PDB-3v3c: Crystal Structure of Chloroplast ATP synthase c-ring from Pisum s...

ID or keywords:

Entry

Database: PDB / ID: 3v3c

Title

Crystal Structure of Chloroplast ATP synthase c-ring from Pisum sativum

Components

ATP synthase subunit c, chloroplastic

Keywords

PHOTOSYNTHESIS / c-ring / Proton translocation / proton binding

Function / homology

Function and homology information

chloroplast thylakoid membrane / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / lipid binding
Similarity search - Function

Biological species

Pisum sativum (garden pea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.402 Å

Authors

Saroussi, S. / Nelson, N.

Citation

Journal: Plos One / Year: 2012
Title: Structure and flexibility of the C-ring in the electromotor of rotary F(o)F(1)-ATPase of pea chloroplasts.
Authors: Saroussi, S. / Schushan, M. / Ben-Tal, N. / Junge, W. / Nelson, N.

History

Deposition	Dec 13, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 3, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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 / _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	3v3c.cif.gz	385.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3v3c.ent.gz	322.2 KB	Display	PDB format
PDBx/mmJSON format	3v3c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3v3c_validation.pdf.gz	701.5 KB	Display	wwPDB validaton report
Full document	3v3c_full_validation.pdf.gz	724.7 KB	Display
Data in XML	3v3c_validation.xml.gz	36.4 KB	Display
Data in CIF	3v3c_validation.cif.gz	52.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v3/3v3c ftp://data.pdbj.org/pub/pdb/validation_reports/v3/3v3c	HTTPS FTP

-
Related structure data

Similar structure data	2w5j-d 6tqj-d 2wie-1 2xqs-1 4fp7-d 2vqz-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	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #219 - Mar 2018 Vacuolar ATPase similarity (7) #145 - Jan 2012 Messenger RNA Capping similarity (1) #86 - Feb 2007 Exosomes similarity (1) #72 - Dec 2005 ATP Synthase similarity (8) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: ATP synthase subunit c, chloroplastic

B: ATP synthase subunit c, chloroplastic

C: ATP synthase subunit c, chloroplastic

D: ATP synthase subunit c, chloroplastic

E: ATP synthase subunit c, chloroplastic

F: ATP synthase subunit c, chloroplastic

G: ATP synthase subunit c, chloroplastic

H: ATP synthase subunit c, chloroplastic

I: ATP synthase subunit c, chloroplastic

J: ATP synthase subunit c, chloroplastic

K: ATP synthase subunit c, chloroplastic

L: ATP synthase subunit c, chloroplastic

M: ATP synthase subunit c, chloroplastic

N: ATP synthase subunit c, chloroplastic

hetero molecules

111 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	139.130, 102.380, 122.430
Angle α, β, γ (deg.)	90.000, 101.220, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	E-105- YT3
2	1	L-110- YT3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	N
2	1	A
3	1	B
4	1	C
5	1	D
6	1	E
7	1	F
8	1	G
9	1	H
10	1	I
11	1	J
12	1	K
13	1	L
14	1	M

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO

Dom-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	VAL	VAL	chain 'N' and (resseq 3:81 )	N	N	3 - 81	1 - 79
2	VAL	VAL	chain 'A' and (resseq 3:81 )	A	A	3 - 81	1 - 79
3	VAL	VAL	chain 'B' and (resseq 3:81 )	B	B	3 - 81	1 - 79
4	VAL	VAL	chain 'C' and (resseq 3:81 )	C	C	3 - 81	1 - 79
5	VAL	VAL	chain 'D' and (resseq 3:81 )	D	D	3 - 81	1 - 79
6	VAL	VAL	chain 'E' and (resseq 3:81 )	E	E	3 - 81	1 - 79
7	PRO	PRO	chain 'F' and (resseq 3:79 )	F	F	3 - 79	1 - 77
8	VAL	VAL	chain 'G' and (resseq 3:81 )	G	G	3 - 81	1 - 79
9	VAL	VAL	chain 'H' and (resseq 3:81 )	H	H	3 - 81	1 - 79
10	VAL	VAL	chain 'I' and (resseq 3:81 )	I	I	3 - 81	1 - 79
11	VAL	VAL	chain 'J' and (resseq 3:81 )	J	J	3 - 81	1 - 79
12	VAL	VAL	chain 'K' and (resseq 3:81 )	K	K	3 - 81	1 - 79
13	VAL	VAL	chain 'L' and (resseq 3:81 )	L	L	3 - 81	1 - 79
14	VAL	VAL	chain 'M' and (resseq 3:81 )	M	M	3 - 81	1 - 79

#1: Protein	ATP synthase subunit c, chloroplastic / ATP synthase F(0) sector subunit c / ATPase subunit III / F-type ATPase subunit c / F-ATPase ...ATP synthase F(0) sector subunit c / ATPase subunit III / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein Mass: 7790.104 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Details: chloroplast / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P08212
#2: Sugar	ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG) Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅₁H₉₆O₁₅
#3: Chemical	ChemComp-YT3 / YTTRIUM (III) ION Mass: 88.906 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Y
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.92 Å³/Da / Density % sol: 68.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 100mM Na-acetate (pH 4.5), 50mM MgCl2, 50mM NaCl, 10mM Yttrium chloride and 14-24% PEG 550 Mono, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2011

Radiation

Monochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.4→29.32 Å / Num. obs: 23125 / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / B_iso Wilson estimate: 48 Å² / R_merge(I) obs: 0.167 / Net I/σ(I): 6.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Diffraction-ID	% possible all
3.4-3.58	4.3	0.033	27.1	718	1	23.4
3.4-3.58	4.5	1.921	1	3379	1	22.1

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
SCALA		data scaling
PHASER		phasing
PHENIX	1.7.2_869	refinement
PDB_EXTRACT	3.1	data extraction
XDS		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.402→28.889 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 1.42 / σ(F): 1.34 / Phase error: 35.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3215	1044	5.18 %
R_work	0.2995	-	-
obs	0.3006	20148	86.59 %

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 0.001 Å² / k_sol: 0.207 e/Å³

Displacement parameters

B_iso max: 563.6 Å² / B_iso mean: 92.7648 Å² / B_iso min: 7.04 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-19.5646 Å²	-0 Å²	5.3136 Å²
2-	-	-32.4647 Å²	0 Å²
3-	-	-	-16.4348 Å²

Refinement step

Cycle: LAST / Resolution: 3.402→28.889 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7492	0	86	0	7578

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7661
X-RAY DIFFRACTION	f_angle_d	1.03	10457
X-RAY DIFFRACTION	f_chiral_restr	0.133	1367
X-RAY DIFFRACTION	f_plane_restr	0.005	1311
X-RAY DIFFRACTION	f_dihedral_angle_d	16.268	2574

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	N	532	X-RAY DIFFRACTION	POSITIONAL	0.165
1	2	A	532	X-RAY DIFFRACTION	POSITIONAL	0.165
1	3	B	527	X-RAY DIFFRACTION	POSITIONAL	0.174
1	4	C	520	X-RAY DIFFRACTION	POSITIONAL	0.058
1	5	D	533	X-RAY DIFFRACTION	POSITIONAL	0.093
1	6	E	533	X-RAY DIFFRACTION	POSITIONAL	0.084
1	7	F	512	X-RAY DIFFRACTION	POSITIONAL	0.041
1	8	G	533	X-RAY DIFFRACTION	POSITIONAL	0.04
1	9	H	530	X-RAY DIFFRACTION	POSITIONAL	0.04
1	10	I	530	X-RAY DIFFRACTION	POSITIONAL	0.04
1	11	J	536	X-RAY DIFFRACTION	POSITIONAL	0.04
1	12	K	532	X-RAY DIFFRACTION	POSITIONAL	0.053
1	13	L	536	X-RAY DIFFRACTION	POSITIONAL	0.04
1	14	M	536	X-RAY DIFFRACTION	POSITIONAL	0.048

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.4021-3.5812	0.3544	47	0.4189	689	736	22
3.5812-3.8051	0.3651	162	0.3504	2800	2962	90
3.8051-4.0981	0.3157	166	0.2927	3142	3308	99
4.0981-4.5091	0.2774	174	0.2607	3102	3276	99
4.5091-5.1584	0.3007	160	0.2389	3135	3295	99
5.1584-6.4869	0.2971	185	0.294	3113	3298	99
6.4869-28.89	0.3709	150	0.3423	3123	3273	96

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	0.1016	0.0503	-0.1153	-0.0009	-0.0332	0.0891	0.0431	-0.0942	-0.0062	-0.0262	0.0178	0.0046	-0.013	0.078	0.2199	-0.2319	-0.4106	0.3369	0.5916	0.3848	-0.2004	-15.6719	-17.4777	22.4089
2	0.2106	-0.1284	0.2847	0.4413	-0.1938	0.416	0.1099	0.1191	0.0906	0.0029	0.2244	-0.0079	-0.1892	-0.0457	0.3958	1.141	-0.0412	-0.3607	0.9715	0.0903	0.1646	-7.3509	-19.4601	19.2902
3	0.1085	-0.0014	-0.0881	0.0029	0.0116	0.1093	0.0163	-0.207	0.0014	0.0966	-0.0123	-0.0721	-0.0224	0.0979	0.0415	-0.2688	0.1749	0.3857	0.6107	0.0028	-0.1283	-15.962	-25.2066	21.7123
4	0.1702	-0.034	0.1395	0.1896	0.0588	0.1893	-0.0228	-0.1761	0.047	0.2325	0.0575	-0.067	-0.0304	0.1134	0.0505	1.0486	-0.0529	-0.4463	1.0153	-0.1061	0.2035	-8.4866	-30.7018	20.7739
5	0.0561	-0.0333	-0.0028	0.0425	0.0411	0.103	-0.0245	-0.0729	0.023	0.0603	0.1114	0.021	-0.0135	-0.0264	0.2988	0.3425	0.4325	-0.0085	0.6508	-0.2547	-0.1367	-18.8579	-32.1688	23.568
6	0.0317	-0.0247	-0.0155	0.0907	0.0322	0.0354	-0.1374	-0.1361	0.0007	0.1263	0.0738	-0.0671	0.0863	0.1186	-0.353	0.4072	0.2851	-0.2073	0.4193	-0.5153	0.1114	-14.7503	-40.2215	23.2103
7	0.5096	-0.0902	0.7039	0.0394	0.0174	0.9488	0.0398	0.1085	-0.0757	-0.2338	-0.1051	0.1565	-0.0256	-0.0782	-0.2704	0.4953	0.7193	-0.2761	0.0552	-0.5571	0.2462	-23.697	-36.8217	27.4929
8	0.1135	-0.0009	-0.0345	0.1948	0.0412	0.0447	0.0151	0.1688	-0.1386	-0.3073	-0.1789	0.3157	-0.0696	-0.1289	-0.368	0.4177	-0.0699	-0.5131	0.1307	-0.3099	0.333	-22.464	-45.7499	29.4672
9	0.1179	-0.018	-0.0402	0.4232	0.1358	0.1061	-0.0444	0.1064	-0.1115	-0.2558	-0.0855	0.3693	-0.0324	-0.1605	-0.494	0.3146	0.3283	0.0091	-0.2448	-0.0514	0.2842	-30.0245	-38.5191	31.4573
10	0.1786	-0.0215	-0.0936	0.0211	0.0481	0.2011	-0.1054	0.0796	0.0157	-0.0422	0.1415	0.0517	0.2465	0.0059	0.0191	0.4424	-0.0866	-0.2172	0.0973	-0.1126	0.2399	-32.4247	-46.5772	34.8935
11	0.0763	0.0886	-0.035	0.2484	-0.0652	0.0273	0.0169	-0.1933	0.0707	0.2296	0.0296	-0.1156	-0.0569	0.0039	0.1255	0.6202	-0.6249	-0.7985	-0.0457	-0.0084	-0.0478	-38.2749	-39.8626	39.15
12	0.1679	0.0582	-0.0874	0.0386	-0.0427	0.0344	-0.1025	-0.1803	-0.1299	-0.1591	0.0062	0.1343	0.0479	0.0612	-0.3775	-0.1552	-0.4848	0.2713	0.5112	0.4168	-0.1023	-41.4747	-32.019	38.6821
13	0.2444	0.0091	-0.1077	0.0872	-0.0094	0.0373	-0.0305	-0.0832	-0.2113	-0.1847	-0.1808	0.0323	0.0281	0.0976	-0.4767	-0.2914	0.0161	0.1016	0.7403	0.0184	0.1472	-47.8008	-34.0454	45.044
14	0.1475	0.0582	-0.0944	0.0318	-0.0578	0.3397	0.0286	-0.2739	-0.0124	-0.0472	-0.044	-0.0711	-0.0561	0.3028	-0.0157	-0.1529	-0.0948	0.2101	0.7587	-0.0866	-0.0814	-44.7582	-25.1265	39.9723
15	0.2967	0.1365	-0.1585	0.469	-0.1213	0.1113	-0.0477	-0.0268	-0.0115	-0.2433	0.1396	0.5636	-0.0295	-0.1026	-0.124	-0.0157	0.3615	-0.1032	0.8068	-0.113	0.424	-50.3029	-23.2251	47.49
16	0.1559	-0.0621	-0.1348	0.0344	0.0479	0.101	0.0666	-0.0618	0.1594	0.0015	0.1579	-0.2516	-0.0565	0.1016	0.3833	-0.15	0.3966	0.3189	1.0716	-0.2126	0.2787	-44.7964	-17.3445	39.9969
17	0.2321	0.0826	0.0185	0.3983	-0.1181	0.1697	0.0105	0.0346	0.1522	-0.1139	0.1236	0.4092	-0.0439	-0.0292	0.1393	0.3165	0.4831	-0.154	1.0577	-0.0331	0.5202	-49.137	-11.7725	46.2246
18	0.0982	-0.09	-0.0903	0.1047	0.0769	0.0617	0.1096	0.1395	-0.039	-0.1136	-0.1284	0.064	-0.0898	-0.0715	0.0664	0.4245	0.7641	-0.0216	0.9969	-0.4434	0.2041	-41.3733	-10.4507	38.6837
19	0.0446	0.0076	0.0151	0.057	-0.0012	0.1162	-0.0507	-0.0896	0.0403	0.0699	0.1299	-0.1025	0.0414	0.0174	0.2019	1.0368	0.433	-0.4489	0.572	-0.1406	0.3261	-43.721	-2.3849	42.3882
20	0.0193	-0.1195	0.0421	0.1067	0.0257	-0.0088	0.1054	-0.0668	0.1126	0.068	0.0703	-0.1479	-0.0737	0.1095	0.6354	0.1984	0.528	-0.0438	-0.3106	-0.7259	-0.0389	-36.2536	-5.6246	35.4105
21	0.1131	-0.0106	-0.0699	0.0975	0.0033	0.0308	0.0789	-0.1605	0.0891	-0.0433	0.0926	0.0345	-0.0076	-0.0869	0.318	0.5858	0.5411	-0.5232	0.4767	0.2088	0.2916	-34.7668	3.2707	37.8787
22	0.0734	-0.0902	-0.0402	0.2875	0.0563	0.0284	0.0423	-0.1283	0.0867	0.2732	0.1541	-0.2799	0.0241	0.101	0.8173	0.9113	0.1463	-0.5388	0.0313	-0.3192	0.3455	-29.9391	-3.9152	31.3949
23	0.1964	0.0214	0.0322	0.324	0.0409	0.0354	-0.1413	-0.1331	-0.0433	-0.0163	-0.0982	-0.0722	-0.0999	0.0538	-0.1875	0.6814	-0.0287	-0.0333	0.351	0.231	0.2714	-25.5857	4.2227	31.0528
24	0.089	0.1084	-0.0096	0.1763	-0.0296	0.0723	0.1553	-0.1189	-0.0274	-0.0597	-0.0403	-0.0207	0.0103	0.0487	0.3373	0.8256	-0.7947	-0.5816	0.21	0.3268	0.5002	-23.5855	-5.7079	27.3994
25	0.0823	-0.0131	-0.0602	0.0913	-0.0492	0.0595	-0.0174	0.0245	0.0262	-0.288	-0.0896	-0.0275	0.0063	0.0525	-0.2377	0.5803	-0.4037	-0.093	0.6175	0.7602	0.0595	-16.1278	-0.0583	26.2473
26	0.0915	0.0469	-0.0495	0.0709	-0.0408	0.0248	0.016	-0.0898	-0.0495	0.053	-0.0556	-0.2535	-0.0295	0.2038	0.1277	-0.056	-0.5419	0.0698	0.3358	0.4295	0.1077	-18.4926	-10.5774	24.1805
27	0.1009	-0.0123	-0.1158	0.117	-0.0082	0.1243	0.0595	-0.0077	-0.0862	0.0096	-0.1684	0.0166	0.0042	0.0978	-0.2073	0.3164	0.1122	0.2091	0.8938	0.1707	0.1072	-10.1027	-8.4326	21.1332

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 3:41)	A	3 - 41
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 42:81)	A	42 - 81
3	X-RAY DIFFRACTION	3	chain 'B' and (resseq 3:41)	B	3 - 41
4	X-RAY DIFFRACTION	4	chain 'B' and (resseq 42:81)	B	42 - 81
5	X-RAY DIFFRACTION	5	chain 'C' and (resseq 3:41)	C	3 - 41
6	X-RAY DIFFRACTION	6	chain 'C' and (resseq 42:81)	C	42 - 81
7	X-RAY DIFFRACTION	7	chain 'D' and (resseq 3:41)	D	3 - 41
8	X-RAY DIFFRACTION	8	chain 'D' and (resseq 42:81)	D	42 - 81
9	X-RAY DIFFRACTION	9	chain 'E' and (resseq 3:41)	E	3 - 41
10	X-RAY DIFFRACTION	10	chain 'E' and (resseq 42:81)	E	42 - 81
11	X-RAY DIFFRACTION	11	chain 'F'	F	3 - 79
12	X-RAY DIFFRACTION	12	chain 'G' and (resseq 3:41)	G	3 - 41
13	X-RAY DIFFRACTION	13	chain 'G' and (resseq 42:81)	G	42 - 81
14	X-RAY DIFFRACTION	14	chain 'H' and (resseq 3:41)	H	3 - 41
15	X-RAY DIFFRACTION	15	chain 'H' and (resseq 42:81)	H	42 - 81
16	X-RAY DIFFRACTION	16	chain 'I' and (resseq 3:41)	I	3 - 41
17	X-RAY DIFFRACTION	17	chain 'I' and (resseq 42:81)	I	42 - 81
18	X-RAY DIFFRACTION	18	chain 'J' and (resseq 3:41)	J	3 - 41
19	X-RAY DIFFRACTION	19	chain 'J' and (resseq 42:81)	J	42 - 81
20	X-RAY DIFFRACTION	20	chain 'K' and (resseq 3:41)	K	3 - 41
21	X-RAY DIFFRACTION	21	chain 'K' and (resseq 42:81)	K	42 - 81
22	X-RAY DIFFRACTION	22	chain 'L' and (resseq 3:41)	L	3 - 41
23	X-RAY DIFFRACTION	23	chain 'L' and (resseq 42:81)	L	42 - 81
24	X-RAY DIFFRACTION	24	chain 'M' and (resseq 3:41)	M	3 - 41
25	X-RAY DIFFRACTION	25	chain 'M' and (resseq 42:81)	M	42 - 81
26	X-RAY DIFFRACTION	26	chain 'N' and (resseq 3:41)	N	3 - 41
27	X-RAY DIFFRACTION	27	chain 'N' and (resseq 42:81)	N	42 - 81

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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