PDB-3rv5: Crystal structure of human cardiac troponin C regulatory domain i...

ID or keywords:

Entry

Database: PDB / ID: 3rv5

Title

Crystal structure of human cardiac troponin C regulatory domain in complex with cadmium and deoxycholic acid

Components

Troponin C, slow skeletal and cardiac muscles

Keywords

CONTRACTILE PROTEIN / helix-loop-helix EF-hand motif / Metal ion coordination / calcium sensor

Function / homology

Function and homology information

diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed /

troponin T binding / cardiac Troponin complex /

troponin complex /

regulation of muscle contraction / transition between fast and slow fiber / Striated Muscle Contraction / response to metal ion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Li, A.Y. / Lee, J. / Borek, D. / Otwinowski, Z. / Tibbits, G. / Paetzel, M.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Crystal structure of cardiac troponin C regulatory domain in complex with cadmium and deoxycholic Acid reveals novel conformation.
Authors: Li, A.Y. / Lee, J. / Borek, D. / Otwinowski, Z. / Tibbits, G.F. / Paetzel, M.

History

Deposition	May 6, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 31, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 26, 2011	Group: Database references
Revision 1.2	Nov 16, 2011	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3rv5.cif.gz	147.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3rv5.ent.gz	128 KB	Display	PDB format
PDBx/mmJSON format	3rv5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rv/3rv5 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/3rv5	HTTPS FTP

-
Related structure data

Related structure data	1ap4 1j1d 1lxf 1mxl 1spy 1wrk
Similar structure data	3soj-2 1z5f-d 4oeb-2 6myk-1 1e21-d 3m1b-6 6myk-4 2eg1-d 6nez-1 3vux-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#185 - May 2015 Titin similarity (1) #18 - Jun 2001 Myosin similarity (1) #44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: Troponin C, slow skeletal and cardiac muscles

B: Troponin C, slow skeletal and cardiac muscles

C: Troponin C, slow skeletal and cardiac muscles

D: Troponin C, slow skeletal and cardiac muscles

hetero molecules

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

1

A: Troponin C, slow skeletal and cardiac muscles

hetero molecules

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

2

B: Troponin C, slow skeletal and cardiac muscles

hetero molecules

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

3

C: Troponin C, slow skeletal and cardiac muscles

hetero molecules

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

4

D: Troponin C, slow skeletal and cardiac muscles

hetero molecules

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

5

A: Troponin C, slow skeletal and cardiac muscles

B: Troponin C, slow skeletal and cardiac muscles

hetero molecules

A: Troponin C, slow skeletal and cardiac muscles

B: Troponin C, slow skeletal and cardiac muscles

hetero molecules

C: Troponin C, slow skeletal and cardiac muscles

D: Troponin C, slow skeletal and cardiac muscles

hetero molecules

C: Troponin C, slow skeletal and cardiac muscles

D: Troponin C, slow skeletal and cardiac muscles

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.844, 81.783, 100.469
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Troponin C, slow skeletal and cardiac muscles / / TN-C Mass: 10398.569 Da / Num. of mol.: 4 / Fragment: N-terminal domain (N-cTnC), UNP residues 1-89 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC, TNNC1, TNNC1 (Amino acids 1-89) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63316
#2: Chemical	... ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cd
#3: Chemical	ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID / Deoxycholic acid Mass: 392.572 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂₄H₄₀O₄ / Comment: detergent*YM
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.56 Å³/Da / Density % sol: 51.96 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM Tris-HCl (pH 8), 50 mM cadmium sulfate, 900 mM sodium acetate (reservoir) and 50 mM deoxycholic acid (additive), VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98066 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 30, 2008 / Details: vertical collimating mirror
Radiation	Monochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98066 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 22061 / Num. obs: 21706 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / R_merge(I) obs: 0.067 / Net I/σ(I): 28.4
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.176 / Mean I/σ(I) obs: 5.7 / % possible all: 99.1

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
SHELXS		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.2→33.01 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.879 / SU B: 7.948 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28148	1128	5.1 %	RANDOM
R_work	0.22541	-	-	-
obs	0.22826	20909	98.47 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 41.299 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.69 Å²	0 Å²	0 Å²
2-	-	1.52 Å²	0 Å²
3-	-	-	-0.84 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→33.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2518	0	164	133	2815

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.032	0.023	2815
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.887	2.05	3661
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.976	5	318
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.992	27.273	132
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.301	15	488
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.612	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	430
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1934
X-RAY DIFFRACTION	r_gen_planes_other
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	1.338	1.5	1638
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.509	2	2554
X-RAY DIFFRACTION	r_scbond_it	4.03	3	1173
X-RAY DIFFRACTION	r_scangle_it	4.325	4.5	1107
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.265	84	-
R_work	0.236	1541	-
obs	-	-	98.84 %

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	2.0341	0.3324	-0.1029	1.6549	0.3967	3.3316	0.0115	0.4064	0.1484	-0.4134	-0.0036	0.2872	-0.0986	-0.1668	-0.008	0.2294	-0.0029	0.0099	0.2204	-0.006	0.2493	38.1437	13.2906	-16.7578
2	3.7571	-1.3302	0.486	3.2705	0.2382	3.3306	-0.0916	0.1619	-0.4296	-0.1505	0.0238	-0.0945	0.265	0.0545	0.0677	0.1499	-0.0011	-0.0047	0.1291	-0.0014	0.1304	32.4587	12.6204	-5.8927
3	3.6671	0.8747	-0.2187	0.4912	0.1645	0.224	-0.005	-0.037	-0.1104	0.0196	-0.019	-0.0497	0.0625	0.0242	0.024	0.1043	0.0035	-0.0018	0.0949	0.0023	0.0837	23.3977	20.441	-1.5538
4	7.1442	-1.9721	0.919	0.6144	-0.2048	0.1582	0.06	0.3946	0.2741	-0.143	-0.0931	-0.0642	-0.0855	0.0719	0.033	0.2375	-0.0107	-0.0001	0.1829	0.0007	0.1765	23.6065	31.1948	-7.3507
5	1.4758	0.5345	0.5802	2.6514	1.4951	3.2255	0.0456	0.0211	0.2948	-0.138	-0.0259	-0.0213	-0.3822	-0.0492	-0.0196	0.1156	-0.0006	0.0014	0.1231	0.009	0.1233	10.8696	24.7572	-7.3017
6	11.1501	3.6866	-0.8972	4.8615	-5.3387	9.2685	-0.0871	0.5307	-0.101	-0.5952	-0.105	-0.7424	0.2605	0.5725	0.1921	0.3895	-0.0215	0.1796	0.2557	-0.0314	0.4993	16.46	23.6766	-17.4914
7	2.1332	0.774	-1.7699	1.5728	0.5664	3.3923	0.0179	0.0525	0.0455	-0.1079	0.07	-0.3738	0.1156	0.3153	-0.0879	0.3098	0.0108	0.0295	0.2919	0.0471	0.3301	11.9422	19.879	-32.6952
8	1.0288	-0.1056	0.759	1.9603	0.4323	1.8174	-0.0054	0.175	-0.0422	-0.2069	-0.0067	-0.0834	0.0741	0.0588	0.0122	0.1111	0.0015	0.0047	0.1324	-0.0006	0.1358	3.9297	13.6954	-15.8513
9	0.2098	1.0053	-1.1999	8.7481	-10.0051	11.6937	0.0428	0.1011	0.0976	-0.0423	-0.039	-0.1144	-0.1703	0.1227	-0.0038	0.2682	0.0049	0.0283	0.2566	-0.0023	0.2704	4.3356	1.701	-21.3899
10	3.8534	1.6672	3.8056	2.1319	2.2794	4.1828	0.0463	0.0854	-0.1708	0.0059	0.0139	-0.1043	0.1467	0.1022	-0.0603	0.1851	0.0026	0.0099	0.1801	0.0066	0.1847	9.6069	0.0544	-11.6031
11	0.8893	1.1658	-0.9456	6.8597	-2.8472	3.3231	0.0021	-0.2268	-0.3632	0.2233	-0.0907	-0.2978	0.398	0.1476	0.0886	0.1428	-0.0159	-0.0401	0.1666	0.0434	0.2257	10.5572	7.4583	-2.7898
12	5.4176	-2.8669	1.6768	5.334	1.2648	2.3582	0.1057	0.5174	-0.138	-0.4333	-0.0073	-0.4713	0.1764	0.4455	-0.0984	0.285	0.0331	0.1482	0.1126	0.0302	0.2329	16.7273	10.4754	-8.4178
13	4.8341	-0.9204	-1.1188	0.5003	0.0202	2.147	-0.0025	0.0232	0.0784	0.0359	0.019	0.254	0.0381	-0.3006	-0.0165	0.2074	0.0023	0.0043	0.1683	-0.0012	0.243	-12.0093	20.4839	-16.5263
14	2.0187	-0.008	0.8318	2.0602	1.9552	9.1553	0.0013	-0.1172	0.1239	0.0927	0.0023	0.0532	-0.1877	-0.0288	-0.0036	0.1598	0.0015	-0.0003	0.1553	0.0095	0.1952	-6.001	18.5386	-34.8117
15	1.9599	-0.401	1.6658	1.62	0.5347	6.0381	-0.0092	-0.3199	-0.0871	0.2941	0.0116	-0.0761	0.1093	0.078	-0.0024	0.2186	-0.0061	0.0056	0.2176	0.0019	0.2441	-3.9019	9.4839	-31.1489
16	0.3438	-0.2485	0.9993	0.2269	-0.6839	2.9376	0.0224	-0.1048	-0.0626	-0.0387	0.0638	0.164	0.0356	-0.3406	-0.0862	0.3069	-0.0002	-0.001	0.3019	-0.0035	0.3233	-10.7547	1.6027	-38.3804
17	3.0815	-0.0317	1.3782	1.9721	-1.0343	2.6978	-0.0301	0.139	-0.3973	-0.0174	-0.0526	0.1114	0.2879	0.0368	0.0826	0.1888	-0.0118	0.001	0.1845	0.0028	0.1846	-14.1356	10.3035	-44.3062
18	11.5459	2.6787	-0.6316	4.0671	-4.6306	6.9528	0.0615	-0.5234	0.0593	0.5055	0.0426	0.4016	-0.107	-0.4299	-0.1041	0.4718	-0.0435	0.1029	0.3403	-0.0343	0.4131	-20.9651	9.1824	-35.8811
19	0.9811	0.3195	-1.5224	0.857	-0.6594	3.9503	-0.0183	-0.3421	-0.1341	0.3766	-0.007	0.0102	0.1817	0.0956	0.0253	0.231	-0.0002	-0.0045	0.2721	0.0258	0.232	-38.1639	12.6177	-36.982
20	4.9505	2.5291	-3.9865	1.5885	-2.3827	3.6536	-0.0656	0.1105	-0.0935	-0.075	0.0278	0.0441	0.0936	-0.0667	0.0378	0.1581	0.0064	-0.0077	0.151	-0.0037	0.1592	-22.9686	15.0556	-48.403
21	5.267	-0.108	-0.1375	0.5348	-0.5338	0.7815	0.0296	-0.0071	0.1515	0.0908	0.0335	0.1909	-0.1351	-0.2182	-0.0631	0.2126	-0.0005	-0.0055	0.2123	-0.0305	0.2164	-28.214	23.8753	-47.8129
22	0.6637	-0.0666	0.1153	0.0799	-0.0391	0.0723	-0.0487	-0.3343	0.2067	0.1322	0.0243	0.0392	-0.101	-0.0968	0.0244	0.3019	0.0048	0.0068	0.2913	-0.0074	0.285	-21.0317	32.8202	-44.0039
23	2.926	-1.9878	0.9236	2.5089	-2.9644	5.2494	0.0268	-0.0573	0.3652	0.1894	-0.1032	-0.2969	-0.4547	0.388	0.0764	0.161	-0.0014	0.0075	0.1687	-0.0186	0.1671	-11.483	25.378	-45.7351
24	2.6085	0.2502	0.4763	5.2074	6.0366	7.9707	-0.0456	-0.603	0.4005	0.3388	-0.1636	0.4256	-0.1382	-0.5383	0.2092	0.3987	0.1019	0.1051	0.2835	0.064	0.2851	-15.6725	22.9815	-37.1273

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 15
2	X-RAY DIFFRACTION	2	A	16 - 25
3	X-RAY DIFFRACTION	3	A	26 - 48
4	X-RAY DIFFRACTION	4	A	49 - 63
5	X-RAY DIFFRACTION	5	A	64 - 80
6	X-RAY DIFFRACTION	6	A	81 - 85
7	X-RAY DIFFRACTION	7	B	5 - 19
8	X-RAY DIFFRACTION	8	B	20 - 48
9	X-RAY DIFFRACTION	9	B	49 - 54
10	X-RAY DIFFRACTION	10	B	55 - 64
11	X-RAY DIFFRACTION	11	B	65 - 74
12	X-RAY DIFFRACTION	12	B	75 - 82
13	X-RAY DIFFRACTION	13	C	3 - 19
14	X-RAY DIFFRACTION	14	C	20 - 35
15	X-RAY DIFFRACTION	15	C	36 - 51
16	X-RAY DIFFRACTION	16	C	52 - 67
17	X-RAY DIFFRACTION	17	C	68 - 79
18	X-RAY DIFFRACTION	18	C	80 - 85
19	X-RAY DIFFRACTION	19	D	5 - 23
20	X-RAY DIFFRACTION	20	D	24 - 33
21	X-RAY DIFFRACTION	21	D	34 - 51
22	X-RAY DIFFRACTION	22	D	52 - 65
23	X-RAY DIFFRACTION	23	D	66 - 76
24	X-RAY DIFFRACTION	24	D	77 - 82

-
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