|86 - B\|104 }	B	86 - 104
12	X-RAY DIFFRACTION	12	{ B\|105 - B\|119 }	B	105 - 119
13	X-RAY DIFFRACTION	13	{ B\|120 - B\|172 }	B	120 - 172
14	X-RAY DIFFRACTION	14	{ B\|173 - B\|202 }	B	173 - 202
15	X-RAY DIFFRACTION	15	{ B\|203 - B\|234 }	B	203 - 234
16	X-RAY DIFFRACTION	16	{ B\|235 - B\|242 }	B	235 - 242
17	X-RAY DIFFRACTION	17	{ B\|243 - B\|277 }	B	243 - 277
18	X-RAY DIFFRACTION	18	{ B\|278 - B\|281 }	B	278 - 281
19	X-RAY DIFFRACTION	19	{ B\|282 - B\|304 }	B	282 - 304
20	X-RAY DIFFRACTION	20	{ B\|305 - B\|327 }	B	305 - 327
21	X-RAY DIFFRACTION	21	{ C\|39 - C\|42 }	C	39 - 42
22	X-RAY DIFFRACTION	22	{ C\|43 - C\|81 }	C	43 - 81
23	X-RAY DIFFRACTION	23	{ C\|82 - C\|94 }	C	82 - 94
24	X-RAY DIFFRACTION	24	{ C\|95 - C\|142 }	C	95 - 142
25	X-RAY DIFFRACTION	25	{ C\|143 - C\|150 }	C	143 - 150
26	X-RAY DIFFRACTION	26	{ C\|151 - C\|214 }	C	151 - 214
27	X-RAY DIFFRACTION	27	{ C\|215 - C\|229 }	C	215 - 229
28	X-RAY DIFFRACTION	28	{ C\|230 - C\|264 }	C	230 - 264
29	X-RAY DIFFRACTION	29	{ C\|265 - C\|282 }	C	265 - 282
30	X-RAY DIFFRACTION	30	{ C\|283 - C\|384 }	C	283 - 384
31	X-RAY DIFFRACTION	31	{ D\|39 - D\|42 }	D	39 - 42
32	X-RAY DIFFRACTION	32	{ D\|43 - D\|81 }	D	43 - 81
33	X-RAY DIFFRACTION	33	{ D\|82 - D\|94 }	D	82 - 94
34	X-RAY DIFFRACTION	34	{ D\|95 - D\|142 }	D	95 - 142
35	X-RAY DIFFRACTION	35	{ D\|143 - D\|150 }	D	143 - 150
36	X-RAY DIFFRACTION	36	{ D\|151 - D\|214 }	D	151 - 214
37	X-RAY DIFFRACTION	37	{ D\|215 - D\|229 }	D	215 - 229
38	X-RAY DIFFRACTION	38	{ D\|230 - D\|264 }	D	230 - 264
39	X-RAY DIFFRACTION	39	{ D\|265 - D\|282 }	D	265 - 282
40	X-RAY DIFFRACTION	40	{ D\|283 - D\|384 }	D	283 - 384
41	X-RAY DIFFRACTION	41	{ E\|86 - E\|104 }	E	86 - 104
42	X-RAY DIFFRACTION	42	{ E\|105 - E\|119 }	E	105 - 119
43	X-RAY DIFFRACTION	43	{ E\|120 - E\|172 }	E	120 - 172
44	X-RAY DIFFRACTION	44	{ E\|173 - E\|202 }	E	173 - 202
45	X-RAY DIFFRACTION	45	{ E\|203 - E\|234 }	E	203 - 234
46	X-RAY DIFFRACTION	46	{ E\|235 - E\|242 }	E	235 - 242
47	X-RAY DIFFRACTION	47	{ E\|243 - E\|277 }	E	243 - 277
48	X-RAY DIFFRACTION	48	{ E\|278 - E\|281 }	E	278 - 281
49	X-RAY DIFFRACTION	49	{ E\|282 - E\|304 }	E	282 - 304
50	X-RAY DIFFRACTION	50	{ E\|305 - E\|327 }	E	305 - 327
51	X-RAY DIFFRACTION	51	{ F\|39 - F\|42 }	F	39 - 42
52	X-RAY DIFFRACTION	52	{ F\|43 - F\|81 }	F	43 - 81
53	X-RAY DIFFRACTION	53	{ F\|82 - F\|94 }	F	82 - 94
54	X-RAY DIFFRACTION	54	{ F\|95 - F\|142 }	F	95 - 142
55	X-RAY DIFFRACTION	55	{ F\|143 - F\|150 }	F	143 - 150
56	X-RAY DIFFRACTION	56	{ F\|151 - F\|214 }	F	151 - 214
57	X-RAY DIFFRACTION	57	{ F\|215 - F\|229 }	F	215 - 229
58	X-RAY DIFFRACTION	58	{ F\|230 - F\|264 }	F	230 - 264
59	X-RAY DIFFRACTION	59	{ F\|265 - F\|282 }	F	265 - 282
60	X-RAY DIFFRACTION	60	{ F\|283 - F\|384 }	F	283 - 384
61	X-RAY DIFFRACTION	61	{ G\|86 - G\|104 }	G	86 - 104
62	X-RAY DIFFRACTION	62	{ G\|105 - G\|119 }	G	105 - 119
63	X-RAY DIFFRACTION	63	{ G\|120 - G\|172 }	G	120 - 172
64	X-RAY DIFFRACTION	64	{ G\|173 - G\|202 }	G	173 - 202
65	X-RAY DIFFRACTION	65	{ G\|203 - G\|234 }	G	203 - 234
66	X-RAY DIFFRACTION	66	{ G\|235 - G\|242 }	G	235 - 242
67	X-RAY DIFFRACTION	67	{ G\|243 - G\|277 }	G	243 - 277
68	X-RAY DIFFRACTION	68	{ G\|278 - G\|281 }	G	278 - 281
69	X-RAY DIFFRACTION	69	{ G\|282 - G\|304 }	G	282 - 304
70	X-RAY DIFFRACTION	70	{ G\|305 - G\|327 }	G	305 - 327
71	X-RAY DIFFRACTION	71	{ H\|86 - H\|104 }	H	86 - 104
72	X-RAY DIFFRACTION	72	{ H\|105 - H\|119 }	H	105 - 119
73	X-RAY DIFFRACTION	73	{ H\|120 - H\|172 }	H	120 - 172
74	X-RAY DIFFRACTION	74	{ H\|173 - H\|202 }	H	173 - 202
75	X-RAY DIFFRACTION	75	{ H\|203 - H\|234 }	H	203 - 234
76	X-RAY DIFFRACTION	76	{ H\|235 - H\|242 }	H	235 - 242
77	X-RAY DIFFRACTION	77	{ H\|243 - H\|277 }	H	243 - 277
78	X-RAY DIFFRACTION	78	{ H\|278 - H\|281 }	H	278 - 281
79	X-RAY DIFFRACTION	79	{ H\|282 - H\|304 }	H	282 - 304
80	X-RAY DIFFRACTION	80	{ H\|305 - H\|327 }	H	305 - 327

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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

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