PDB-5luq: Crystal Structure of Human DNA-dependent Protein Kinase Catalytic...

ID or keywords:

Entry

Database: PDB / ID: 5luq

Title

Crystal Structure of Human DNA-dependent Protein Kinase Catalytic Subunit (DNA-PKcs)

Components

C-terminal fragment of KU80 (KU80ct194)
DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit

Keywords

TRANSFERASE / DNA-PKcs / Kinase / DNA repair / NHEJ / double strand break repair / HEAT repeat

Function / homology

Function and homology information

positive regulation of platelet formation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / immature B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex ...positive regulation of platelet formation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / immature B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / regulation of epithelial cell proliferation / IRF3-mediated induction of type I IFN / telomere capping / regulation of hematopoietic stem cell differentiation / U3 snoRNA binding / T cell lineage commitment / negative regulation of cGAS/STING signaling pathway / maturation of 5.8S rRNA / B cell lineage commitment / double-strand break repair via alternative nonhomologous end joining / positive regulation of double-strand break repair via nonhomologous end joining / ectopic germ cell programmed cell death / somitogenesis / mitotic G1 DNA damage checkpoint signaling / activation of innate immune response / telomere maintenance / positive regulation of erythrocyte differentiation / negative regulation of protein phosphorylation / positive regulation of translation / response to gamma radiation / protein-DNA complex / Nonhomologous End-Joining (NHEJ) / small-subunit processome / peptidyl-threonine phosphorylation / protein destabilization / protein modification process / regulation of circadian rhythm / brain development / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / rhythmic process / E3 ubiquitin ligases ubiquitinate target proteins / heart development / T cell differentiation in thymus / double-stranded DNA binding / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / nucleolus / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 4.3 Å

Authors

Sibanda, B.L. / Chirgadze, D.Y. / Ascher, D.B. / Blundell, T.L.

Funding support

United Kingdom, 1items

Citation

Journal: Science / Year: 2017
Title: DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair.
Authors: Sibanda, B.L. / Chirgadze, D.Y. / Ascher, D.B. / Blundell, T.L.

History

Deposition	Sep 9, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 1, 2017	Group: Database references
Revision 1.2	Mar 28, 2018	Group: Source and taxonomy / Category: entity_src_gen / entity_src_nat Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _entity_src_nat.common_name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5luq.cif.gz	3 MB	Display	PDBx/mmCIF format
PDB format	pdb5luq.ent.gz	2.6 MB	Display	PDB format
PDBx/mmJSON format	5luq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5luq_validation.pdf.gz	559.5 KB	Display	wwPDB validaton report
Full document	5luq_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5luq_validation.xml.gz	333.1 KB	Display
Data in CIF	5luq_validation.cif.gz	437.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lu/5luq ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5luq	HTTPS FTP

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Related structure data

Similar structure data	6zh6-d 6zfp-d 4425 11216 7k17-1 6zh8-d 5w1r-d 22622 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	#122 - Feb 2010 Enhanceosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (3) #148 - Apr 2012 Ras Protein similarity (8) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit

K: C-terminal fragment of KU80 (KU80ct194)

B: DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit

S: C-terminal fragment of KU80 (KU80ct194)

972 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit

K: C-terminal fragment of KU80 (KU80ct194)

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

2

B: DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit

S: C-terminal fragment of KU80 (KU80ct194)

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

Unit cell

Length a, b, c (Å)	169.120, 132.640, 296.590
Angle α, β, γ (deg.)	90.00, 105.53, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit / DNA-PKcs / DNPK1 / p460 Mass: 469618.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa References: UniProt: P78527, non-specific serine/threonine protein kinase
#2: Protein	C-terminal fragment of KU80 (KU80ct194) Mass: 16621.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGAT3 / Production host: Escherichia coli BL21(DE3) (bacteria)

#1: Protein

DNA-dependent protein kinase catalytic subunit,DNA-dependent Protein Kinase Catalytic Subunit,DNA-dependent protein kinase catalytic subunit / DNA-PKcs / DNPK1 / p460

Mass: 469618.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural)

Homo sapiens (human) / Cell line: HeLa
References: UniProt: P78527, non-specific serine/threonine protein kinase

#2: Protein

C-terminal fragment of KU80 (KU80ct194)

Mass: 16621.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Plasmid: pGAT3 / Production host:

Escherichia coli BL21(DE3) (bacteria)

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	3.27	62
2	3.27	62

Crystal grow

Temperature (K)	Crystal-ID	Method	Details	PH range
293	1	vapor diffusion, hanging drop	0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 18% PEG 8000	6.2-6.7
293	2	vapor diffusion, hanging drop	0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 8% PEG 8000	6.2-6.7

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ESRF	ID29	1	0.9791
SYNCHROTRON	ESRF	ID23-1	2	0.9791

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 6M-F	1	PIXEL	May 23, 2012
DECTRIS PILATUS 6M-F	2	PIXEL	Jun 25, 2011

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97915	1
2	0.9791	1

Reflection

Resolution: 4.3→49.92 Å / Num. obs: 84530 / % possible obs: 99.9 % / Redundancy: 35.2 % / R_merge(I) obs: 0.16 / Net I/σ(I): 15.4

Reflection shell

Resolution: 4.3→4.41 Å / Redundancy: 13.1 % / R_merge(I) obs: 0.936 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 4.3→49.92 Å / SU ML: 1.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 55.75

	R_factor	Num. reflection	% reflection
R_free	0.437	1978	2.34 %
R_work	0.3862	-	-
obs	0.3874	84530	97.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 4.3→49.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	59694	0	0	0	59694

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	60886
X-RAY DIFFRACTION	f_angle_d	1.542	82328
X-RAY DIFFRACTION	f_dihedral_angle_d	14.868	37258
X-RAY DIFFRACTION	f_chiral_restr	0.068	9336
X-RAY DIFFRACTION	f_plane_restr	0.011	10524

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 (%)
4.3-4.4075	0.4411	134	0.4466	5463	X-RAY DIFFRACTION	91
4.4075-4.5266	0.4963	135	0.4432	5631	X-RAY DIFFRACTION	95
4.5266-4.6597	0.5077	140	0.4477	5752	X-RAY DIFFRACTION	96
4.6597-4.81	0.5102	140	0.458	5782	X-RAY DIFFRACTION	97
4.81-4.9818	0.4783	142	0.4617	5842	X-RAY DIFFRACTION	97
4.9818-5.181	0.4999	135	0.4535	5859	X-RAY DIFFRACTION	98
5.181-5.4166	0.5099	145	0.4549	5943	X-RAY DIFFRACTION	99
5.4166-5.7018	0.5191	140	0.4605	5941	X-RAY DIFFRACTION	99
5.7018-6.0584	0.4567	134	0.4628	6007	X-RAY DIFFRACTION	99
6.0584-6.5253	0.5304	147	0.4571	5986	X-RAY DIFFRACTION	100
6.5253-7.1802	0.4666	142	0.4413	6008	X-RAY DIFFRACTION	100
7.1802-8.2152	0.4546	144	0.3883	6061	X-RAY DIFFRACTION	100
8.2152-10.3352	0.3607	148	0.2844	6087	X-RAY DIFFRACTION	100
10.3352-49.9234	0.3788	152	0.3318	6190	X-RAY DIFFRACTION	100

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	0.6182	-0.2092	0.3796	0.2659	-0.1376	0.3206	-0.1841	-0.8431	-0.5397	1.1482	0.5762	-0.0335	0.5243	-0.0831	0.1665	2.0213	0.8059	-0.4009	2.1286	-0.6683	1.3029	39.0522	-30.5557	88.0704
2	0.0973	-0.0661	-0.111	0.0463	0.0636	0.1204	-0.1299	-0.1555	0.1683	0.1241	0.129	0.1446	0.1578	0.3468	0.1361	1.8937	1.1563	0.5539	3.6237	-1.3805	0.7496	55.5157	-13.8908	99.6993
3	0.2189	-0.1099	0.0042	0.1601	0.1918	0.2904	-0.0857	-0.9782	0.7312	0.579	-0.0831	-0.8395	1.3429	-0.346	0.0004	2.4516	0.698	-0.1767	3.102	-0.3451	1.675	79.7448	-13.7805	88.2267
4	0.078	-0.0716	0.0842	0.0486	-0.0726	0.0401	-0.4432	-0.8084	-0.2967	0.332	0.1017	-1.0906	0.3227	-0.4255	-0.0005	2.4453	0.6522	-0.6748	2.3025	-0.1327	2.348	82.2607	-10.5758	64.6066
5	0.874	0.042	-0.0642	0.7074	0.6442	3.1195	-1.0263	0.2321	-0.0243	0.0923	0.0427	0.3462	1.1901	-0.7267	-1.834	1.2852	0.3899	0.5314	0.6917	0.1826	1.0809	68.71	-7.9233	47.8809
6	0.3307	0.0321	0.085	0.2741	-0.4058	0.4225	-0.2779	0.7832	-0.4249	-0.7115	0.3614	0.6246	0.8064	-0.7527	0.1914	1.7276	-0.4314	-0.2726	0.0567	0.3863	0.8533	70.227	-7.739	33.4802
7	0.1937	-0.0649	-0.1689	-0.0102	0.0667	0.102	-0.0362	0.5042	0.3042	0.4236	-0.3428	0.3406	-0.4922	0.1871	0.0002	1.4674	0.3607	0.2777	2.0707	0.7673	2.4366	64.9794	10.359	34.0397
8	0.4658	-0.0047	-0.0194	0.3123	0.0539	0.3443	0.5151	-0.0682	0.2089	0.6203	0.434	0.265	0.7814	-0.7858	0.7608	0.4858	1.2441	1.0196	3.9521	-0.3994	0.9681	44.2615	7.2171	30.1705
9	0.2092	-0.087	-0.2503	0.0398	0.1403	0.2727	1.748	0.0826	0.3087	-0.2194	0.5562	0.0924	0.3277	-0.3576	0.0103	2.3198	0.3939	-0.5798	4.1617	-0.7459	3.1419	24.2336	-19.674	7.6635
10	0.2061	-0.3008	-0.3005	0.2456	0.1464	0.119	-0.2156	-1.802	-0.3048	0.6789	0.9616	-0.2693	0.4463	0.7204	0.1211	1.2705	-0.5507	0.3053	2.6428	1.0695	1.4371	43.0167	-20.1238	7.947
11	0.375	-0.361	-0.2807	0.579	0.4232	0.3355	0.0192	0.0554	-0.3618	-0.1273	0.2035	-0.7348	-0.3664	0.0645	0.0689	-1.2366	-0.9493	2.1277	2.6592	1.2546	0.0071	66.99	-7.4949	-3.9255
12	0.1926	0.1326	-0.2022	0.0267	-0.0937	0.1838	-0.9011	0.4694	0.5804	0.6682	-0.0083	-1.4966	-0.7466	0.303	0.0001	2.1595	0.4189	-0.0192	2.1957	0.436	2.5096	82.6046	16.0866	-2.604
13	0.0209	-0.0923	0.0159	0.0323	-0.0993	0.0595	-1.0659	-0.3831	-0.0733	0.2997	-0.527	-0.9962	0.7551	0.6952	-0.0013	1.9592	-0.2427	-0.2033	2.0279	0.5342	3.2703	88.7074	17.2333	13.3704
14	0.0814	0.0642	0.1683	0.1465	0.0564	0.1409	-0.3382	-1.7727	0.6051	0.4749	1.0076	0.0046	0.5467	0.3521	0.0009	2.8533	0.0613	-0.2983	1.5566	-0.4417	2.566	96.9016	17.2069	37.3366
15	0.7283	-0.853	0.5101	0.8461	0.3816	0.7682	-0.2545	-0.6649	-0.376	1.4751	1.1229	0.2415	0.9988	-0.7287	0.9871	-0.8607	1.4988	-1.0285	-0.0785	0.6743	0.2446	103.4733	-13.2837	51.2569
16	0.0028	0.0155	-0.0086	0.1516	-0.122	0.1335	0.0646	0.1432	0.0961	-0.1025	-0.1802	0.4397	0.1314	0.0109	0.0812	1.9148	0.9567	0.253	1.8249	0.6233	1.8315	87.4149	-17.6282	42.3351
17	0.0845	-0.2101	-0.0764	0.2804	0.3052	-0.05	0.4815	0.0114	0.3535	0.0986	-0.1952	-0.5929	0.6323	0.6395	-0.7379	0.7116	0.1529	-0.1506	0.1186	-0.4422	1.0522	95.9667	-44.892	51.3078
18	0.378	0.3935	0.0074	0.3421	-0.4084	0.9256	0.6648	-0.7144	-0.0623	0.3271	-0.012	-0.1333	0.2542	0.2559	0.0004	1.7815	0.3063	0.1268	1.5813	-0.2813	1.8022	65.7711	-66.7094	54.8756
19	0.1944	0.2686	0.1493	0.1648	-0.0841	0.3009	-0.086	-0.0757	0.8849	-0.8573	-0.61	0.5897	-0.6689	-1.1821	-3.119	-0.3458	0.2975	1.6828	2.128	0.6765	-0.3918	16.1063	-44.0757	58.1714
20	0.0396	-0.1157	0.0792	0.2729	-0.0209	0.2205	-0.1722	0.4713	0.0343	-0.3894	0.0983	0.7621	0.1869	-0.2335	0.0143	1.163	-1.5404	0.0892	3.0997	1.5197	2.8442	17.1989	-32.3659	25.5646
21	0.0568	-0.0261	0.071	0.0954	-0.0148	0.0547	0.1264	-0.6855	0.1394	0.0511	0.5194	-0.8089	0.3881	0.2296	0.0022	2.9599	-0.1703	-1.3435	3.8952	-0.9747	2.7927	41.2758	-35.2943	29.0494
22	0.0429	0.0628	0.0101	0.0795	0.1091	0.0288	0.7423	0.2985	-0.6022	-0.3613	0.4649	-0.6542	0.4554	0.5938	0.0014	1.1573	-0.1859	0.5836	3.2554	0.7905	2.6255	35.9002	-33.5348	13.2183
23	1.698	-0.3045	0.5498	0.0268	-0.1374	0.9973	-1.0191	-0.0254	1.5072	-0.3008	0.3261	-0.4281	-0.8872	-1.2784	-0.3067	0.4684	-0.3284	0.9174	3.8496	1.5581	2.7469	7.2579	-8.5245	19.4489
24	0.0961	-0.1121	0.0243	0.0673	-0.0232	0.0973	-0.4877	-0.0209	0.2559	-0.33	-0.6584	1.1646	0.1687	0.1154	-0.0001	3.1831	0.6493	0.0452	4.4507	1.1781	2.509	-0.195	19.3837	26.5569
25	0.041	0.0235	0.0449	0.2941	0.1568	0.1389	0.2622	-0.6535	-0.1847	0.0951	-0.6707	-0.5372	-0.3522	0.7837	-0.8223	1.1091	0.0687	0.2765	2.7094	0.8667	1.1829	9.0056	11.4864	46.2455
26	0.0908	-0.0541	-0.0528	0.31	0.3208	0.1497	-0.1691	-1.1067	0.1671	0.6591	-0.5523	0.3456	0.0016	-0.0257	-0.0052	2.6345	0.8869	-0.7569	2.6606	-0.6397	2.6169	28.8576	16.4727	43.177
27	0.036	-0.0877	-0.0363	0.1366	0.0966	0.07	-1.7082	-0.2036	0.6217	-0.1408	-0.3085	-0.0655	-0.7462	0.815	-0	3.6719	1.2284	-0.8215	2.4283	-0.4257	2.6964	20.9778	40.4893	33.4782
28	0.3952	0.3719	-0.3534	0.3401	-0.2581	0.3593	0.3223	0.355	0.9593	0.1417	0.3828	-0.2874	-0.8807	-0.7085	0.3993	1.0609	0.8904	0.5903	1.9895	-1.271	1.2609	19.3561	53.4881	19.0601
29	0.0293	-0.1121	0.0467	0.1218	-0.0538	0.1623	-0.1535	-0.2717	0.7627	0.7027	-0.1167	-0.2141	-1.3288	1.0975	-0.0076	1.9503	0.465	-0.2807	2.4128	-0.4763	2.5856	41.8078	40.7979	-1.4242
30	0.0751	-0.1307	-0.1036	0.137	0.0163	-0.0063	0.2917	1.3723	0.0344	-0.7066	0.4489	-0.0219	0.3433	-0.4676	-0.0002	2.3965	-0.3982	0.2566	2.6588	-0.1089	1.6044	41.0761	17.1044	-31.9316
31	-0.0017	-0.0618	0.0957	0.863	-0.177	0.7613	-0.1916	-1.2873	-0.2398	0.1504	-0.2338	-0.8428	-0.3005	0.2501	-0.825	0.7436	0.3265	1.7887	1.4818	0.3949	0.4525	48.4626	11.7741	-4.954
32	0.0366	-0.0859	0.0169	0.3127	0.0068	0.0837	0.4777	0.9745	0.1795	1.1766	-0.6247	-0.1943	0.1145	0.8148	-0.0063	2.3044	0.28	-0.4531	2.2852	0.1456	1.2455	32.4026	19.905	0.8266
33	0.9397	0.6839	-0.1335	1.3632	0.9652	1.9941	-0.5519	0.8801	0.1613	-0.5707	-0.6369	0.8658	-0.6218	-1.1597	-1.0826	1.1324	-1.4356	0.1204	3.8085	1.228	0.9939	10.7958	1.6316	-11.1168
34	0.0672	0.1316	-0.1498	0.0304	-0.1922	0.1229	-0.662	0.2746	0.4953	0.1019	-0.8815	-0.7345	0.5297	0.5912	-0.0094	0.4973	0.3122	0.0485	2.4354	0.1205	1.9733	19.0279	12.9315	-1.8924
35	0.2277	0.2074	0.2561	0.4075	0.3541	0.2653	0.2937	-0.8052	-0.0249	-1.3277	-0.2901	-0.3811	0.9663	0.4202	-0.0013	1.7816	0.5163	-0.2901	2.8136	-0.1031	2.3529	13.7202	25.2047	-6.0894
36	1.3194	0.0298	0.2419	0.2977	-0.1038	0.3697	-0.4316	-0.5671	0.695	0.3268	-0.2192	0.3469	-0.751	-0.4591	-0.4582	2.0585	-0.2729	-0.0725	3.9208	0.2137	1.2528	-43.1758	95.0508	142.9455
37	0.1407	-0.0222	0.0787	0.3545	0.1086	0.3535	0.1834	0.0584	0.1132	0.9231	0.0237	0.3401	0.1238	0.4732	0.3606	1.7865	0.7951	0.9575	2.311	0.3558	0.7941	-59.3173	72.874	144.6662
38	0.0633	0.0081	0.2521	0.1461	0.0723	0.3082	-0.7541	-0.2096	-1.0225	-0.1112	0.0806	0.5777	0.2638	0.5889	-0.0002	2.1187	0.5766	0.6477	2.9839	0.0385	2.006	-67.2449	60.2319	122.7989
39	0.1511	-0.1815	-0.0074	0.1099	-0.0111	-0.0648	0.9265	-0.9794	1.131	-0.3321	-0.276	-0.2572	0.0383	-0.0584	0.0003	2.1236	0.4984	-0.347	2.5306	0.2836	1.8003	-51.779	48.8926	109.2844
40	0.1195	-0.3763	0.0107	1.0041	-0.1294	-0.0201	-0.0137	-0.2171	0.5696	-0.2842	-0.2166	-1.3249	-0.5707	0.2071	-0.1375	0.9699	0.8567	1.0316	0.0983	-0.3382	0.9875	-29.4985	47.4147	110.5107
41	0.9706	-0.5846	-0.2693	0.6607	-0.0059	0.8488	0.3359	1.0881	0.2721	-0.9775	0.0063	-0.5692	-0.1251	0.9727	1.4345	1.1755	1.88	-0.5044	1.4859	0.3266	0.9942	-19.5201	40.995	102.4836
42	0.7899	-0.1537	0.6065	0.339	-0.3226	0.6395	0.5644	-0.9588	-1.1388	0.4723	-0.1015	0.5158	0.217	-1.2871	0.0948	2.8092	0.8184	0.4346	1.7893	-0.4725	1.5548	-17.5405	28.7422	115.5422
43	0.0477	-0.1669	0.063	0.1618	-0.2013	0.6186	0.356	0.4226	0.2166	-0.0493	-0.4897	-0.4595	-1.5329	0.117	-0.1177	1.5238	0.0196	0.0898	2.3616	0.3131	-0.195	-1.325	38.7116	126.4733
44	0.5729	0.1847	-0.2653	0.6175	-0.2249	0.1473	0.7267	0.0837	0.5063	0.292	0.3072	0.3249	0.6738	0.6442	0.3425	1.9682	1.0479	0.3215	3.2165	-1.3109	1.8299	29.3686	61.3869	113.6436
45	0.0028	-0.1432	-0.0315	0.3052	0.0928	0.1241	-1.2453	-0.7184	-1.5814	-0.703	-0.1494	0.4735	0.0685	1.4982	-0.0136	2.5223	0.0958	0.0424	1.4159	0.2823	1.8445	17.5945	54.4377	100.6163
46	0.2343	0.2931	-0.0924	0.564	-0.06	0.0853	0.3465	1.1978	1.2694	-1.3204	0.2771	1.1762	1.0677	0.5483	0.1121	2.473	1.2004	-0.1817	1.9135	-1.1267	1.5024	12.0699	29.4316	85.4433
47	0.6475	-0.0316	-0.3914	0.4931	-0.0789	0.2967	-0.7008	0.6201	-1.0217	0.3245	0.214	0.4977	0.3815	-0.3421	0.1093	1.8191	1.9916	-0.6373	0.2134	-0.7337	2.8582	0.8586	3.8726	88.6073
48	0.2633	0.2565	-0.2088	0.407	-0.3926	0.4275	0.3078	-0.0571	0.5801	-1.0126	0.8229	-0.3414	-0.227	-0.1928	0.9087	2.9271	0.0681	-0.795	-0.242	-0.9291	2.6734	-15.8257	5.8422	92.1669
49	0.1005	-0.0025	0.0094	0.088	0.0059	-0.0307	0.3417	0.0011	-0.3885	1.0838	0.016	0.3387	0.4652	-1.6488	0.0001	2.7335	-0.112	0.0491	1.5294	-0.1679	2.7765	-39.6368	10.8132	100.413
50	0.3709	-0.3379	0.4191	1.0493	-0.4771	0.6009	0.0671	-0.1802	0.4432	1.3323	0.8235	0.2617	0.5948	-0.6608	-0.1739	-0.0827	1.1904	-0.4775	-0.844	0.3676	0.9816	-55.057	38.4259	87.1932
51	0.169	0.0307	-0.0031	0.0237	-0.0211	-0.001	-0.2057	-0.1107	0.6208	0.4753	0.2944	-0.1936	-0.7798	0.1468	-0.0033	2.5122	0.0031	0.8232	1.7997	0.4802	2.6096	-37.0024	45.5208	91.3717
52	0.6409	-0.2139	0.2943	0.0581	0.1531	1.8859	-0.0189	-0.356	-0.1974	0.4379	0.7385	-0.1975	1.1086	0.3429	1.4878	-0.1871	0.4556	0.2164	-0.3866	-0.1225	0.3663	-50.0829	68.0434	75.1221
53	0.2923	-1.0572	0.5454	0.0324	1.1238	0.4956	-0.5602	-0.9094	0.1126	0.8548	0.228	-0.7234	0.2791	-0.3157	-0.0166	2.1901	0.2743	-0.4017	1.5587	-0.2365	1.1921	-33.9488	100.5678	83.618
54	0.3721	-0.011	-0.3357	0.7533	0.0267	0.35	-0.1069	-1.0415	0.6763	0.1547	-0.3289	-0.2664	-0.9647	0.2144	-1.6025	2.5949	0.6487	-0.6583	0.9082	-0.6971	1.1503	-5.308	104.2741	130.0672
55	0.7148	-0.2768	0.1535	0.1389	0.1115	0.5876	-0.6558	-0.5707	0.2139	-0.4904	-0.6523	0.0261	0.3305	0.4167	-0.2001	2.614	0.5991	0.877	0.3148	0.3436	2.6768	19.3444	81.8951	119.0534
56	0.0791	0.0139	0.1268	0.0923	-0.0465	0.1309	0.4631	1.3297	0.1946	0.2349	-0.864	0.5168	-0.0013	0.3616	0.0004	2.7109	0.7951	0.5886	3.0215	-0.7825	3.0614	3.1602	74.978	102.1332
57	0.0251	-0.0087	-0.0103	0.0877	-0.0649	0.0304	-0.1523	0.3878	-0.2474	-0.0281	-0.4272	0.7197	0.1949	-0.0339	-0.0005	3.2945	0.6583	-0.2734	2.0988	0.2913	2.6529	18.0138	68.8924	101.0362
58	0.0836	-0.0382	-0.2395	0.4567	0.2551	0.2495	-0.41	-0.6448	-0.3422	0.597	1.0381	-0.9241	0.8207	1.0364	0.0003	2.7535	0.2732	0.037	1.7091	0.0445	1.3906	29.9953	65.214	136.4934
59	0.4379	-0.2139	0.2186	0.1071	-0.0949	0.1152	-1.1431	0.2573	0.9198	0.3165	-1.0728	0.054	-0.4637	0.5892	-0.022	3.3877	0.2002	-0.1605	2.8875	-0.1873	1.5132	29.142	49.1863	161.6777
60	0.0872	-0.0674	0.038	0.126	0.0162	0.3499	-0.0979	-0.0325	0.2798	0.0197	-0.354	0.4021	-1.1447	0.1387	0.6629	2.7912	0.9477	-0.7873	2.365	-0.6696	0.8951	6.3252	57.3117	160.8644
61	0.1169	-0.0935	-0.0291	0.2175	-0.0938	0.053	1.1465	-0.322	1.0634	-0.1725	-0.8134	-0.0284	1.5307	-0.6391	0	1.8985	-0.5024	-0.548	1.9631	0.2725	2.2526	-2.3298	41.7006	148.2615
62	0.1036	-0.0364	-0.1414	-0.1325	-0.1723	0.2174	0.4127	-0.2073	0.4426	1.8887	0.097	-0.8212	0.0661	-1.3224	0.0001	2.0615	0.0679	-0.2703	1.9014	0.4664	2.7621	10.1825	22.8316	162.2882
63	0.1413	0.2051	0.039	0.4686	0.2158	0.176	-0.1981	-0.662	-0.594	0.7759	0.1878	-0.2262	0.2777	0.4382	0.0998	1.5465	0.0002	-0.4331	1.8545	1.063	2.4207	23.7716	7.1961	162.3982
64	0.3391	-0.1296	-0.1256	0.2007	0.0395	0.1066	0.4134	0.7308	-0.1464	0.1738	-1.2834	0.0855	0.0646	-0.0753	-0.0004	2.1647	0.0576	0.1255	2.6519	-0.4867	3.154	26.027	2.8246	130.2669
65	0.2741	-0.0011	-0.0386	0.1793	0.0354	0.0866	-0.0539	1.7583	-0.0854	-0.8188	0.1716	0.2523	0.1438	-0.5795	0.0002	2.905	-0.0975	0.5382	3.1916	-1.1549	2.9408	50.8467	14.8161	102.3319
66	0.4139	-0.5271	0.3172	0.674	-0.4965	0.3505	-0.5251	0.6526	0.2104	1.3441	-0.1932	-0.8908	0.5317	0.1054	-0.1571	2.7856	0.6834	0.4936	2.5327	0.0587	1.2144	24.4364	21.7757	108.3255
67	0.0787	-0.0557	0.07	-0.072	0.0034	0.0247	0.0426	0.5409	-1.1703	0.1345	0.3229	0.0517	0.9068	0.0995	-0.0001	1.165	-0.5928	-0.4926	1.9647	0.2567	2.1859	29.6286	24.7898	126.3898
68	0.1671	0.0733	-0.0609	-0.0046	-0.0676	0.2842	-0.1603	-0.1844	-0.1062	1.1281	0.0558	-0.254	-0.5226	-0.2072	0.0001	1.7674	0.0803	-0.459	2.0613	-0.3422	2.5533	52.0529	45.2224	124.3387
69	-0.0217	-0.076	0.0084	0.1493	0.0996	0.0021	-0.7203	0.4482	-0.5432	-1.1031	0.026	-0.1578	0.4753	1.3052	-0.0011	1.2644	0.1314	0.7608	1.6963	0.0601	1.3711	39.5269	35.3043	130.0278
70	0.4136	0.1918	-0.2201	0.0782	-0.2859	0.4535	-1.2945	1.0477	1.2409	-0.038	0.1967	-0.3011	-0.3917	0.7273	-0.0027	2.9194	0.4566	-1.0954	2.8156	0.0749	2.6709	46.2869	26.3899	138.2406
71	0.0278	-0.0168	-0.0384	0.0298	0.0128	0.0009	0.1456	0.462	-0.2207	0.0151	0.1514	0.0695	0.3184	0.2749	-0.0002	4.8023	0.3817	-1.2551	3.8987	0.5063	3.4193	46.5468	-56.8974	49.7977
72	0.02	-0.0009	-0.0153	0.0125	-0.0133	0.0166	-0.0682	-0.2894	0.002	0.0962	0.0883	0.0977	-0.0266	0.0223	-0.0001	2.0564	0.202	0.5673	2.9576	0.2462	2.8007	89.2903	-81.0468	44.2304
73	0.0173	0.0267	-0.001	0.0018	-0.001	0.0128	-0.3055	0.1901	0.0105	-0.7557	-0.6386	-0.3083	-0.204	0.1358	0.002	2.2622	0.1168	1.3026	2.8472	0.3167	3.4317	-19.2682	97.9106	101.5621
74	0.0262	0.0338	0.0094	0.0292	0.0041	0.0142	-0.0079	-0.1336	-0.218	0.3585	-0.2813	-0.2734	-0.2366	-0.2769	0.0003	1.1203	-0.0725	-0.1335	1.5366	-0.4353	1.6912	-39.7248	99.4018	55.9924

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 10 through 144)
2	X-RAY DIFFRACTION	2	(chain 'A' and resid 145 through 236)
3	X-RAY DIFFRACTION	3	(chain 'A' and resid 237 through 379)
4	X-RAY DIFFRACTION	4	(chain 'A' and resid 380 through 471)
5	X-RAY DIFFRACTION	5	(chain 'A' and resid 472 through 542)
6	X-RAY DIFFRACTION	6	(chain 'A' and resid 543 through 630)
7	X-RAY DIFFRACTION	7	(chain 'A' and resid 631 through 722)
8	X-RAY DIFFRACTION	8	(chain 'A' and resid 723 through 878)
9	X-RAY DIFFRACTION	9	(chain 'A' and resid 879 through 904)
10	X-RAY DIFFRACTION	10	(chain 'A' and resid 905 through 1045)
11	X-RAY DIFFRACTION	11	(chain 'A' and resid 1046 through 1180)
12	X-RAY DIFFRACTION	12	(chain 'A' and resid 1213 through 1308)
13	X-RAY DIFFRACTION	13	(chain 'A' and resid 1323 through 1420)
14	X-RAY DIFFRACTION	14	(chain 'A' and resid 1421 through 1526)
15	X-RAY DIFFRACTION	15	(chain 'A' and resid 1548 through 1763)
16	X-RAY DIFFRACTION	16	(chain 'A' and resid 1787 through 1822)
17	X-RAY DIFFRACTION	17	(chain 'A' and resid 1856 through 1975)
18	X-RAY DIFFRACTION	18	(chain 'A' and resid 1976 through 2310)
19	X-RAY DIFFRACTION	19	(chain 'A' and resid 2311 through 2514)
20	X-RAY DIFFRACTION	20	(chain 'A' and resid 2515 through 2576)
21	X-RAY DIFFRACTION	21	(chain 'A' and resid 2602 through 2665)
22	X-RAY DIFFRACTION	22	(chain 'A' and resid 2774 through 2802)
23	X-RAY DIFFRACTION	23	(chain 'A' and resid 2803 through 2943)
24	X-RAY DIFFRACTION	24	(chain 'A' and resid 2944 through 3006)
25	X-RAY DIFFRACTION	25	(chain 'A' and resid 3008 through 3095)
26	X-RAY DIFFRACTION	26	(chain 'A' and resid 3096 through 3199)
27	X-RAY DIFFRACTION	27	(chain 'A' and resid 3227 through 3314)
28	X-RAY DIFFRACTION	28	(chain 'A' and resid 3315 through 3405)
29	X-RAY DIFFRACTION	29	(chain 'A' and resid 3406 through 3576)
30	X-RAY DIFFRACTION	30	(chain 'A' and resid 3577 through 3680)
31	X-RAY DIFFRACTION	31	(chain 'A' and resid 3681 through 3755)
32	X-RAY DIFFRACTION	32	(chain 'A' and resid 3756 through 3808)
33	X-RAY DIFFRACTION	33	(chain 'A' and resid 3809 through 3894)
34	X-RAY DIFFRACTION	34	(chain 'A' and resid 3895 through 3972)
35	X-RAY DIFFRACTION	35	(chain 'A' and resid 3973 through 4128)
36	X-RAY DIFFRACTION	36	(chain 'B' and resid 10 through 144)
37	X-RAY DIFFRACTION	37	(chain 'B' and resid 145 through 236)
38	X-RAY DIFFRACTION	38	(chain 'B' and resid 237 through 379)
39	X-RAY DIFFRACTION	39	(chain 'B' and resid 380 through 471)
40	X-RAY DIFFRACTION	40	(chain 'B' and resid 472 through 542)
41	X-RAY DIFFRACTION	41	(chain 'B' and resid 543 through 630)
42	X-RAY DIFFRACTION	42	(chain 'B' and resid 631 through 722)
43	X-RAY DIFFRACTION	43	(chain 'B' and resid 723 through 878)
44	X-RAY DIFFRACTION	44	(chain 'B' and resid 879 through 904)
45	X-RAY DIFFRACTION	45	(chain 'B' and resid 905 through 1045)
46	X-RAY DIFFRACTION	46	(chain 'B' and resid 1046 through 1180)
47	X-RAY DIFFRACTION	47	(chain 'B' and resid 1213 through 1308)
48	X-RAY DIFFRACTION	48	(chain 'B' and resid 1323 through 1420)
49	X-RAY DIFFRACTION	49	(chain 'B' and resid 1421 through 1526)
50	X-RAY DIFFRACTION	50	(chain 'B' and resid 1548 through 1763)
51	X-RAY DIFFRACTION	51	(chain 'B' and resid 1787 through 1822)
52	X-RAY DIFFRACTION	52	(chain 'B' and resid 1856 through 1975)
53	X-RAY DIFFRACTION	53	(chain 'B' and resid 1976 through 2310)
54	X-RAY DIFFRACTION	54	(chain 'B' and resid 2311 through 2514)
55	X-RAY DIFFRACTION	55	(chain 'B' and resid 2515 through 2576)
56	X-RAY DIFFRACTION	56	(chain 'B' and resid 2602 through 2665)
57	X-RAY DIFFRACTION	57	(chain 'B' and resid 2774 through 2802)
58	X-RAY DIFFRACTION	58	(chain 'B' and resid 2803 through 2943)
59	X-RAY DIFFRACTION	59	(chain 'B' and resid 2944 through 3006)
60	X-RAY DIFFRACTION	60	(chain 'B' and resid 3008 through 3095)
61	X-RAY DIFFRACTION	61	(chain 'B' and resid 3096 through 3199)
62	X-RAY DIFFRACTION	62	(chain 'B' and resid 3227 through 3314)
63	X-RAY DIFFRACTION	63	(chain 'B' and resid 3315 through 3405)
64	X-RAY DIFFRACTION	64	(chain 'B' and resid 3406 through 3576)
65	X-RAY DIFFRACTION	65	(chain 'B' and resid 3577 through 3680)
66	X-RAY DIFFRACTION	66	(chain 'B' and resid 3681 through 3755)
67	X-RAY DIFFRACTION	67	(chain 'B' and resid 3756 through 3808)
68	X-RAY DIFFRACTION	68	(chain 'B' and resid 3809 through 3894)
69	X-RAY DIFFRACTION	69	(chain 'B' and resid 3895 through 3972)
70	X-RAY DIFFRACTION	70	(chain 'B' and resid 3973 through 4128)
71	X-RAY DIFFRACTION	71	(chain 'K' and resid 101 through 133)
72	X-RAY DIFFRACTION	72	(chain 'K' and resid 201 through 221)
73	X-RAY DIFFRACTION	73	(chain 'S' and resid 101 through 133)
74	X-RAY DIFFRACTION	74	(chain 'S' and resid 201 through 221)

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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

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Jul 12, 2017. Major update of PDB

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Yorodumi