PDB-4fd2: Crystal structure of the C-terminal domain of ClpB

ID or keywords:

Entry

Database: PDB / ID: 4fd2

Title

Crystal structure of the C-terminal domain of ClpB

Components

Chaperone protein ClpB

Keywords

CHAPERONE / AAA domain

Function / homology

Function and homology information

response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Biter, A.B. / Lee, S. / Sung, N. / Tsai, F.T.F.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for intersubunit signaling in a protein disaggregating machine.
Authors: Biter, A.B. / Lee, S. / Sung, N. / Tsai, F.T.

History

Deposition	May 25, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 18, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 22, 2012	Group: Database references
Revision 1.2	Apr 18, 2018	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	4fd2.cif.gz	384.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4fd2.ent.gz	321.4 KB	Display	PDB format
PDBx/mmJSON format	4fd2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4fd2_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	4fd2_full_validation.pdf.gz	1.3 MB	Display
Data in XML	4fd2_validation.xml.gz	38.3 KB	Display
Data in CIF	4fd2_validation.cif.gz	50.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fd/4fd2 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/4fd2	HTTPS FTP

-
Related structure data

Related structure data	4fctC 4fcvC 4fcwC C: citing same article (ref.)
Similar structure data	4fcv-1 4fcw-3 3tfl-d 4fct-d 4fcv-3 6xu4-2 6oa3-d 6nk2-d 4p6e-3 3t1f-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) 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

4fctC

4fcvC

4fcwC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (4) #176 - Aug 2014 Dynein similarity (4) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

A: Chaperone protein ClpB

B: Chaperone protein ClpB

D: Chaperone protein ClpB

hetero molecules

106 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chaperone protein ClpB

hetero molecules

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

2

B: Chaperone protein ClpB

hetero molecules

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

3

D: Chaperone protein ClpB

hetero molecules

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

Unit cell

Length a, b, c (Å)	129.775, 129.775, 129.401
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	D
1	2	A
2	2	B
3	2	D
1	3	A
2	3	B
3	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	545 - 756
2	1	1	4	B	545 - 756
3	1	1	4	D	545 - 756
1	1	2	4	A	757 - 852
2	1	2	4	B	757 - 852
3	1	2	4	D	757 - 852
1	1	3	4	A	853
2	1	3	4	B	853
3	1	3	4	D	853

NCS ensembles :

ID
1
2
3

#1: Protein	Chaperone protein ClpB Mass: 34931.223 Da / Num. of mol.: 3 / Fragment: UNP residues 545-852 / Mutation: E668A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: clpB, TTHA1487 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL CodonPlus / References: UniProt: Q9RA63
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM

#1: Protein

Chaperone protein ClpB

Mass: 34931.223 Da / Num. of mol.: 3 / Fragment: UNP residues 545-852 / Mutation: E668A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: clpB, TTHA1487 / Plasmid: pET24 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL CodonPlus / References: UniProt: Q9RA63

#2: Chemical

ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE

Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 58.99 %
Crystal grow	Temperature: 294 K / Method: hanging drop / pH: 5 Details: citric acid, isopropanol, pH 5.0, hanging drop, temperature 294K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9786 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9786 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.497
1	1	h+k,-k,-l	2	0.503

Reflection

Resolution: 3→50 Å / Num. obs: 24567

-
Processing

Software

Name	Version	Classification	NB
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→42.48 Å / Cor.coef. F_o:F_c: 0.901 / Cor.coef. F_o:F_c free: 0.882 / Occupancy max: 1 / Occupancy min: 1 / SU B: 72.784 / SU ML: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE

	R_factor	Num. reflection	% reflection
R_free	0.298	1001	4.1 %
R_work	0.278	-	-
obs	0.279	24567	98.8 %

Solvent computation

Solvent model: MASK

Displacement parameters

B_iso mean: 109.45 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-25.04 Å²	0 Å²	0 Å²
2-	-	-25.04 Å²	0 Å²
3-	-	-	50.07 Å²

Refinement step

Cycle: LAST / Resolution: 3→42.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7386	0	81	0	7467

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	7599
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.515	2.001	10284
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.745	5	921
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.023	22.623	366
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.35	15	1368
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.958	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	1161
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5718
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	1.707	1.5	4599
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.225	2	7431
X-RAY DIFFRACTION	r_scbond_it	3.985	3	3000
X-RAY DIFFRACTION	r_scangle_it	7.443	4.5	2853
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1702	medium positional	0.15	0.5
1	2	B	1702	medium positional	0.18	0.5
1	3	D	1702	medium positional	0.14	0.5
2	1	A	760	medium positional	0.12	0.5
2	2	B	760	medium positional	0.2	0.5
2	3	D	760	medium positional	0.15	0.5
3	1	A	27	medium positional	0.32	0.5
3	2	B	27	medium positional	0.4	0.5
3	3	D	27	medium positional	0.53	0.5
1	1	A	1702	medium thermal	1.5	2
1	2	B	1702	medium thermal	1.02	2
1	3	D	1702	medium thermal	0.84	2
2	1	A	760	medium thermal	1.4	2
2	2	B	760	medium thermal	1.24	2
2	3	D	760	medium thermal	0.59	2
3	1	A	27	medium thermal	0.2	2
3	2	B	27	medium thermal	0.29	2
3	3	D	27	medium thermal	0.21	2

LS refinement shell

Resolution: 3→3.08 Å

	R_factor	Num. reflection	% reflection
R_free	0.325	81	-
R_work	0.355	1696	-
obs	-	-	97.53 %

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	14.7635	13.4796	-1.9313	23.4111	-5.2274	1.0309	0.3374	0.9198	-0.7641	0.4823	-0.4809	-0.7095	0.0301	0.3771	0.1435	0.4111	0.2569	0.0374	0.5226	0.0271	0.0436	-48.4804	-2.8295	41.3899
2	3.0239	0.8251	1.1028	2.4797	0.1019	1.8345	0.08	0.1287	0.2115	-0.3104	-0.1758	0.2051	-0.249	0.0796	0.0958	0.4081	-0.0155	0.0541	0.5499	0.0579	0.1808	-55.9172	7.3322	37.4749
3	7.9238	-5.3171	-6.6102	42.8971	-8.8245	6.2052	-0.7124	-0.3763	2.073	-4.367	3.3573	3.6502	1.4961	-0.6493	-2.6449	1.9179	-0.3563	-0.6659	0.8976	0.2566	0.9235	-67.6004	25.4094	30.4338
4	2.9666	-24.3745	7.0618	68.8646	-28.0721	15.8944	-2.4043	1.3486	-1.2115	6.9868	-1.3222	1.5535	-2.3902	-0.4457	3.7266	1.1008	0.4155	0.5029	1.8312	-0.148	3.9076	-68.6007	23.9254	20.9087
5	6.2041	1.0279	2.4081	1.525	-1.2415	2.6271	-0.1112	-0.0205	0.8032	0.0905	0.0163	0.3068	-0.2569	-0.0804	0.0949	0.448	0.1035	0.0555	0.5466	0.0464	0.2361	-64.4884	13.178	34.3742
6	30.2297	-7.3139	17.031	10.4819	-3.8443	18.4936	0.2387	-3.6177	-0.6391	0.4823	-0.5998	0.7311	0.6535	-1.034	0.3612	0.333	-0.212	0.199	0.8502	0.0141	0.1044	-54.8987	13.2649	57.0878
7	7.561	1.2435	-3.6866	0.501	-0.5006	2.7282	0.0194	-0.1726	-0.2898	0.1142	-0.1016	-0.117	-0.0416	0.1837	0.0822	0.4356	0.0105	-0.0335	0.4198	0.0996	0.3181	-29.2677	12.1431	36.1919
8	11.332	8.5892	4.7576	15.0753	3.2632	1.6619	-0.0088	-0.0573	0.0806	0.7422	-0.0708	0.6735	-0.0176	-0.2114	0.0795	0.5113	0.1613	0.0887	0.6207	-0.1602	0.0875	-43.1383	-5.8435	-37.0306
9	0.1931	-0.0816	-0.8021	3.567	-0.9947	2.0445	-0.04	-0.0788	-0.0359	0.341	-0.0101	-0.4432	-0.1297	0.1865	0.0502	0.672	0.0094	0.0165	0.6624	-0.0503	0.5161	-30.833	-7.4677	-32.8015
10	4.7765	-5.7543	-4.2821	4.4634	7.3159	55.0495	-1.3872	-0.6548	-0.5646	1.1984	0.5658	0.1907	-1.7815	4.1225	0.8215	0.7174	-0.0848	0.07	1.3684	0.2957	1.7801	-10.1777	-9.8297	-20.5239
11	5.687	0.5316	0.9633	5.7287	-0.9292	0.724	-0.0788	-0.0569	-0.1773	0.1166	0.1417	-0.9823	0.0773	0.4161	-0.0629	0.5857	0.0732	-0.058	0.6937	-0.0916	0.4747	-21.672	-12.9355	-28.622
12	23.7923	-13.5413	9.9332	18.3518	-8.7219	6.5858	0.2899	2.4456	-0.0217	-1.2721	-0.7307	-0.4307	0.5596	0.2194	0.4408	0.6739	0.1368	0.3036	0.9724	-0.1157	0.1443	-24.9725	-2.3437	-51.5397
13	2.452	-0.4524	-0.4694	2.3262	0.8996	2.9853	-0.2202	0.1802	0.0473	-0.2206	-0.1664	0.4996	-0.331	-0.0834	0.3867	0.5972	0.0029	-0.0762	0.6954	-0.0143	0.4558	-37.2648	6.5815	-35.0756
14	3.4658	-2.5609	-0.9892	4.8516	0.6795	4.5955	-0.1375	0.1113	0.379	-0.0315	0.4001	0.2617	0.2049	-0.1254	-0.2626	0.6545	-0.0962	-0.0409	0.5413	-0.0573	0.6137	-41.3794	24.5318	-29.075
15	34.9651	-2.5568	3.162	5.9388	2.3117	1.0181	0.778	-0.0304	0.9447	-0.8053	-0.8724	-0.1529	-0.3175	-0.2949	0.0944	0.4548	-0.1228	-0.0358	0.2982	0.0481	0.0206	-38.2017	-3.1318	-1.7965
16	2.8824	-0.0001	-0.8024	2.5213	0.6547	1.9315	-0.0028	0.1611	-0.5465	-0.3085	-0.0385	0.1445	0.2366	-0.2975	0.0412	0.4281	0.0228	-0.0539	0.4388	-0.0065	0.1783	-43.2464	-14.6548	-5.7228
17	1.005	-2.7216	1.6544	4.1442	-1.8016	-0.0364	0.4174	0.5634	-0.4214	-0.9557	-0.428	0.3093	0.3572	0.216	0.0106	1.3189	-0.2578	0.065	1.1511	-0.2015	1.3305	-52.1687	-33.919	-17.2652
18	3.0627	-3.1135	-0.6817	5.2135	3.1972	3.1695	0.2615	0.0994	-0.9589	-0.1153	-0.2911	0.7866	0.3484	-0.3977	0.0295	0.5731	-0.0607	-0.0939	0.4221	-0.0204	0.2991	-43.3478	-25.4147	-9.7066
19	10.3035	-2.2356	4.988	25.3438	17.3934	17.7046	-1.8868	-1.8958	-0.2814	1.0951	2.1743	-1.4618	-0.5134	0.7941	-0.2875	0.4295	0.264	-0.1042	0.6998	0.2408	0.595	-49.4831	-16.7788	13.2936
20	9.4105	-6.3314	4.4395	12.4714	-1.9665	4.751	-0.3254	-1.1149	-0.1253	0.2734	0.3133	0.2993	0.041	-0.2731	0.0121	0.3922	-0.1223	0.1308	0.4858	0.0355	0.1003	-48.1383	-9.8032	4.9597
21	3.1978	-2.5766	1.2123	3.5899	-2.5563	4.8366	0.0174	0.0076	0.2812	-0.1147	-0.151	-0.3097	-0.2328	-0.1105	0.1336	0.4211	-0.0237	-0.0309	0.4866	-0.0719	0.3816	-63.9043	9.9587	-9.989

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	545 - 573
2	X-RAY DIFFRACTION	2	A	574 - 628
3	X-RAY DIFFRACTION	3	A	629 - 640
4	X-RAY DIFFRACTION	4	A	641 - 651
5	X-RAY DIFFRACTION	5	A	652 - 712
6	X-RAY DIFFRACTION	6	A	713 - 743
7	X-RAY DIFFRACTION	7	A	744 - 852
8	X-RAY DIFFRACTION	8	B	545 - 573
9	X-RAY DIFFRACTION	9	B	574 - 628
10	X-RAY DIFFRACTION	10	B	629 - 651
11	X-RAY DIFFRACTION	11	B	652 - 708
12	X-RAY DIFFRACTION	12	B	709 - 743
13	X-RAY DIFFRACTION	13	B	744 - 780
14	X-RAY DIFFRACTION	14	B	781 - 852
15	X-RAY DIFFRACTION	15	D	545 - 573
16	X-RAY DIFFRACTION	16	D	574 - 628
17	X-RAY DIFFRACTION	17	D	629 - 651
18	X-RAY DIFFRACTION	18	D	652 - 708
19	X-RAY DIFFRACTION	19	D	709 - 743
20	X-RAY DIFFRACTION	20	D	744 - 763
21	X-RAY DIFFRACTION	21	D	764 - 852

-
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