PDB-9pzi: Crystal Structure of synthetic antibody COP-2 in complex with the...

ID or keywords:

Entry

Database: PDB / ID: 9pzi

Title

Crystal Structure of synthetic antibody COP-2 in complex with the C-terminal domain of Clostridium perfringens enterotoxin

Components

COP-2 Heavy chain
COP-2 Light chain
Heat-labile enterotoxin B chain

Keywords

IMMUNE SYSTEM/TOXIN / ENTEROTOXIN / SYNTHETIC ANTIBODY / TOXIN / IMMUNE SYSTEM-TOXIN complex

Function / homology

Clostridium enterotoxin / Clostridium enterotoxin / toxin activity / extracellular region / Heat-labile enterotoxin B chain

Function and homology information

Biological species

Homo sapiens (human)

Clostridium perfringens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Vecchio, A.J. / Ogbu, C.P. / Kapoor, S.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35GM138368	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01GM117372	United States

Citation

Journal: Protein Sci / Year: 2025
Title: Structures of a synthetic antibody selected against and bound to the C-terminal domain of Clostridium perfringens enterotoxin.
Authors: Chinemerem P Ogbu / Nicolas Manuel Goldbach / Martin Pacesa / Srajan Kapoor / Bruno E Correia / Alex J Vecchio /

Abstract: Clostridium perfringens enterotoxin (CpE) causes cytotoxic gastrointestinal disease in mammalian epithelium by binding membrane protein receptors called claudins. Claudins direct the formation of ...

History

Deposition	Aug 11, 2025	Deposition site: RCSB / Processing site: RCSB
Supersession	Aug 20, 2025	ID: 9MXI
Revision 1.0	Aug 20, 2025	Provider: repository / Type: Initial release
Revision 1.1	Sep 24, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9pzi.cif.gz	930.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9pzi.ent.gz	791.3 KB	Display	PDB format
PDBx/mmJSON format	9pzi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9pzi_validation.pdf.gz	489.3 KB	Display	wwPDB validaton report
Full document	9pzi_full_validation.pdf.gz	515.1 KB	Display
Data in XML	9pzi_validation.xml.gz	71.9 KB	Display
Data in CIF	9pzi_validation.cif.gz	93.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pz/9pzi ftp://data.pdbj.org/pub/pdb/validation_reports/pz/9pzi	HTTPS FTP

-
Related structure data

Related structure data	52864C 9ihcC C: citing same article (ref.)
Similar structure data	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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

C: COP-2 Light chain

D: COP-2 Heavy chain

A: COP-2 Light chain

B: COP-2 Heavy chain

E: COP-2 Light chain

F: COP-2 Heavy chain

G: Heat-labile enterotoxin B chain

I: Heat-labile enterotoxin B chain

H: Heat-labile enterotoxin B chain

207 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: COP-2 Light chain

D: COP-2 Heavy chain

H: Heat-labile enterotoxin B chain

defined by author&software
Evidence: gel filtration, The orientation in the crystal in crystal induced and not present in solution, only a single COP-2/cCpE is in solution as verified by SEC and cryo-EM
69 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: COP-2 Light chain

B: COP-2 Heavy chain

I: Heat-labile enterotoxin B chain

defined by author&software
69 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: COP-2 Light chain

F: COP-2 Heavy chain

G: Heat-labile enterotoxin B chain

defined by author&software
69 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	111.475, 198.520, 115.800
Angle α, β, γ (deg.)	90.00, 109.72, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	A-308- HOH

#1: Antibody	COP-2 Light chain Mass: 26053.135 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	COP-2 Heavy chain Mass: 27799.080 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein	Heat-labile enterotoxin B chain Mass: 15114.945 Da / Num. of mol.: 3 / Fragment: C-terminal domain (UNP residues 192-319) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01558
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 63 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 200 mM sodium chloride, 1.75 M ammonium sulfate, and 100 mM sodium cacodylate pH 6.6

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033167 Å / Relative weight: 1
Reflection	Resolution: 2.5→29.74 Å / Num. obs: 81028 / % possible obs: 99.1 % / Redundancy: 2 % / B_iso Wilson estimate: 45.06 Å² / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.066 / R_pim(I) all: 0.066 / R_rim(I) all: 0.093 / Net I/σ(I): 6.96
Reflection shell	Resolution: 2.5→2.589 Å / Redundancy: 2 % / R_merge(I) obs: 0.535 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 8034 / CC_1/2: 0.506 / CC star: 0.82 / R_pim(I) all: 0.535 / R_rim(I) all: 0.757 / % possible all: 98.32

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
DIALS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→29.74 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.27 / Stereochemistry target values: ML / Details: TLS, NCS and secondary structure restraints

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2248	3974	4.91 %	Random
R_work	0.1783	-	-	-
obs	-	80904	99.15 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 55.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→29.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12804	0	0	323	13127

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	13116
X-RAY DIFFRACTION	f_angle_d	1.45	17865
X-RAY DIFFRACTION	f_dihedral_angle_d	7.494	1805
X-RAY DIFFRACTION	f_chiral_restr	0.072	2010
X-RAY DIFFRACTION	f_plane_restr	0.012	2267

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 (%)
2.5-2.53	0.3403	172	0.2723	2742	X-RAY DIFFRACTION	99
2.53-2.56	0.333	150	0.2649	2665	X-RAY DIFFRACTION	98
2.56-2.6	0.3167	154	0.2683	2706	X-RAY DIFFRACTION	98
2.6-2.63	0.307	159	0.2516	2670	X-RAY DIFFRACTION	98
2.63-2.67	0.2897	159	0.24	2662	X-RAY DIFFRACTION	97
2.67-2.71	0.2844	174	0.2248	2709	X-RAY DIFFRACTION	99
2.71-2.75	0.2609	155	0.2118	2740	X-RAY DIFFRACTION	100
2.75-2.8	0.2472	141	0.2121	2757	X-RAY DIFFRACTION	100
2.8-2.84	0.2482	163	0.2001	2765	X-RAY DIFFRACTION	100
2.84-2.9	0.262	122	0.2076	2781	X-RAY DIFFRACTION	100
2.9-2.95	0.2352	140	0.2147	2732	X-RAY DIFFRACTION	100
2.95-3.01	0.2981	118	0.2216	2804	X-RAY DIFFRACTION	100
3.01-3.08	0.2684	136	0.2177	2739	X-RAY DIFFRACTION	100
3.08-3.15	0.2839	139	0.1971	2802	X-RAY DIFFRACTION	100
3.15-3.23	0.2429	138	0.198	2729	X-RAY DIFFRACTION	100
3.23-3.32	0.2541	135	0.1885	2794	X-RAY DIFFRACTION	99
3.32-3.41	0.2389	134	0.1854	2728	X-RAY DIFFRACTION	99
3.41-3.52	0.2187	131	0.1805	2748	X-RAY DIFFRACTION	99
3.52-3.65	0.1996	181	0.1778	2692	X-RAY DIFFRACTION	99
3.65-3.79	0.2022	155	0.1679	2722	X-RAY DIFFRACTION	99
3.79-3.97	0.1931	146	0.1622	2719	X-RAY DIFFRACTION	98
3.97-4.17	0.2223	113	0.149	2777	X-RAY DIFFRACTION	100
4.17-4.44	0.1475	122	0.1336	2814	X-RAY DIFFRACTION	100
4.44-4.78	0.1598	126	0.1238	2776	X-RAY DIFFRACTION	100
4.78-5.26	0.1657	128	0.1291	2786	X-RAY DIFFRACTION	100
5.26-6.01	0.1954	144	0.1619	2778	X-RAY DIFFRACTION	100
6.01-7.55	0.213	134	0.186	2736	X-RAY DIFFRACTION	98
7.55-29.74	0.2218	105	0.1627	2858	X-RAY DIFFRACTION	100

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	1.7267	0.2134	0.4804	6.7982	-0.1613	1.4329	-0.1267	0.216	0.1395	-0.3833	0.3558	0.0916	-0.1654	0.0895	-0.1617	0.3731	-0.0302	0.0228	0.541	-0.0193	0.3171	5.48	59.244	-40.137
2	2.1523	0.3858	0.0532	3.028	-0.7011	2.9263	-0.0438	0.1715	0.2714	0.2391	0.148	0.0591	-0.4594	-0.1987	-0.0576	0.3269	-0.0068	0.0261	0.4207	0.005	0.3006	6.657	66.138	-31.628
3	4.0913	-0.5558	1.1147	2.9321	1.8771	3.551	0.2414	-0.2641	-0.6676	0.4522	-0.2019	-0.4583	0.7382	0.0462	-0.0739	0.4339	-0.0091	0.0176	0.3877	0.0041	0.3949	9.616	55.892	-26.14
4	2.254	0.0001	0.6598	1.7922	1.239	1.9646	0.0783	0.4475	-0.0161	-0.1268	-0.1327	-0.105	-0.183	0.0405	0.0323	0.3366	-0.0281	0.0298	0.4471	0.0106	0.3103	7.11	61.593	-33.231
5	0.8968	1.5081	1.2168	7.886	4.0094	2.2962	0.1174	-0.2345	-0.5242	-0.3587	-0.242	0.0531	-0.4385	-0.1908	0.1089	0.4122	-0.034	0.0411	0.3898	-0.0499	0.3911	0.955	41.649	-41.385
6	4.7121	-1.5739	-1.0921	0.6649	0.8154	1.5998	-1.2068	-0.6539	-0.7763	0.3705	0.4288	-0.1062	1.227	-0.8579	0.6205	0.6756	-0.2346	0.2662	0.8938	-0.1386	1.0051	-23.971	28.044	-29.399
7	7.7309	1.3918	-1.5046	1.1582	-0.6507	1.3849	0.4188	0.1276	-0.1263	0.134	-0.3858	0.6512	0.0441	-0.1177	0.0318	0.5346	-0.0644	0.0725	0.5308	-0.2056	0.7154	-15.247	33.941	-40.264
8	6.8597	0.9093	0.5305	3.298	0.5658	4.9441	0.4071	1.1648	0.3932	-0.7985	-0.5226	1.1843	0.6954	-0.6758	-0.0323	0.7548	0.0442	-0.0141	0.8467	-0.1758	0.8605	-24.294	35.375	-42.209
9	1.4756	1.5527	-0.9022	1.7463	-0.8778	1.0334	0.1109	-0.9567	-0.248	0.1603	-0.2638	0.3575	0.0306	-0.1755	0.1317	0.5121	-0.0477	0.0723	0.5689	-0.1973	0.6794	-14.903	35.998	-34.979
10	5.3942	1.7509	0.1493	1.5186	0.0097	0.099	-0.553	0.0895	-1.1804	-0.2432	0.2046	0.6016	0.5579	-0.7489	0.2713	0.6518	-0.138	0.0344	0.7565	-0.2955	1.3136	-26.27	26.381	-41.396
11	8.5007	2.9016	-3.3047	3.6289	-1.8169	4.3717	-0.4772	0.9764	-0.9892	0.2107	0.2482	0.2381	0.661	-0.834	0.3971	0.5492	-0.0474	0.0609	0.5374	-0.263	0.8499	-15.223	25.554	-44.026
12	1.7169	1.4456	2.3333	3.1221	0.009	4.982	0.1148	-0.3727	-0.3732	0.3568	-0.0682	0.1766	0.5337	-0.3184	-0.0442	0.394	-0.0269	0.0939	0.4458	-0.0767	0.2782	-12.652	58.674	-15.328
13	2.3178	0.2481	-0.2762	2.3183	0.1991	1.5892	-0.0329	0.2302	0.0664	-0.0385	0.0194	0.1103	-0.339	-0.1649	0.0085	0.3032	0.0168	0.0302	0.3692	-0.0137	0.2386	-5.89	67.871	-17.845
14	3.2704	-0.1354	-1.3592	4.2163	1.376	0.9944	-0.1172	0.3119	0.2615	-0.1283	-0.2761	0.2413	-0.2593	-0.4233	0.3283	0.3829	-0.0218	0.0462	0.3712	-0.01	0.3051	-13.086	67.107	-15.152
15	2.5587	0.954	0.1693	2.2774	0.0956	1.2976	-0.0183	-0.2425	-0.304	0.0298	-0.1253	-0.0287	0.078	-0.1837	0.0524	0.3679	0.0252	0.057	0.3483	-0.0612	0.3033	-1.619	62.639	-20.869
16	8.3874	-4.8617	0.4833	8.9289	2.2847	6.6316	0.7799	-0.8664	-0.8207	0.0173	-0.2389	0.3172	0.7979	-0.6384	-0.4318	0.6118	-0.1274	0.1714	0.6592	0.1106	0.9705	-19.203	26.923	-25.897
17	3.2019	0.0076	-0.5092	4.0487	1.4225	3.5696	-0.1726	-1.0112	-0.5016	0.799	0.0742	0.1602	0.5992	0.3527	0.1008	0.5779	-0.037	0.081	0.7209	0.0225	0.5694	-14.729	35.749	-23.214
18	0.8923	-0.5918	0.3353	1.6572	0.6587	0.6992	-0.0939	-0.7053	-0.4368	0.4763	-0.3184	0.0086	0.1525	0.4094	0.2179	1.0923	0.0273	0.3504	1.096	0.2995	1.1575	-19.155	31.797	-15.789
19	2.1558	-1.0148	-0.8313	3.0729	-1.9448	4.9402	0.0488	-0.1275	0.4222	0.4989	0.191	0.1562	-0.4726	-0.3303	-0.0796	0.3713	-0.0302	-0.0645	0.3261	-0.0521	0.4969	5.595	31.375	-53.107
20	3.055	-0.2179	-0.7746	4.5548	-0.3383	1.3189	-0.0248	-0.1357	0.2881	0.1779	-0.1136	-0.0876	0.0625	0.1214	0.1408	0.2707	-0.0049	-0.0402	0.2632	-0.0051	0.3697	10.078	22.539	-56.823
21	0.4625	0.0296	0.2681	3.1569	-1.104	2.8927	0.0146	-0.066	-0.0552	-0.0851	-0.2656	0.0247	0.2695	0.2339	0.1359	0.307	0.0256	-0.0136	0.2617	0.0103	0.4406	4.704	22.994	-55.917
22	0.6477	-1.9006	1.5463	5.4166	-4.5358	3.9319	0.1799	0.2685	-0.2855	0.2879	0.2409	0.5288	0.2276	-0.2993	-0.5738	0.3581	0.0176	-0.0353	0.3207	0.0318	0.504	1.356	41.264	-68.049
23	5.8035	1.2359	1.2129	1.9645	0.1374	1.6903	-0.212	0.6798	0.1766	-0.0664	0.1852	0.5421	-0.0512	-0.3936	0.0126	0.4299	-0.0188	-0.0356	0.6783	0.1927	0.5843	-17.621	40.852	-80.454
24	3.6573	-1.0431	1.0358	3.5893	-1.3289	3.6394	-0.08	0.3363	0.781	-0.1521	0.4685	0.5358	-0.8626	-0.9397	-0.5382	0.5636	0.0631	-0.0132	0.6751	0.1745	0.8715	-23.776	44.578	-74.811
25	8.7603	0.2621	2.042	0.2216	-0.1573	2.2148	0.0828	0.334	-0.399	-0.0728	0.126	0.0598	0.0337	-0.2559	-0.3244	0.5045	-0.0499	-0.0312	0.4843	0.1596	0.6918	-14.141	37.889	-76.96
26	3.9899	0.0941	2.2549	1.0484	0.8569	2.3673	-0.5796	0.846	1.1627	-0.5859	0.3442	1.1722	-0.6726	-0.5591	0.2723	0.5164	-0.0427	-0.1712	0.8723	0.3545	0.8764	-19.41	49.415	-82.493
27	2.4552	-0.4608	0.9136	2.594	-1.1013	2.0626	0.0097	0.0126	-0.1219	-0.1485	0.1443	0.6398	0.111	-0.2106	-0.113	0.3609	-0.041	-0.0622	0.2307	-0.0018	0.5505	-5.96	9.202	-59.739
28	3.0998	-2.0605	-0.4225	1.7791	0.9205	1.0549	0.068	0.628	-0.4554	-0.5517	-0.4112	0.7985	0.0019	-0.6038	0.2555	0.7854	-0.1449	-0.1769	1.1947	-0.0639	0.6716	-17.896	32.79	-88.582
29	3.8253	0.2572	0.4933	3.7837	-1.1659	2.5798	-0.3135	0.809	-1.0402	-0.9201	0.3277	-0.0166	0.5947	-0.019	-0.0956	0.5876	-0.1585	-0.0847	0.6436	-0.0747	0.7665	-13.92	26.923	-83.271
30	1.0863	0.4007	-0.7561	3.5552	0.7689	4.7167	-0.2488	-0.1757	0.1191	0.066	-0.1145	0.0697	0.3939	-0.2266	0.3425	0.3418	0.0115	0.0156	0.4512	0.1265	0.336	5.857	56.174	-71.222
31	3.341	-0.737	-0.8609	3.6029	0.3543	2.7156	0.1859	0.0904	-0.0282	-0.6169	0.036	-0.3508	-0.0483	0.2761	-0.1309	0.3316	-0.0128	0.0139	0.3003	0.0514	0.2844	7.46	60.796	-81.238
32	2.3087	0.3073	0.4187	1.1645	-1.0382	4.0108	0.0495	-0.2103	-0.1508	0.0704	0.1172	-0.0319	-0.0808	0.0937	-0.1695	0.3237	0.0083	0.0178	0.3354	0.0341	0.3295	8.545	64.447	-75.752
33	1.3361	-0.8453	-1.9051	1.0684	1.5748	2.9214	-0.0686	-0.2655	-0.1142	-0.0848	-0.1835	0.0488	0.5	-0.5683	0.4267	0.46	0.0084	0.0531	0.5152	0.0048	0.3888	1.032	63.677	-55.039
34	1.7843	0.6834	0.1752	1.2662	-0.0981	0.053	-0.0297	0.0125	0.6276	-0.0884	-0.0585	0.6802	-0.4031	-0.5509	-0.2813	0.6061	0.9204	-0.2181	1.7612	-0.2602	0.7607	-23.454	82.186	-49.626
35	4.1739	-0.3443	-0.3815	1.5431	0.3424	0.2451	0.3577	-0.4695	-0.4059	-0.3444	-0.2162	-0.0142	-0.5624	-2.0304	-0.0378	0.5133	0.2632	-0.1265	1.5775	0.0754	0.1911	-15.209	68.997	-48.825
36	3.2844	1.4538	-4.2261	1.9535	-1.6767	5.4472	0.3017	-0.7242	-0.2893	0.6682	0.2651	0.7911	0.002	-2.6537	-0.0578	0.6728	0.0615	0.0905	1.9297	0.2541	0.5563	-24.312	66.756	-48.86
37	2.7101	-1.8845	-0.5128	1.5107	0.4812	0.256	0.1638	-0.266	0.5617	0.2446	0.0764	0.0799	-0.5257	-1.7363	-0.0614	0.5573	0.2713	0.0165	1.604	0.0616	0.4226	-14.858	72.306	-53.247
38	4.1159	-0.4043	-2.7484	0.5992	0.7117	2.064	0.2367	-1.3167	-0.3486	0.6085	0.018	0.1532	-1.0851	-2.0148	0.1808	0.6891	0.507	0.1634	1.9729	-0.1018	0.2417	-20.368	70.913	-40.689
39	3.5424	-1.492	-0.8325	1.3786	0.2108	2.5557	-0.1001	-0.0832	0.0604	0.0312	0.1677	0.0633	-0.2897	-0.3707	-0.0957	0.3653	0.0607	-0.0046	0.332	0.0771	0.2939	-6.323	73.808	-85.503
40	2.5502	1.6228	2.5901	1.2069	1.2026	3.4897	-0.0473	-0.822	0.2101	0.6625	0.1476	0.0117	-0.7236	-1.1267	0.396	1.4118	1.004	-0.5517	1.3809	-0.1804	0.3569	-16.795	82.255	-52.894
41	4.2676	0.2282	1.1554	0.3112	0.1281	4.1514	-0.7792	-0.2783	1.0281	0.2422	0.411	-0.008	-2.4441	-1.1618	0.2279	1.1338	0.3901	-0.1847	0.7107	-0.0417	0.5964	-13.998	83.803	-60.139
42	4.1483	-0.713	0.6266	2.3065	1.2038	2.1395	-0.1083	-0.1517	-0.5459	1.1868	-0.6143	-0.6567	-0.4252	0.9396	0.464	0.4372	0.0393	0.0108	0.4226	-0.0182	0.4481	21.28	62.977	-101.675
43	3.5378	0.5793	0.02	2.8048	-1.5025	4.1626	-0.0218	0.4409	0.1716	-0.7006	-0.3842	-0.1405	-0.0477	0.7043	0.2009	0.4746	0.0679	0.0016	0.3443	-0.0121	0.3223	16.27	71.58	-118.223
44	1.316	-0.3381	0.6585	2.5685	0.1012	3.3636	0.1102	0.0886	-0.0855	-0.1501	0.0117	0.066	0.1324	-0.163	-0.1156	0.3387	0.0364	0.0343	0.3419	0.0209	0.3326	10.593	65.748	-105.224
45	2.2719	0.1611	0.0329	1.9686	-0.4769	3.5704	0.0064	0.0555	-0.1482	-0.2535	0.0144	-0.0389	0.3404	-0.1023	-0.0141	0.3836	0.0237	0.0105	0.3443	-0.0297	0.3206	10.101	65.145	-109.879
46	2.2166	1.7094	0.2741	7.5644	-0.3742	1.4517	-0.1205	-0.1012	0.1467	0.0126	-0.0634	-0.5858	0.1217	0.319	0.0832	0.4597	-0.0747	-0.0605	0.5646	0.0587	0.4444	-18.086	94.865	-96.473
47	5.9132	1.959	-1.2695	1.6341	-0.9043	3.5411	0.2983	-0.7404	-0.0967	1.4153	-0.3215	0.4242	-0.0023	-0.2942	0.127	0.5241	0.0051	-0.1129	0.4578	0.1007	0.4576	-23.877	83.74	-90.91
48	2.1202	0.4767	-0.2435	3.1486	-1.05	2.6236	0.1146	-0.1632	0.1092	0.1945	-0.1694	0.3054	0.0273	-0.0253	0.0766	0.3772	-0.024	-0.0302	0.3131	-0.0058	0.3699	-27.107	97.328	-96.78
49	2.742	0.3102	-0.6209	2.703	-0.7293	2.9701	0.077	-0.1933	0.3226	0.3871	-0.1576	0.1953	-0.2761	0.0666	0.0542	0.4505	-0.0303	-0.0086	0.3147	0.0435	0.374	-27.686	94.404	-93.538
50	5.9828	0.3313	0.8103	7.2123	-1.5516	1.0756	0.2455	-1.3515	-0.752	2.1341	0.5013	-0.9165	0.2243	-0.0085	-0.6271	1.1281	0.0907	-0.1382	0.7523	0.0504	0.8089	19.892	78.525	-71.542
51	3.7206	-0.1318	-0.1499	3.8006	-1.5042	5.7023	0.0163	0.2949	0.4803	-0.0842	0.092	-0.0798	-0.4064	-0.4262	-0.2624	0.4492	0.0748	0.1	0.3214	0.0011	0.4755	23.814	93.204	-100.353
52	1.5403	0.0289	-0.9458	2.6147	-0.3881	2.9098	0.1627	-0.1079	0.2236	0.0382	-0.0309	-0.1304	-0.2079	0.1361	-0.113	0.4017	0.0147	0.0464	0.2788	-0.0335	0.3603	30.792	85.632	-92.848
53	2.5344	-0.7181	-1.5529	1.7459	0.0378	7.4006	0.115	-0.6021	0.1588	0.2316	-0.2989	0.1795	-0.9884	0.3475	0.2054	0.5232	-0.0474	0.1342	0.2945	-0.0627	0.5706	29.943	94.957	-90.855

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN C AND RESID 2:50 )	C	2 - 50
2	X-RAY DIFFRACTION	2	( CHAIN C AND RESID 51:63 )	C	51 - 63
3	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 64:86 )	C	64 - 86
4	X-RAY DIFFRACTION	4	( CHAIN C AND RESID 87:127 )	C	87 - 127
5	X-RAY DIFFRACTION	5	( CHAIN C AND RESID 128:139 )	C	128 - 139
6	X-RAY DIFFRACTION	6	( CHAIN C AND RESID 140:154 )	C	140 - 154
7	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 155:176 )	C	155 - 176
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 177:189 )	C	177 - 189
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 190:212 )	C	190 - 212
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 213:223 )	C	213 - 223
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 224:237 )	C	224 - 237
12	X-RAY DIFFRACTION	12	( CHAIN D AND RESID 4:43 )	D	4 - 43
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 44:93 )	D	44 - 93
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 94:117 )	D	94 - 117
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 118:158 )	D	118 - 158
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 159:173 )	D	159 - 173
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 174:242 )	D	174 - 242
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 243:252 )	D	243 - 252
19	X-RAY DIFFRACTION	19	( CHAIN A AND RESID 2:50 )	A	2 - 50
20	X-RAY DIFFRACTION	20	( CHAIN A AND RESID 51:100 )	A	51 - 100
21	X-RAY DIFFRACTION	21	( CHAIN A AND RESID 101:127 )	A	101 - 127
22	X-RAY DIFFRACTION	22	( CHAIN A AND RESID 128:139 )	A	128 - 139
23	X-RAY DIFFRACTION	23	( CHAIN A AND RESID 140:176 )	A	140 - 176
24	X-RAY DIFFRACTION	24	( CHAIN A AND RESID 177:189 )	A	177 - 189
25	X-RAY DIFFRACTION	25	( CHAIN A AND RESID 190:212 )	A	190 - 212
26	X-RAY DIFFRACTION	26	( CHAIN A AND RESID 213:237 )	A	213 - 237
27	X-RAY DIFFRACTION	27	( CHAIN B AND RESID 4:158 )	B	4 - 158
28	X-RAY DIFFRACTION	28	( CHAIN B AND RESID 159:173 )	B	159 - 173
29	X-RAY DIFFRACTION	29	( CHAIN B AND RESID 174:252 )	B	174 - 252
30	X-RAY DIFFRACTION	30	( CHAIN E AND RESID 2:50 )	E	2 - 50
31	X-RAY DIFFRACTION	31	( CHAIN E AND RESID 51:63 )	E	51 - 63
32	X-RAY DIFFRACTION	32	( CHAIN E AND RESID 64:127 )	E	64 - 127
33	X-RAY DIFFRACTION	33	( CHAIN E AND RESID 128:139 )	E	128 - 139
34	X-RAY DIFFRACTION	34	( CHAIN E AND RESID 140:154 )	E	140 - 154
35	X-RAY DIFFRACTION	35	( CHAIN E AND RESID 155:176 )	E	155 - 176
36	X-RAY DIFFRACTION	36	( CHAIN E AND RESID 177:189 )	E	177 - 189
37	X-RAY DIFFRACTION	37	( CHAIN E AND RESID 190:212 )	E	190 - 212
38	X-RAY DIFFRACTION	38	( CHAIN E AND RESID 213:237 )	E	213 - 237
39	X-RAY DIFFRACTION	39	( CHAIN F AND RESID 4:163 )	F	4 - 163
40	X-RAY DIFFRACTION	40	( CHAIN F AND RESID 164:184 )	F	164 - 184
41	X-RAY DIFFRACTION	41	( CHAIN F AND RESID 185:252 )	F	185 - 252
42	X-RAY DIFFRACTION	42	( CHAIN G AND RESID 201:210 )	G	201 - 210
43	X-RAY DIFFRACTION	43	( CHAIN G AND RESID 211:227 )	G	211 - 227
44	X-RAY DIFFRACTION	44	( CHAIN G AND RESID 228:284 )	G	228 - 284
45	X-RAY DIFFRACTION	45	( CHAIN G AND RESID 285:322 )	G	285 - 322
46	X-RAY DIFFRACTION	46	( CHAIN I AND RESID 200:217 )	I	200 - 217
47	X-RAY DIFFRACTION	47	( CHAIN I AND RESID 218:227 )	I	218 - 227
48	X-RAY DIFFRACTION	48	( CHAIN I AND RESID 228:284 )	I	228 - 284
49	X-RAY DIFFRACTION	49	( CHAIN I AND RESID 285:321 )	I	285 - 321
50	X-RAY DIFFRACTION	50	( CHAIN H AND RESID 197:204 )	H	197 - 204
51	X-RAY DIFFRACTION	51	( CHAIN H AND RESID 205:227 )	H	205 - 227
52	X-RAY DIFFRACTION	52	( CHAIN H AND RESID 228:302 )	H	228 - 302
53	X-RAY DIFFRACTION	53	( CHAIN H AND RESID 303:322 )	H	303 - 322

-
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