PDB-2xoc: C-terminal cysteine-rich domain of human CHFR bound to mADPr

ID or keywords:

Entry

Database: PDB / ID: 2xoc

Title

C-terminal cysteine-rich domain of human CHFR bound to mADPr

Components

E3 UBIQUITIN-PROTEIN LIGASE CHFR

Keywords

LIGASE / ZINC-BINDING / POLY(ADP-RIBOSE) MITOSIS / ANTEPHASE CHECKPOINT / CELL CYCLE

Function / homology

Function and homology information

meiotic spindle checkpoint signaling / mitotic G2/M transition checkpoint / positive regulation of protein ubiquitination / protein destabilization / RING-type E3 ubiquitin transferase / PML body / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.89 Å

Authors

Oberoi, J. / Bayliss, R.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Structural Basis of Poly(Adp-Ribose) Recognition by the Multizinc Binding Domain of Checkpoint with Forkhead-Associated and Ring Domains (Chfr).
Authors: Oberoi, J. / Richards, M.W. / Crumpler, S. / Brown, N. / Blagg, J. / Bayliss, R.

History

Deposition	Aug 11, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 29, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jun 9, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 23, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2xoc.cif.gz	201.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2xoc.ent.gz	160.4 KB	Display	PDB format
PDBx/mmJSON format	2xoc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xo/2xoc ftp://data.pdbj.org/pub/pdb/validation_reports/xo/2xoc	HTTPS FTP

-
Related structure data

Related structure data	2xoyC 2xozC 2xp0C 1lgp 1lgq C: citing same article (ref.)
Similar structure data	2xoz-1 2xoy-2 2xp0-1 2xoz-2 2xoy-1 2xp0-2 3a7u-d 7ll8-d 4az9-1 5f2u-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (2) #163 - Jul 2013 HIV Capsid similarity (2) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: E3 UBIQUITIN-PROTEIN LIGASE CHFR

B: E3 UBIQUITIN-PROTEIN LIGASE CHFR

hetero molecules

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

1

A: E3 UBIQUITIN-PROTEIN LIGASE CHFR

hetero molecules

defined by author&software
30.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: E3 UBIQUITIN-PROTEIN LIGASE CHFR

hetero molecules

defined by software
29.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	161.540, 51.700, 82.360
Angle α, β, γ (deg.)	90.00, 105.76, 90.00
Int Tables number	5
Space group name H-M	C121

-
Protein , 1 types, 2 molecules AB

#1: Protein	E3 UBIQUITIN-PROTEIN LIGASE CHFR / CHECKPOINT WITH FORKHEAD AND RING FINGER DOMAINS PROTEIN / RING FINGER PROTEIN 196 / CHFR Mass: 29268.252 Da / Num. of mol.: 2 / Fragment: CYSTEINE-RICH REGION, RESIDUES 407-663 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CODONPLUS RIL BL21(DE3) References: UniProt: Q96EP1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

#1: Protein

E3 UBIQUITIN-PROTEIN LIGASE CHFR / CHECKPOINT WITH FORKHEAD AND RING FINGER DOMAINS PROTEIN / RING FINGER PROTEIN 196 / CHFR

Mass: 29268.252 Da / Num. of mol.: 2 / Fragment: CYSTEINE-RICH REGION, RESIDUES 407-663
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HOMO SAPIENS (human) / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): CODONPLUS RIL BL21(DE3)
References: UniProt: Q96EP1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

-
Non-polymers , 5 types, 724 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#5: Chemical	ChemComp-ADE / ADENINE Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₅N₅
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has protein modification	Y
Sequence details	N-TERMINAL 'GAM' SEQUENCE FROM VECTOR. SEQUENCE MATCHES UNIPROT ENTRY Q96EP1 WITH THE EXCEPTION OF ...N-TERMINAL 'GAM' SEQUENCE FROM VECTOR. SEQUENCE MATCHES UNIPROT ENTRY Q96EP1 WITH THE EXCEPTION OF THE VECTOR SEQUENCE RESIDUES AND A NATURALLY OCCURRING VARIANT AT .POSITION 497

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 57.05 % / Description: NONE
Crystal grow	Details: 12% PEG 20000, 0.1M MES PH 6.5 0.1M KCL

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.89→49.22 Å / Num. obs: 52431 / % possible obs: 99.5 % / Observed criterion σ(I): 6 / Redundancy: 3.3 % / B_iso Wilson estimate: 18.7 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 8.7
Reflection shell	Resolution: 1.89→1.99 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.89→32.513 Å / SU ML: 0.21 / σ(F): 0.03 / Phase error: 17.9 / Stereochemistry target values: ML
Details: MADPR LIGAND (ID CODE APR) WAS MODELLED AS ADE AND ADP.

	R_factor	Num. reflection	% reflection
R_free	0.1935	4322	8.5 %
R_work	0.168	-	-
obs	0.1702	50629	96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.629 Å² / k_sol: 0.342 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.4562 Å²	0 Å²	0.6611 Å²
2-	-	3.3716 Å²	0 Å²
3-	-	-	-1.9154 Å²

Refinement step

Cycle: LAST / Resolution: 1.89→32.513 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3391	0	67	710	4168

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3585
X-RAY DIFFRACTION	f_angle_d	0.845	4875
X-RAY DIFFRACTION	f_dihedral_angle_d	18.73	1316
X-RAY DIFFRACTION	f_chiral_restr	0.057	511
X-RAY DIFFRACTION	f_plane_restr	0.003	636

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 (%)
1.89-1.9115	0.2617	113	0.2336	1422	X-RAY DIFFRACTION	88
1.9115-1.934	0.2834	142	0.2379	1437	X-RAY DIFFRACTION	91
1.934-1.9576	0.2748	127	0.2247	1480	X-RAY DIFFRACTION	92
1.9576-1.9823	0.228	135	0.2027	1472	X-RAY DIFFRACTION	91
1.9823-2.0084	0.2366	127	0.1962	1468	X-RAY DIFFRACTION	93
2.0084-2.0359	0.2278	137	0.1917	1464	X-RAY DIFFRACTION	92
2.0359-2.065	0.2218	138	0.1935	1503	X-RAY DIFFRACTION	93
2.065-2.0958	0.1973	124	0.1806	1459	X-RAY DIFFRACTION	94
2.0958-2.1286	0.2098	131	0.1761	1558	X-RAY DIFFRACTION	95
2.1286-2.1635	0.2255	138	0.1724	1565	X-RAY DIFFRACTION	95
2.1635-2.2008	0.225	120	0.1623	1507	X-RAY DIFFRACTION	95
2.2008-2.2408	0.1825	156	0.1638	1558	X-RAY DIFFRACTION	96
2.2408-2.2839	0.1876	150	0.1589	1534	X-RAY DIFFRACTION	97
2.2839-2.3305	0.1752	155	0.1643	1519	X-RAY DIFFRACTION	97
2.3305-2.3811	0.1843	144	0.1691	1573	X-RAY DIFFRACTION	97
2.3811-2.4365	0.189	148	0.1678	1560	X-RAY DIFFRACTION	98
2.4365-2.4974	0.1979	174	0.1738	1564	X-RAY DIFFRACTION	98
2.4974-2.5649	0.1785	145	0.1621	1558	X-RAY DIFFRACTION	98
2.5649-2.6403	0.2353	149	0.169	1549	X-RAY DIFFRACTION	98
2.6403-2.7255	0.2071	151	0.1659	1603	X-RAY DIFFRACTION	99
2.7255-2.8229	0.2109	151	0.1752	1603	X-RAY DIFFRACTION	99
2.8229-2.9358	0.2017	150	0.1729	1575	X-RAY DIFFRACTION	98
2.9358-3.0694	0.2086	151	0.1714	1561	X-RAY DIFFRACTION	99
3.0694-3.231	0.2213	156	0.1664	1620	X-RAY DIFFRACTION	99
3.231-3.4333	0.183	150	0.1596	1571	X-RAY DIFFRACTION	98
3.4333-3.698	0.1777	152	0.1402	1591	X-RAY DIFFRACTION	98
3.698-4.0695	0.1525	151	0.1397	1592	X-RAY DIFFRACTION	98
4.0695-4.6569	0.1658	148	0.1348	1571	X-RAY DIFFRACTION	96
4.6569-5.8616	0.1401	154	0.1477	1593	X-RAY DIFFRACTION	97
5.8616-32.5179	0.1566	155	0.1686	1677	X-RAY DIFFRACTION	99

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	0.3675	0.2102	0.0374	0.5162	-0.0658	0.5424	0.288	-0.0689	0.1153	-0.1199	-0.0874	-0.0059	0.1693	-0.1593	-0.027	0.2519	0.0487	0.0885	0.2618	0.013	0.2424	27.3315	24.0486	52.0346
2	0.1916	-0.0446	-0.0874	0.2229	0.1105	0.0774	0.0664	0.2314	-0.0406	0.0624	-0.0752	0.4237	-0.0519	-0.2019	-0.0085	0.1215	0.07	0.0303	0.1673	0.0527	0.2005	33.945	27.4717	38.8058
3	0.1569	0.0967	-0.0655	0.109	0.0844	0.1917	-0.0137	-0.0198	0.0203	0.0142	0.0519	0.0316	-0.0336	0.0519	-0.0258	0.0839	0.038	-0.0005	0.1228	0.0295	0.0868	45.3309	25.3354	36.9558
4	0.372	-0.1048	-0.0735	0.2322	-0.1688	0.2155	-0.0156	-0.1285	-0.0497	0.1023	0.0334	-0.001	0.0421	0.0171	-0.0138	0.0847	-0.0049	-0.014	0.0928	0.0047	0.0624	64.5177	9.8199	28.6262
5	0.884	-0.1308	-0.1118	0.7107	0.2005	0.4374	-0.1171	-0.0208	0.3565	-0.2153	0.2468	-0.1878	-0.09	0.0522	-0.1074	0.1696	-0.032	-0.0081	0.088	-0.0195	0.1456	62.6706	25.3608	23.7317
6	0.198	-0.019	-0.1464	0.0196	0.1018	0.2865	0.0292	0.0602	0.0115	-0.0048	0.0306	0.0007	-0.0871	-0.0514	-0.0234	0.1003	0.0058	-0.0117	0.0861	0.0197	0.0824	53.772	20.9482	24.3189
7	0.1856	0.233	0.0375	0.1544	0.2374	0.2643	0.0457	0.0829	-0.0711	0.0642	0.0777	-0.0426	0.0278	0.0667	-0.0726	0.0666	-0.0114	-0.0326	0.0524	-0.0158	0.0878	64.418	3.7992	16.3787
8	0.1833	-0.0946	-0.0747	0.3146	0.3709	0.4636	0.1819	0.3846	0.0901	0.0347	-0.181	-0.2087	-0.022	-0.025	-0.0052	0.1254	-0.0398	-0.0405	0.1527	0.0104	0.0327	58.6692	8.0401	3.5444
9	0.6001	-0.1022	0.4773	0.2784	0.0881	0.8103	-0.1333	-0.0368	0.1	0.1193	-0.0336	-0.1313	0.2023	-0.3252	0.163	0.1159	-0.0727	0.0204	0.1982	-0.075	0.1005	6.9336	-11.4127	32.2124
10	0.2849	0.1982	-0.121	0.3928	0.0866	0.1917	-0.0661	0.1921	-0.059	-0.0556	0.0085	0.0257	0.1011	-0.1179	0.0479	0.1021	-0.0335	0.0118	0.2506	-0.0291	0.1086	12.0337	-13.5708	17.5198
11	0.1543	-0.0832	-0.1362	0.1082	0.0715	0.2233	0.0043	-0.0877	0.042	0.0357	-0.0245	-0.0179	0.0186	-0.0543	0.0126	0.0428	-0.0209	0.0074	0.0569	-0.0112	0.0385	31.3786	-9.9076	15.846
12	0.3157	-0.0252	0.0746	0.1036	-0.0011	0.1607	-0.0308	0.0217	0.0224	-0.0295	0.027	-0.0212	-0.0493	-0.0082	-0.0017	0.0465	-0.0173	0.0128	0.0195	0.0043	0.029	40.6222	-7.6884	4.3177
13	0.0689	-0.0488	-0.0064	0.1015	0.0468	0.0523	0.1106	0.024	-0.1555	0.0052	0.0093	-0.3249	0.0022	0.0542	-0.0926	0.1452	-0.0061	-0.0193	0.0449	-0.0095	0.1922	56.9665	-19.3012	7.6153
14	0.1035	-0.0482	-0.0176	0.0619	0.0163	0.0021	0.1084	0.0003	-0.2533	-0.0935	-0.0014	-0.185	0.2005	0.1713	-0.1071	0.1558	0.0205	-0.0319	0.0636	-0.0512	0.1666	53.6482	-24.1407	0.278

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 425:477)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 478:500)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 501:543)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 544:571)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 572:588)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 589:617)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 618:657)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 658:663)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 425:476)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 477:507)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 508:557)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 558:630)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 631:655)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 656:663)

-
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, 2 molecules AB

-
Non-polymers , 5 types, 724 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, 2 molecules AB

-Non-polymers , 5 types, 724 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, 2 molecules AB

-
Non-polymers , 5 types, 724 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