PDB-7zx0: Crystal structure of Pol theta polymerase domain in complex with ...

ID or keywords:

Entry

Database: PDB / ID: 7zx0

Title

Crystal structure of Pol theta polymerase domain in complex with compound 5

Components

DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')
DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')
DNA polymerase theta

Keywords

TRANSFERASE / DNA polymerase / protein-DNA complex / DNA repair / inhibitor

Function / homology

Function and homology information

double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / replication fork processing / mitochondrial nucleoid / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / somatic hypermutation of immunoglobulin genes ...
Similarity search - Function

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.99 Å

Authors

Krajewski, W.W. / Turnbull, A.P. / Willis, S. / Charles, M. / Stockley, M. / Heald, R.A.

Funding support

1items

Citation

Journal: J.Med.Chem. / Year: 2022
Title: Discovery, Characterization, and Structure-Based Optimization of Small-Molecule In Vitro and In Vivo Probes for Human DNA Polymerase Theta.
Authors: Stockley, M.L. / Ferdinand, A. / Benedetti, G. / Blencowe, P. / Boyd, S.M. / Calder, M. / Charles, M.D. / Edwardes, L.V. / Ekwuru, T. / Finch, H. / Galbiati, A. / Geo, L. / Grande, D. / ...

History

Deposition	May 19, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 12, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 19, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 9, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7zx0.cif.gz	869.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7zx0.ent.gz		Display	PDB format
PDBx/mmJSON format	7zx0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7zx0_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	7zx0_full_validation.pdf.gz	2.6 MB	Display
Data in XML	7zx0_validation.xml.gz	129.9 KB	Display
Data in CIF	7zx0_validation.cif.gz	177.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zx/7zx0 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/7zx0	HTTPS FTP

-
Related structure data

Related structure data	7zusSC 7zx1C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #91 - Jul 2007 Thymine Dimers similarity (7) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #3 - Mar 2000 DNA Polymerase similarity (8) #150 - Jun 2012 Sliding Clamps similarity (2) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (7)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (8)
#150 - Jun 2012
Sliding Clamps
similarity (2)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

AAA: DNA polymerase theta

BBB: DNA polymerase theta

CCC: DNA polymerase theta

DDD: DNA polymerase theta

EEE: DNA polymerase theta

FFF: DNA polymerase theta

GGG: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

HHH: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

III: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

JJJ: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

KKK: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

LLL: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

MMM: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

NNN: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

OOO: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

PPP: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

QQQ: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

RRR: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

hetero molecules

547 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: DNA polymerase theta

GGG: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

HHH: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

hetero molecules

defined by author&software
91.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: DNA polymerase theta

III: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

JJJ: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

hetero molecules

defined by author&software
91.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

CCC: DNA polymerase theta

KKK: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

LLL: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

hetero molecules

defined by author&software
91.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

DDD: DNA polymerase theta

MMM: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

NNN: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

hetero molecules

defined by author&software
91.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

EEE: DNA polymerase theta

OOO: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

PPP: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

hetero molecules

defined by author&software
91.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

FFF: DNA polymerase theta

QQQ: DNA (5'-D(P*TP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*C)-3')

RRR: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*(DDG))-3')

hetero molecules

defined by author&software
91.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.050, 172.020, 288.610
Angle α, β, γ (deg.)	90.000, 91.260, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	VAL	VAL	AAA	A	1824 - 2590	5 - 726
2	1	1	SER	SER	VAL	VAL	BBB	B	1824 - 2590	5 - 726
3	2	2	SER	SER	VAL	VAL	AAA	A	1824 - 2590	5 - 726
4	2	2	SER	SER	VAL	VAL	CCC	C	1824 - 2590	5 - 726
5	3	3	SER	SER	VAL	VAL	AAA	A	1824 - 2590	5 - 726
6	3	3	SER	SER	VAL	VAL	DDD	D	1824 - 2590	5 - 726
7	4	4	SER	SER	VAL	VAL	AAA	A	1824 - 2590	5 - 726
8	4	4	SER	SER	VAL	VAL	EEE	E	1824 - 2590	5 - 726
9	5	5	SER	SER	VAL	VAL	AAA	A	1824 - 2590	5 - 726
10	5	5	SER	SER	VAL	VAL	FFF	F	1824 - 2590	5 - 726
11	6	6	SER	SER	VAL	VAL	BBB	B	1824 - 2590	5 - 726
12	6	6	SER	SER	VAL	VAL	CCC	C	1824 - 2590	5 - 726
13	7	7	SER	SER	VAL	VAL	BBB	B	1824 - 2590	5 - 726
14	7	7	SER	SER	VAL	VAL	DDD	D	1824 - 2590	5 - 726
15	8	8	SER	SER	VAL	VAL	BBB	B	1824 - 2590	5 - 726
16	8	8	SER	SER	VAL	VAL	EEE	E	1824 - 2590	5 - 726
17	9	9	SER	SER	VAL	VAL	BBB	B	1824 - 2590	5 - 726
18	9	9	SER	SER	VAL	VAL	FFF	F	1824 - 2590	5 - 726
19	10	10	SER	SER	VAL	VAL	CCC	C	1824 - 2590	5 - 726
20	10	10	SER	SER	VAL	VAL	DDD	D	1824 - 2590	5 - 726
21	11	11	SER	SER	VAL	VAL	CCC	C	1824 - 2590	5 - 726
22	11	11	SER	SER	VAL	VAL	EEE	E	1824 - 2590	5 - 726
23	12	12	SER	SER	VAL	VAL	CCC	C	1824 - 2590	5 - 726
24	12	12	SER	SER	VAL	VAL	FFF	F	1824 - 2590	5 - 726
25	13	13	SER	SER	VAL	VAL	DDD	D	1824 - 2590	5 - 726
26	13	13	SER	SER	VAL	VAL	EEE	E	1824 - 2590	5 - 726
27	14	14	SER	SER	VAL	VAL	DDD	D	1824 - 2590	5 - 726
28	14	14	SER	SER	VAL	VAL	FFF	F	1824 - 2590	5 - 726
29	15	15	SER	SER	VAL	VAL	EEE	E	1824 - 2590	5 - 726
30	15	15	SER	SER	VAL	VAL	FFF	F	1824 - 2590	5 - 726
31	16	16	DT	DT	DC	DC	GGG	G	2 - 17	1 - 16
32	16	16	DT	DT	DC	DC	III	I	2 - 17	1 - 16
33	17	17	DT	DT	DC	DC	GGG	G	2 - 17	1 - 16
34	17	17	DT	DT	DC	DC	KKK	K	2 - 17	1 - 16
35	18	18	DT	DT	DC	DC	GGG	G	2 - 17	1 - 16
36	18	18	DT	DT	DC	DC	MMM	M	2 - 17	1 - 16
37	19	19	DT	DT	DC	DC	GGG	G	2 - 17	1 - 16
38	19	19	DT	DT	DC	DC	OOO	O	2 - 17	1 - 16
39	20	20	DT	DT	DC	DC	GGG	G	2 - 17	1 - 16
40	20	20	DT	DT	DC	DC	QQQ	Q	2 - 17	1 - 16
41	21	21	DG	DG	DDG	DDG	HHH	H	1 - 13	1 - 13
42	21	21	DG	DG	DDG	DDG	JJJ	J	1 - 13	1 - 13
43	22	22	DG	DG	DDG	DDG	HHH	H	1 - 13	1 - 13
44	22	22	DG	DG	DDG	DDG	LLL	L	1 - 13	1 - 13
45	23	23	DG	DG	DDG	DDG	HHH	H	1 - 13	1 - 13
46	23	23	DG	DG	DDG	DDG	NNN	N	1 - 13	1 - 13
47	24	24	DG	DG	DDG	DDG	HHH	H	1 - 13	1 - 13
48	24	24	DG	DG	DDG	DDG	PPP	P	1 - 13	1 - 13
49	25	25	DG	DG	DDG	DDG	HHH	H	1 - 13	1 - 13
50	25	25	DG	DG	DDG	DDG	RRR	R	1 - 13	1 - 13
51	26	26	DT	DT	DC	DC	III	I	2 - 17	1 - 16
52	26	26	DT	DT	DC	DC	KKK	K	2 - 17	1 - 16
53	27	27	DT	DT	DC	DC	III	I	2 - 17	1 - 16
54	27	27	DT	DT	DC	DC	MMM	M	2 - 17	1 - 16
55	28	28	DT	DT	DC	DC	III	I	2 - 17	1 - 16
56	28	28	DT	DT	DC	DC	OOO	O	2 - 17	1 - 16
57	29	29	DT	DT	DC	DC	III	I	2 - 17	1 - 16
58	29	29	DT	DT	DC	DC	QQQ	Q	2 - 17	1 - 16
59	30	30	DG	DG	DDG	DDG	JJJ	J	1 - 13	1 - 13
60	30	30	DG	DG	DDG	DDG	LLL	L	1 - 13	1 - 13
61	31	31	DG	DG	DDG	DDG	JJJ	J	1 - 13	1 - 13
62	31	31	DG	DG	DDG	DDG	NNN	N	1 - 13	1 - 13
63	32	32	DG	DG	DDG	DDG	JJJ	J	1 - 13	1 - 13
64	32	32	DG	DG	DDG	DDG	PPP	P	1 - 13	1 - 13
65	33	33	DG	DG	DDG	DDG	JJJ	J	1 - 13	1 - 13
66	33	33	DG	DG	DDG	DDG	RRR	R	1 - 13	1 - 13
67	34	34	DT	DT	DC	DC	KKK	K	2 - 17	1 - 16
68	34	34	DT	DT	DC	DC	MMM	M	2 - 17	1 - 16
69	35	35	DT	DT	DC	DC	KKK	K	2 - 17	1 - 16
70	35	35	DT	DT	DC	DC	OOO	O	2 - 17	1 - 16
71	36	36	DT	DT	DC	DC	KKK	K	2 - 17	1 - 16
72	36	36	DT	DT	DC	DC	QQQ	Q	2 - 17	1 - 16
73	37	37	DG	DG	DDG	DDG	LLL	L	1 - 13	1 - 13
74	37	37	DG	DG	DDG	DDG	NNN	N	1 - 13	1 - 13
75	38	38	DG	DG	DDG	DDG	LLL	L	1 - 13	1 - 13
76	38	38	DG	DG	DDG	DDG	PPP	P	1 - 13	1 - 13
77	39	39	DG	DG	DDG	DDG	LLL	L	1 - 13	1 - 13
78	39	39	DG	DG	DDG	DDG	RRR	R	1 - 13	1 - 13
79	40	40	DT	DT	DC	DC	MMM	M	2 - 17	1 - 16
80	40	40	DT	DT	DC	DC	OOO	O	2 - 17	1 - 16
81	41	41	DT	DT	DC	DC	MMM	M	2 - 17	1 - 16
82	41	41	DT	DT	DC	DC	QQQ	Q	2 - 17	1 - 16
83	42	42	DG	DG	DDG	DDG	NNN	N	1 - 13	1 - 13
84	42	42	DG	DG	DDG	DDG	PPP	P	1 - 13	1 - 13
85	43	43	DG	DG	DDG	DDG	NNN	N	1 - 13	1 - 13
86	43	43	DG	DG	DDG	DDG	RRR	R	1 - 13	1 - 13
87	44	44	DT	DT	DC	DC	OOO	O	2 - 17	1 - 16
88	44	44	DT	DT	DC	DC	QQQ	Q	2 - 17	1 - 16
89	45	45	DG	DG	DDG	DDG	PPP	P	1 - 13	1 - 13
90	45	45	DG	DG	DDG	DDG	RRR	R	1 - 13	1 - 13

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56
29	Local NCS retraints between domains: 57 58
30	Local NCS retraints between domains: 59 60
31	Local NCS retraints between domains: 61 62
32	Local NCS retraints between domains: 63 64
33	Local NCS retraints between domains: 65 66
34	Local NCS retraints between domains: 67 68
35	Local NCS retraints between domains: 69 70
36	Local NCS retraints between domains: 71 72
37	Local NCS retraints between domains: 73 74
38	Local NCS retraints between domains: 75 76
39	Local NCS retraints between domains: 77 78
40	Local NCS retraints between domains: 79 80
41	Local NCS retraints between domains: 81 82
42	Local NCS retraints between domains: 83 84
43	Local NCS retraints between domains: 85 86
44	Local NCS retraints between domains: 87 88
45	Local NCS retraints between domains: 89 90

-
Protein , 1 types, 6 molecules AAABBBCCCDDDEEEFFF

#1: Protein	DNA polymerase theta / DNA polymerase eta Mass: 81771.719 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLQ, POLH / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS / References: UniProt: O75417, DNA-directed DNA polymerase

#1: Protein

DNA polymerase theta / DNA polymerase eta

Mass: 81771.719 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: POLQ, POLH / Plasmid: pET21a / Production host:

Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS / References: UniProt: O75417, DNA-directed DNA polymerase

-
DNA chain , 2 types, 12 molecules GGGIIIKKKMMMOOOQQQHHHJJJLLLNNNPPPRRR

#2: DNA chain	DNA (5'-D(PTPTPCPCPAPAPTPGPAPCPAPGPCPCPGPC)-3') Mass: 4843.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain	DNA (5'-D(GPCPGPGPCPTPGPTPCPAPTPTP(DDG))-3') Mass: 3982.596 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source*: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 14 molecules

#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE Mass: 491.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-K7X / 2-[5-bromanyl-3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]oxy-~{N}-ethyl-~{N}-(3-methylphenyl)ethanamide Mass: 456.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₁₇BrF₃N₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 59.3 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.9 Details: 15% (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.9, 0.2 M sodium citrate tribasic dihydrate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97623 Å / Relative weight: 1
Reflection	Resolution: 2.93→147.75 Å / Num. obs: 122599 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC_1/2: 0.998 / R_rim(I) all: 0.084 / Net I/σ(I): 13.1
Reflection shell	Resolution: 2.93→3.01 Å / Num. unique obs: 9044 / CC_1/2: 0.472 / R_rim(I) all: 1.169

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7ZUS

7zus

Resolution: 2.99→50.005 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.911 / WR_factor R_free: 0.235 / WR_factor R_work: 0.203 / SU B: 21.949 / SU ML: 0.386 / Average fsc free: 0.8642 / Average fsc work: 0.8744 / Cross valid method: FREE R-VALUE / ESU R Free: 0.42
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2519	5815	5.04 %
R_work	0.218	109568	-
all	0.22	-	-
obs	-	115383	99.149 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 97.164 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.623 Å²	0 Å²	0.246 Å²
2-	-	-4.446 Å²	-0 Å²
3-	-	-	-1.187 Å²

Refinement step

Cycle: LAST / Resolution: 2.99→50.005 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29008	3528	214	1	32751

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	33776
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	29643
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.018	0.01	51984
X-RAY DIFFRACTION	r_angle_refined_deg	1.438	1.653	46532
X-RAY DIFFRACTION	r_angle_other_deg	1.236	1.574	68073
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.436	5	3773
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.725	22.555	1401
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.721	15	4829
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.068	15	159
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	4714
X-RAY DIFFRACTION	r_chiral_restr_other	0.025	0.2	5
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	35931
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	7389
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	6261
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	26673
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	15898
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	15921
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	459
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.04	0.2	13
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.23	0.2	29
X-RAY DIFFRACTION	r_nbd_other	0.289	0.2	88
X-RAY DIFFRACTION	r_mcbond_it	7.748	10.399	15188
X-RAY DIFFRACTION	r_mcbond_other	7.748	10.398	15187
X-RAY DIFFRACTION	r_mcangle_it	12.06	15.584	18929
X-RAY DIFFRACTION	r_mcangle_other	12.06	15.584	18930
X-RAY DIFFRACTION	r_scbond_it	7.768	11.005	18588
X-RAY DIFFRACTION	r_scbond_other	7.766	11.005	18585
X-RAY DIFFRACTION	r_scangle_it	12.251	16.429	27603
X-RAY DIFFRACTION	r_scangle_other	12.252	16.429	27601
X-RAY DIFFRACTION	r_lrange_it	17.801	211.493	72337
X-RAY DIFFRACTION	r_lrange_other	17.801	211.492	72338
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.028	0.05	19981
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.026	0.05	20268
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.035	0.05	19943
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.027	0.05	20093
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.026	0.05	20117
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.021	0.05	19953
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.032	0.05	19742
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.02	0.05	20030
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.018	0.05	19923
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.032	0.05	19919
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.024	0.05	20054
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.021	0.05	20100
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.026	0.05	19849
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.027	0.05	19963
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.016	0.05	20009
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.017	0.05	1260
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.008	0.05	1265
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.012	0.05	1266
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.011	0.05	1263
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.01	0.05	1263
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.014	0.05	1152
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.007	0.05	1157
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.009	0.05	1158
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.009	0.05	1156
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.008	0.05	1153
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.014	0.05	1262
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.015	0.05	1263
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.012	0.05	1260
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.012	0.05	1262
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.014	0.05	1153
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.013	0.05	1151
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.009	0.05	1153
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.01	0.05	1153
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.008	0.05	1265
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.007	0.05	1264
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.007	0.05	1265
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.007	0.05	1155
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.008	0.05	1155
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.006	0.05	1154
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.01	0.05	1264
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.009	0.05	1266
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.008	0.05	1155
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.007	0.05	1153
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.006	0.05	1263
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.005	0.05	1154

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.02751	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.02751	0.05009
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.02615	0.05009
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.02615	0.05009
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.03525	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.03525	0.05009
4	7	AAA	X-RAY DIFFRACTION	Local ncs	0.0265	0.05009
4	8	EEE	X-RAY DIFFRACTION	Local ncs	0.0265	0.05009
5	9	AAA	X-RAY DIFFRACTION	Local ncs	0.02596	0.05009
5	10	FFF	X-RAY DIFFRACTION	Local ncs	0.02596	0.05009
6	11	BBB	X-RAY DIFFRACTION	Local ncs	0.02103	0.05009
6	12	CCC	X-RAY DIFFRACTION	Local ncs	0.02103	0.05009
7	13	BBB	X-RAY DIFFRACTION	Local ncs	0.03228	0.05009
7	14	DDD	X-RAY DIFFRACTION	Local ncs	0.03228	0.05009
8	15	BBB	X-RAY DIFFRACTION	Local ncs	0.02032	0.05009
8	16	EEE	X-RAY DIFFRACTION	Local ncs	0.02032	0.05009
9	17	BBB	X-RAY DIFFRACTION	Local ncs	0.01755	0.05009
9	18	FFF	X-RAY DIFFRACTION	Local ncs	0.01755	0.05009
10	19	CCC	X-RAY DIFFRACTION	Local ncs	0.03202	0.05009
10	20	DDD	X-RAY DIFFRACTION	Local ncs	0.03202	0.05009
11	21	CCC	X-RAY DIFFRACTION	Local ncs	0.02366	0.05009
11	22	EEE	X-RAY DIFFRACTION	Local ncs	0.02366	0.05009
12	23	CCC	X-RAY DIFFRACTION	Local ncs	0.0207	0.05009
12	24	FFF	X-RAY DIFFRACTION	Local ncs	0.0207	0.05009
13	25	DDD	X-RAY DIFFRACTION	Local ncs	0.02644	0.05009
13	26	EEE	X-RAY DIFFRACTION	Local ncs	0.02644	0.05009
14	27	DDD	X-RAY DIFFRACTION	Local ncs	0.0275	0.05009
14	28	FFF	X-RAY DIFFRACTION	Local ncs	0.0275	0.05009
15	29	EEE	X-RAY DIFFRACTION	Local ncs	0.0164	0.05009
15	30	FFF	X-RAY DIFFRACTION	Local ncs	0.0164	0.05009
16	31	GGG	X-RAY DIFFRACTION	Local ncs	0.0173	0.05011
16	32	III	X-RAY DIFFRACTION	Local ncs	0.0173	0.05011
17	33	GGG	X-RAY DIFFRACTION	Local ncs	0.00799	0.05011
17	34	KKK	X-RAY DIFFRACTION	Local ncs	0.00799	0.05011
18	35	GGG	X-RAY DIFFRACTION	Local ncs	0.01151	0.05011
18	36	MMM	X-RAY DIFFRACTION	Local ncs	0.01151	0.05011
19	37	GGG	X-RAY DIFFRACTION	Local ncs	0.01064	0.05011
19	38	OOO	X-RAY DIFFRACTION	Local ncs	0.01064	0.05011
20	39	GGG	X-RAY DIFFRACTION	Local ncs	0.01006	0.05011
20	40	QQQ	X-RAY DIFFRACTION	Local ncs	0.01006	0.05011
21	41	HHH	X-RAY DIFFRACTION	Local ncs	0.01376	0.0501
21	42	JJJ	X-RAY DIFFRACTION	Local ncs	0.01376	0.0501
22	43	HHH	X-RAY DIFFRACTION	Local ncs	0.00726	0.0501
22	44	LLL	X-RAY DIFFRACTION	Local ncs	0.00726	0.0501
23	45	HHH	X-RAY DIFFRACTION	Local ncs	0.00904	0.05011
23	46	NNN	X-RAY DIFFRACTION	Local ncs	0.00904	0.05011
24	47	HHH	X-RAY DIFFRACTION	Local ncs	0.00931	0.0501
24	48	PPP	X-RAY DIFFRACTION	Local ncs	0.00931	0.0501
25	49	HHH	X-RAY DIFFRACTION	Local ncs	0.00848	0.0501
25	50	RRR	X-RAY DIFFRACTION	Local ncs	0.00848	0.0501
26	51	III	X-RAY DIFFRACTION	Local ncs	0.01419	0.05011
26	52	KKK	X-RAY DIFFRACTION	Local ncs	0.01419	0.05011
27	53	III	X-RAY DIFFRACTION	Local ncs	0.01542	0.05011
27	54	MMM	X-RAY DIFFRACTION	Local ncs	0.01542	0.05011
28	55	III	X-RAY DIFFRACTION	Local ncs	0.01153	0.05011
28	56	OOO	X-RAY DIFFRACTION	Local ncs	0.01153	0.05011
29	57	III	X-RAY DIFFRACTION	Local ncs	0.0123	0.05011
29	58	QQQ	X-RAY DIFFRACTION	Local ncs	0.0123	0.05011
30	59	JJJ	X-RAY DIFFRACTION	Local ncs	0.0136	0.0501
30	60	LLL	X-RAY DIFFRACTION	Local ncs	0.0136	0.0501
31	61	JJJ	X-RAY DIFFRACTION	Local ncs	0.01257	0.0501
31	62	NNN	X-RAY DIFFRACTION	Local ncs	0.01257	0.0501
32	63	JJJ	X-RAY DIFFRACTION	Local ncs	0.00948	0.0501
32	64	PPP	X-RAY DIFFRACTION	Local ncs	0.00948	0.0501
33	65	JJJ	X-RAY DIFFRACTION	Local ncs	0.01028	0.0501
33	66	RRR	X-RAY DIFFRACTION	Local ncs	0.01028	0.0501
34	67	KKK	X-RAY DIFFRACTION	Local ncs	0.00799	0.05011
34	68	MMM	X-RAY DIFFRACTION	Local ncs	0.00799	0.05011
35	69	KKK	X-RAY DIFFRACTION	Local ncs	0.0072	0.05011
35	70	OOO	X-RAY DIFFRACTION	Local ncs	0.0072	0.05011
36	71	KKK	X-RAY DIFFRACTION	Local ncs	0.00675	0.05011
36	72	QQQ	X-RAY DIFFRACTION	Local ncs	0.00675	0.05011
37	73	LLL	X-RAY DIFFRACTION	Local ncs	0.00729	0.0501
37	74	NNN	X-RAY DIFFRACTION	Local ncs	0.00729	0.0501
38	75	LLL	X-RAY DIFFRACTION	Local ncs	0.00766	0.0501
38	76	PPP	X-RAY DIFFRACTION	Local ncs	0.00766	0.0501
39	77	LLL	X-RAY DIFFRACTION	Local ncs	0.00643	0.0501
39	78	RRR	X-RAY DIFFRACTION	Local ncs	0.00643	0.0501
40	79	MMM	X-RAY DIFFRACTION	Local ncs	0.00955	0.05011
40	80	OOO	X-RAY DIFFRACTION	Local ncs	0.00955	0.05011
41	81	MMM	X-RAY DIFFRACTION	Local ncs	0.00939	0.05011
41	82	QQQ	X-RAY DIFFRACTION	Local ncs	0.00939	0.05011
42	83	NNN	X-RAY DIFFRACTION	Local ncs	0.00808	0.0501
42	84	PPP	X-RAY DIFFRACTION	Local ncs	0.00808	0.0501
43	85	NNN	X-RAY DIFFRACTION	Local ncs	0.00735	0.0501
43	86	RRR	X-RAY DIFFRACTION	Local ncs	0.00735	0.0501
44	87	OOO	X-RAY DIFFRACTION	Local ncs	0.00624	0.05011
44	88	QQQ	X-RAY DIFFRACTION	Local ncs	0.00624	0.05011
45	89	PPP	X-RAY DIFFRACTION	Local ncs	0.00518	0.0501
45	90	RRR	X-RAY DIFFRACTION	Local ncs	0.00518	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.99-3.067	0.356	426	0.344	8103	0.345	8549	0.613	0.634	99.7661	0.323
3.067-3.151	0.348	374	0.326	7912	0.327	8306	0.711	0.722	99.7592	0.298
3.151-3.242	0.302	393	0.287	7727	0.287	8146	0.817	0.812	99.6808	0.257
3.242-3.341	0.277	410	0.255	7412	0.256	7832	0.862	0.87	99.8723	0.224
3.341-3.45	0.297	384	0.253	7299	0.255	7695	0.852	0.879	99.8441	0.225
3.45-3.571	0.281	386	0.24	6937	0.242	7340	0.876	0.895	99.7684	0.214
3.571-3.705	0.276	403	0.241	6770	0.243	7186	0.883	0.893	99.8191	0.215
3.705-3.855	0.249	317	0.22	6467	0.221	6807	0.908	0.913	99.6621	0.197
3.855-4.026	0.241	340	0.206	6224	0.208	6603	0.92	0.924	99.4094	0.184
4.026-4.221	0.248	317	0.202	5993	0.204	6357	0.907	0.925	99.2607	0.185
4.221-4.447	0.218	272	0.179	5600	0.181	5936	0.936	0.945	98.9218	0.168
4.447-4.715	0.206	314	0.169	5272	0.171	5672	0.945	0.953	98.4838	0.16
4.715-5.037	0.203	294	0.174	4990	0.176	5374	0.942	0.949	98.3253	0.167
5.037-5.436	0.235	245	0.18	4662	0.183	4983	0.934	0.95	98.4748	0.173
5.436-5.948	0.279	233	0.222	4302	0.225	4607	0.901	0.921	98.4372	0.211
5.948-6.639	0.256	189	0.234	3879	0.235	4162	0.903	0.918	97.7415	0.227
6.639-7.643	0.246	170	0.21	3418	0.212	3670	0.916	0.929	97.7657	0.21
7.643-9.307	0.217	151	0.184	2911	0.186	3135	0.946	0.953	97.6714	0.197
9.307-12.939	0.209	125	0.195	2288	0.196	2477	0.947	0.954	97.4162	0.215
12.939-50.005	0.345	69	0.295	1370	0.298	1473	0.837	0.886	97.6918	0.321

-
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://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

-
Protein , 1 types, 6 molecules AAABBBCCCDDDEEEFFF

-
DNA chain , 2 types, 12 molecules GGGIIIKKKMMMOOOQQQHHHJJJLLLNNNPPPRRR

-
Non-polymers , 4 types, 14 molecules

-
Details

-
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

-Protein , 1 types, 6 molecules AAABBBCCCDDDEEEFFF

-DNA chain , 2 types, 12 molecules GGGIIIKKKMMMOOOQQQHHHJJJLLLNNNPPPRRR

-Non-polymers , 4 types, 14 molecules

-Details

-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

-
Protein , 1 types, 6 molecules AAABBBCCCDDDEEEFFF

-
DNA chain , 2 types, 12 molecules GGGIIIKKKMMMOOOQQQHHHJJJLLLNNNPPPRRR

-
Non-polymers , 4 types, 14 molecules

-
Details

-
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