PDB-5lcm: STRUCTURE OF the RAD14 DNA-binding domain IN COMPLEX WITH N2-acet...

ID or keywords:

Entry

Database: PDB / ID: 5lcm

Title

STRUCTURE OF the RAD14 DNA-binding domain IN COMPLEX WITH N2-acetylaminonaphtyl- GUANINE CONTAINING DNA

Components

DNA (5'-D(*GP*CP*TP*CP*TP*AP*CP*(AAN)P*TP*CP*AP*TP*CP*A)-3')
DNA (5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*G)-3')
DNA repair protein RAD14

Keywords

DNA BINDING PROTEIN / Nucleotide excision repair DNA damage recognition

Function / homology

Function and homology information

nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair, DNA damage recognition / UV-damage excision repair / Dual incision in TC-NER /

base-excision repair / damaged DNA binding / zinc ion binding /

nucleus
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.9 Å

Authors

Schneider, S. / Ebert, C. / Simon, N. / Carell, T.

Funding support

Germany, 1items

Citation

Journal: Chembiochem / Year: 2017
Title: Structural Insights into the Recognition of N(2) -Aryl- and C8-Aryl DNA Lesions by the Repair Protein XPA/Rad14.
Authors: Ebert, C. / Simon, N. / Schneider, S. / Carell, T.

History

Deposition	Jun 22, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 10, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2017	Group: Database references
Revision 1.2	Jul 26, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 24, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5lcm.cif.gz	165.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5lcm.ent.gz	140.4 KB	Display	PDB format
PDBx/mmJSON format	5lcm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lc/5lcm ftp://data.pdbj.org/pub/pdb/validation_reports/lc/5lcm	HTTPS FTP

-
Related structure data

Related structure data	5lclC C: citing same article (ref.)
Similar structure data	5g33-d 5g34-d 5g32-d 5lcl-d 5a3d-d 5cq9-1 2dpy-2 5g35-d 1phs-d 1cau-d Search similar-shape structures by Omokage search (details) 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	#255 - Mar 2021 Cisplatin and DNA similarity (12) #67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #253 - Jan 2021 Expressome similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #135 - Mar 2011 Integrase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #40 - Apr 2003 RNA Polymerase similarity (2) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #23 - Nov 2001 DNA similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #131 - Nov 2010 Inteins similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #161 - May 2013 Ricin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#255 - Mar 2021
Cisplatin and DNA
similarity (12)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (2)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#161 - May 2013
Ricin
similarity (1)

Deposited unit

A: DNA repair protein RAD14

B: DNA repair protein RAD14

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

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

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	53.041, 53.041, 131.345
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	DNA repair protein RAD14 / Mass: 14224.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: RAD14, YMR201C, YM8325.02C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P28519
#2: DNA chain	DNA (5'-D(GPCPTPCPTPAPCP(AAN)PTPCPAPTPCPA)-3') Mass: 4672.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: DNA chain	DNA (5'-D(GPTPGPAPTPGPAPCPGPTPAPGPAPG)-3') Mass: 4674.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.68 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion Details: 0.2M Ammonium nitrate 40% (v/v) 2-methyl-1,3,-propanediol

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9726 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9726 Å / Relative weight: 1
Reflection	Resolution: 1.9→49.2 Å / Num. obs: 28349 / % possible obs: 99 % / Redundancy: 4.5 % / CC_1/2: 0.99 / R_merge(I) obs: 0.148 / Net I/σ(I): 6.2
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 1.1 / % possible all: 99

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0151	refinement
XDS		data reduction
XDS		data reduction
REFMAC	5.8.0151	phasing

Refinement

Resolution: 1.9→49.2 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.927 / SU B: 11.824 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26868	1370	4.8 %	RANDOM
R_work	0.23113	-	-	-
obs	0.23296	26983	99.44 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 37.009 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.13 Å²	0 Å²	0 Å²
2-	-	-0.13 Å²	0 Å²
3-	-	-	0.27 Å²

Refinement step

Cycle: 1 / Resolution: 1.9→49.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1892	578	2	112	2584

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.016	3263
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2478
X-RAY DIFFRACTION	r_angle_refined_deg	2.184	1.666	4643
X-RAY DIFFRACTION	r_angle_other_deg	1.605	3	5788
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.89	5	235
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.277	24.404	109
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.237	15	367
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.016	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	437
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	2883
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	725
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.959	1.641	922
X-RAY DIFFRACTION	r_mcbond_other	0.958	1.641	921
X-RAY DIFFRACTION	r_mcangle_it	1.395	2.456	1151
X-RAY DIFFRACTION	r_mcangle_other	1.395	2.457	1152
X-RAY DIFFRACTION	r_scbond_it	0.996	1.737	2341
X-RAY DIFFRACTION	r_scbond_other	0.996	1.737	2340
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.619	2.579	3489
X-RAY DIFFRACTION	r_long_range_B_refined	3.752	16.993	4118
X-RAY DIFFRACTION	r_long_range_B_other	3.716	16.829	4099
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.367	110	-
R_work	0.376	1981	-
obs	-	-	99.38 %

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	2.9461	1.8209	-3.1576	2.6335	-3.8187	9.8801	-0.0316	0.1923	-0.2167	-0.1944	0.0737	0.0697	0.5067	0.0756	-0.0421	0.1446	0.01	0.0009	0.0654	-0.021	0.0488	48.3829	49.9577	-66.0174
2	9.0433	-1.1213	-6.0621	0.4118	1.9853	9.6484	0.3841	0.376	0.3101	-0.0858	-0.0043	-0.0764	-0.4531	-0.0517	-0.3799	0.1502	0.0017	0.0342	0.0924	0.0301	0.0262	44.5878	57.9031	-64.7312
3	11.6437	0.5514	1.2394	2.9586	1.2334	1.8228	0.282	0.1298	0.4769	0.0418	-0.1475	0.2576	-0.1256	-0.3549	-0.1345	0.1038	0.0268	0.0397	0.0909	0.066	0.1036	34.4338	58.6983	-48.9801
4	10.617	-1.1074	-7.8793	3.8517	-0.5597	8.1528	-0.1183	-0.2064	-0.4869	0.2632	-0.0623	0.1025	0.4642	-0.0267	0.1807	0.1522	-0.0311	-0.0303	0.0992	0.0347	0.0384	34.6885	47.9474	-47.4871
5	6.5221	-0.6369	4.1616	3.9139	1.5274	10.1586	0.1025	-0.0666	0.2517	0.1279	0.0722	-0.2417	0.0954	-0.0127	-0.1747	0.0623	0.0031	0.0057	0.0717	0.015	0.0373	47.1656	56.5955	-41.6056
6	10.6119	0.8404	1.5543	0.7395	-0.5625	4.6046	0.076	0.2066	0.163	-0.1852	-0.0029	0.1724	-0.0468	-0.3908	-0.0731	0.1106	0.0437	-0.0325	0.0934	0.0086	0.0547	34.5274	54.1804	-55.5937
7	4.0596	-0.8931	2.406	12.5302	4.0173	9.1963	0.0344	0.8381	0.9479	-0.6443	-0.2289	0.2458	-0.6231	-0.6103	0.1945	0.1242	0.0718	-0.0224	0.4732	0.1801	0.4461	22.224	59.0533	-54.9393
8	1.2723	2.8518	-0.4697	11.134	5.493	9.2895	0.1105	-0.1926	0.1016	0.0337	-0.4148	0.4205	-0.5372	-0.0371	0.3044	0.4445	0.1997	-0.0323	0.5656	0.0227	0.6484	19.3157	68.3499	-43.2098
9	1.8214	1.2023	-3.8702	2.117	-4.0009	11.1184	0.1496	-0.1291	0.0887	0.1206	-0.057	-0.1819	0.0139	0.4675	-0.0926	0.1126	0.0259	-0.0492	0.1622	-0.0062	0.0793	29.6028	31.1549	-1.0469
10	0.2444	-0.5821	1.2618	8.1694	-6.2511	8.0765	-0.0171	-0.0693	-0.0849	0.3321	0.4583	0.2236	-0.2001	-0.5211	-0.4412	0.0948	-0.0007	0.0455	0.1504	0.0335	0.0509	21.7326	35.0235	-2.4201
11	2.8174	0.1887	1.0874	10.8412	0.0238	2.9446	-0.0798	0.0229	0.3441	0.0904	0.2802	0.3565	-0.1896	-0.0759	-0.2004	0.0753	0.0166	0.0317	0.0892	0.0218	0.1007	20.8742	45.1399	-18.1097
12	10.6843	-1.4588	1.1355	9.7382	-0.9487	5.6004	0.0875	0.2438	-0.0841	-0.2664	-0.0775	-0.223	0.0272	0.2739	-0.0101	0.1273	-0.0274	0.0354	0.1281	0.0209	0.0227	31.176	46.7591	-21.8583
13	10.2864	9.2598	9.7153	12.5762	11.8165	11.4004	0.1202	0.0256	-0.0975	-0.6315	0.2847	-0.5497	-0.4244	0.2088	-0.4049	0.1368	-0.0068	0.0891	0.1079	0.0042	0.0614	29.9328	37.7872	-17.3788
14	4.461	0.4228	-0.0669	3.9992	4.1569	10.4998	0.165	0.2186	-0.2929	-0.2018	0.0024	0.1475	-0.0143	-0.1735	-0.1674	0.0877	0.0104	-0.0069	0.0614	0.0011	0.0593	21.8037	32.6167	-27.4637
15	1.7973	1.5899	0.3068	10.551	-0.5762	3.5139	-0.0007	-0.2396	0.3933	0.3138	0.1257	0.0779	-0.5222	0.037	-0.125	0.136	0.0186	0.0402	0.1024	-0.0496	0.1172	25.7736	48.3524	-11.9248
16	7.3532	-1.6732	8.3379	2.0883	-3.3086	13.3093	-0.2815	-0.3639	0.6589	0.0368	-0.0017	0.4414	-0.125	-0.9725	0.2832	0.3695	0.0851	0.0805	0.2642	-0.0663	0.4705	14.1638	58.9316	-17.5635
17	3.5382	-2.1866	4.6826	2.567	-0.6469	10.405	-0.1713	-0.3671	-0.2494	0.118	0.3295	0.3183	-0.1297	-0.2163	-0.1582	0.0935	0.0117	0.0309	0.1552	0.0244	0.2183	39.7584	60.995	-40.992
18	10.8213	0.3054	-1.2564	1.9509	-1.2736	1.9943	-0.7053	-0.5627	-0.7447	0.0029	0.2189	0.3126	-0.0575	-0.2638	0.4864	0.2394	-0.0304	0.0087	0.2741	-0.031	0.4678	25.5342	56.2162	-29.9346
19	11.9993	-2.707	-0.7779	4.1994	-4.0804	5.1704	0.8974	0.4802	-0.5171	-0.4514	-0.4554	0.5575	0.2266	0.1571	-0.442	0.3797	0.0532	-0.0902	0.4029	-0.1935	0.4544	16.1437	44.0139	-35.2021
20	1.8417	-2.3823	1.432	3.4456	-1.0134	3.1393	0.2153	0.2329	0.1788	-0.369	-0.2255	-0.2347	0.0064	0.375	0.0102	0.1753	-0.0508	-0.0054	0.1547	0.0278	0.2183	20.4919	42.2518	-29.7276
21	1.0878	0.3049	-0.6735	0.0883	-0.1903	0.4188	0.0081	0.2059	0.0958	-0.0148	0.0379	0.0338	0.0085	-0.1146	-0.046	0.326	0.0181	-0.0174	0.2409	0.0352	0.2981	24.0443	59.2041	-38.2013
22	7.2498	-5.6506	-4.5685	4.7487	4.8221	7.8605	-0.8636	-0.6871	0.4997	0.521	0.4747	-0.1229	-0.3511	0.2293	0.3889	0.5175	-0.0305	0.0756	0.4717	-0.1164	0.4455	37.5844	62.9531	-30.9333

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	188 - 210
2	X-RAY DIFFRACTION	2	A	211 - 225
3	X-RAY DIFFRACTION	3	A	226 - 238
4	X-RAY DIFFRACTION	4	A	239 - 251
5	X-RAY DIFFRACTION	5	A	252 - 266
6	X-RAY DIFFRACTION	6	A	267 - 278
7	X-RAY DIFFRACTION	7	A	279 - 292
8	X-RAY DIFFRACTION	8	A	293 - 302
9	X-RAY DIFFRACTION	9	B	188 - 210
10	X-RAY DIFFRACTION	10	B	211 - 225
11	X-RAY DIFFRACTION	11	B	226 - 238
12	X-RAY DIFFRACTION	12	B	239 - 247
13	X-RAY DIFFRACTION	13	B	248 - 254
14	X-RAY DIFFRACTION	14	B	255 - 266
15	X-RAY DIFFRACTION	15	B	267 - 283
16	X-RAY DIFFRACTION	16	B	284 - 303
17	X-RAY DIFFRACTION	17	C	1 - 4
18	X-RAY DIFFRACTION	18	C	5 - 9
19	X-RAY DIFFRACTION	19	C	10 - 14
20	X-RAY DIFFRACTION	20	D	1 - 6
21	X-RAY DIFFRACTION	21	D	7 - 10
22	X-RAY DIFFRACTION	22	D	11 - 14

-
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

-
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

-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

-
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