PDB-9eht: Crystal Structure of PD-1/retifanlimab complex

ID or keywords:

Entry

Database: PDB / ID: 9eht

Title

Crystal Structure of PD-1/retifanlimab complex

Components

Programmed cell death protein 1
heavy chain
light chain

Keywords

IMMUNE SYSTEM / PD-1 / immune checkpoint / antibody

Function / homology

Function and homology information

negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.544 Å

Authors

Heo, Y.-S.

Funding support

Korea, Republic Of, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of PD-1/retifanlimab complex
Authors: Heo, Y.-S.

History

Deposition	Nov 25, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9eht.cif.gz	465 KB	Display	PDBx/mmCIF format
PDB format	pdb9eht.ent.gz	380.4 KB	Display	PDB format
PDBx/mmJSON format	9eht.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9eht_validation.pdf.gz	464.3 KB	Display	wwPDB validaton report
Full document	9eht_full_validation.pdf.gz	481.4 KB	Display
Data in XML	9eht_validation.xml.gz	67.9 KB	Display
Data in CIF	9eht_validation.cif.gz	94.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eh/9eht ftp://data.pdbj.org/pub/pdb/validation_reports/eh/9eht	HTTPS FTP

-
Related structure data

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	#204 - Dec 2016 PD-1 similarity (4) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (1) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#204 - Dec 2016
PD-1
similarity (4)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#247 - Jul 2020
Myelin-associated Glycoprotein
similarity (1)
#169 - Jan 2014
HIV Envelope Glycoprotein
similarity (1)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)

Deposited unit

A: light chain

B: heavy chain

D: light chain

E: heavy chain

F: Programmed cell death protein 1

J: Programmed cell death protein 1

126 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: light chain

B: heavy chain

J: Programmed cell death protein 1

defined by author&software
Evidence: gel filtration
62.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: light chain

E: heavy chain

F: Programmed cell death protein 1

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

Unit cell

Length a, b, c (Å)	81.500, 93.160, 89.910
Angle α, β, γ (deg.)	90.00, 112.39, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	light chain Mass: 23682.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	heavy chain Mass: 24996.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein	Programmed cell death protein 1 / Protein PD-1 / hPD-1 Mass: 14083.601 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1488 / 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: 2.51 Å³/Da / Density % sol: 51.08 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 35.00 % (w/v) 2,4-methyl pentanediol, 200 mM Sodium chloride, and 100 mM Tris at pH 7.0

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.54→30 Å / Num. obs: 175789 / % possible obs: 95.9 % / Redundancy: 7 % / CC_1/2: 0.998 / Net I/σ(I): 12.8
Reflection shell	Resolution: 1.54→1.6 Å / Num. unique obs: 63212 / CC_1/2: 0.732

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.544→29.294 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2081	8786	5 %
R_work	0.1809	-	-
obs	0.1823	175760	96.61 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.544→29.294 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8380	0	0	1488	9868

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	8587
X-RAY DIFFRACTION	f_angle_d	1.427	11674
X-RAY DIFFRACTION	f_dihedral_angle_d	3.648	5139
X-RAY DIFFRACTION	f_chiral_restr	0.086	1306
X-RAY DIFFRACTION	f_plane_restr	0.012	1498

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 (%)
1.544-1.5611	0.3113	275	0.3062	5226	X-RAY DIFFRACTION	91
1.5611-1.5795	0.306	288	0.2634	5466	X-RAY DIFFRACTION	95
1.5795-1.5987	0.3012	288	0.2553	5464	X-RAY DIFFRACTION	95
1.5987-1.619	0.2761	287	0.2403	5457	X-RAY DIFFRACTION	95
1.619-1.6403	0.2812	287	0.236	5461	X-RAY DIFFRACTION	96
1.6403-1.6627	0.2703	292	0.2377	5534	X-RAY DIFFRACTION	96
1.6627-1.6865	0.2754	288	0.2314	5475	X-RAY DIFFRACTION	96
1.6865-1.7116	0.2215	288	0.2177	5474	X-RAY DIFFRACTION	96
1.7116-1.7384	0.2491	292	0.2148	5552	X-RAY DIFFRACTION	96
1.7384-1.7669	0.2726	289	0.2201	5484	X-RAY DIFFRACTION	96
1.7669-1.7974	0.2528	293	0.2167	5556	X-RAY DIFFRACTION	96
1.7974-1.83	0.2279	290	0.2059	5531	X-RAY DIFFRACTION	96
1.83-1.8652	0.2358	290	0.1992	5527	X-RAY DIFFRACTION	96
1.8652-1.9033	0.2241	292	0.1956	5557	X-RAY DIFFRACTION	96
1.9033-1.9447	0.2207	292	0.1958	5546	X-RAY DIFFRACTION	97
1.9447-1.9899	0.23	294	0.1908	5592	X-RAY DIFFRACTION	97
1.9899-2.0396	0.2088	292	0.1838	5544	X-RAY DIFFRACTION	97
2.0396-2.0948	0.2166	294	0.182	5590	X-RAY DIFFRACTION	97
2.0948-2.1564	0.1932	295	0.1781	5593	X-RAY DIFFRACTION	97
2.1564-2.226	0.2019	293	0.1769	5580	X-RAY DIFFRACTION	97
2.226-2.3055	0.1991	294	0.1799	5599	X-RAY DIFFRACTION	97
2.3055-2.3978	0.1975	296	0.1844	5630	X-RAY DIFFRACTION	97
2.3978-2.5068	0.2213	296	0.1822	5631	X-RAY DIFFRACTION	98
2.5068-2.6389	0.186	298	0.1805	5660	X-RAY DIFFRACTION	98
2.6389-2.8041	0.2046	298	0.1765	5659	X-RAY DIFFRACTION	98
2.8041-3.0205	0.1984	298	0.1768	5677	X-RAY DIFFRACTION	98
3.0205-3.324	0.1944	300	0.1676	5687	X-RAY DIFFRACTION	98
3.324-3.8041	0.1809	298	0.157	5660	X-RAY DIFFRACTION	98
3.8041-4.7894	0.1854	303	0.1471	5753	X-RAY DIFFRACTION	99
4.7894-29.294	0.2036	306	0.18	5809	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	3.6698	1.6599	1.5576	1.5474	0.655	1.5741	-0.0662	0.0766	-0.164	0.0792	0.1094	-0.1055	0.1311	0.1325	-0.071	0.1776	0.0418	0.0029	0.0916	-0.0078	0.1423	-0.2537	55.692	51.8836
2	5.845	-1.2912	4.0627	5.952	-2.6442	6.9692	-0.1944	-0.0349	0.1258	0.1119	0.2641	0.2834	-0.2321	-0.222	-0.1222	0.1614	0.0048	0.0133	0.0713	-0.0037	0.1135	-9.9468	63.871	52.5586
3	3.3235	1.8777	0.8803	1.3416	0.147	1.7017	-0.0204	-0.1254	-0.0301	0.1059	0.037	-0.0059	0.0719	-0.0566	0.0015	0.1698	0.0341	0.018	0.0832	-0.0081	0.1432	-8.5491	56.1106	55.6815
4	2.8448	2.3785	3.0014	2.3362	2.555	3.2594	0.0605	-0.0483	-0.0858	0.0492	0.0108	-0.0914	0.1149	-0.0172	-0.0936	0.1659	0.0026	-0.0041	0.0969	-0.003	0.1345	-6.9466	58.339	44.4366
5	3.2685	2.3009	-0.3789	6.6542	-2.9982	3.8925	-0.0557	0.1849	0.2666	-0.5321	0.2197	0.5786	-0.1493	-0.1423	-0.1831	0.2204	-0.01	-0.0105	0.1317	-0.004	0.1411	-21.2923	68.6436	12.4848
6	0.7705	0.6504	-0.7339	1.2722	-1.1039	3.0276	0.0207	-0.011	0.0053	0.0266	-0.0393	-0.0431	-0.1448	0.2389	0.0167	0.1579	-0.0205	0.0029	0.1409	-0.0035	0.152	-12.1953	60.2096	19.9316
7	0.5618	0.4349	-1.1159	3.2387	-2.5772	5.9357	0.1103	0.0543	0.0351	-0.0603	-0.0798	-0.0378	-0.3039	0.1081	-0.0162	0.1201	-0.0144	-0.0113	0.1062	0.0022	0.1378	-15.4365	62.4489	18.9006
8	2.1153	-0.7426	0.2371	5.5361	-4.3	9.6809	-0.046	0.0733	0.0217	-0.2891	-0.0391	0.0368	0.274	-0.1685	0.0313	0.1084	-0.0331	0.005	0.1129	-0.0219	0.1465	-15.9512	53.3148	14.4939
9	2.2238	-1.343	-0.0925	1.6104	-0.7485	6.4206	-0.0133	0.0846	0.0472	0.0396	0.1519	0.1729	-0.2543	-0.3574	-0.2471	0.1645	0.0008	-0.0247	0.0464	-0.0238	0.1297	-11.0216	83.7124	46.9927
10	2.232	-0.7305	0.136	2.5119	-1.541	1.1465	-0.0852	-0.0196	-0.0271	0.0558	0.0325	0.0055	-0.0003	0.0167	0.0429	0.2104	0.0039	-0.0282	0.0855	-0.0165	0.142	-4.7202	78.3383	54.4267
11	4.3203	-0.8532	1.8569	3.3333	0.4857	6.432	-0.2199	0.1979	0.1658	0.1641	-0.0827	-0.3645	0.1647	0.649	0.2269	0.1799	-0.0233	-0.0382	0.1263	0.0169	0.2236	5.7565	81.5265	53.0022
12	1.2822	0.2779	0.7068	1.2698	0.5377	5.1958	-0.0913	-0.0324	0.1291	0.0405	0.1101	-0.163	-0.3253	0.2795	-0.0311	0.218	0.0014	-0.0254	0.0634	0.0082	0.1796	-2.998	85.9076	49.1929
13	0.9406	-0.2772	0.7198	0.1978	-0.5217	2.312	-0.0148	0.0639	-0.0624	-0.0091	0.0209	-0.013	0.1194	-0.0125	0.021	0.1914	-0.0078	0.0028	0.0644	-0.0125	0.1369	-13.8515	72.9834	39.1036
14	3.5123	2.121	-0.3602	2.9151	-0.3513	1.3291	-0.0169	-0.0068	-0.0774	0.1097	-0.0391	0.002	-0.0838	-0.0026	0.0476	0.1785	-0.0055	-0.001	0.0917	0.0053	0.1309	-23.1927	71.6008	26.4182
15	6.3543	4.6073	0.9368	7.0675	0.4226	2.1765	-0.1065	0.227	0.0699	-0.1214	0.0626	0.4501	-0.0476	-0.2178	0.0634	0.1403	-0.0011	0.0125	0.1349	0.0155	0.1105	-30.0885	69.8106	23.4207
16	6.5036	3.456	1.9864	6.3298	4.7324	6.4621	-0.174	0.458	0.348	-0.9716	-0.1464	0.6409	-0.8299	-0.5051	0.2221	0.2966	-0.0089	-0.0657	0.2106	0.0875	0.2343	-31.2385	74.9467	18.056
17	1.1737	-0.9649	1.7168	1.8388	-2.6772	7.3187	-0.0072	0.0047	-0.0569	0.0747	0.1004	0.1289	0.1071	-0.3905	-0.1052	0.1103	-0.0226	0.0451	0.1718	-0.017	0.127	-13.8555	46.0702	1.3761
18	2.2719	1.4553	3.0038	3.1925	-0.2849	6.3962	0.0467	-0.0468	-0.3756	0.0943	0.0674	-0.2166	0.2627	0.2132	-0.0807	0.1671	0.0152	0.0324	0.1598	-0.0016	0.1427	-2.4799	40.6922	-0.4045
19	0.3696	-0.0036	0.4728	0.302	-0.5277	4.7896	0.0537	-0.0182	-0.0914	-0.0667	0.0221	0.0485	0.5363	-0.1891	-0.0834	0.1718	-0.01	0.0155	0.1426	-0.007	0.1468	-8.8358	40.3265	3.156
20	3.1128	5.3734	-1.4801	9.2804	-1.8409	3.5421	-0.1849	-0.1675	-0.1712	-0.1105	0.2676	-0.777	-0.1706	0.9346	-0.0488	0.2051	0.0046	0.023	0.4798	-0.1221	0.2684	18.7813	52.0288	33.9216
21	1.1154	1.6986	1.2574	4.2591	2.6425	2.8748	-0.0659	0.1411	-0.072	-0.1986	0.1492	-0.123	-0.0764	0.2261	-0.0711	0.1755	0.0267	0.0043	0.2032	-0.0004	0.1316	4.549	49.0416	27.2588
22	5.831	4.1473	1.7321	4.4237	2.0317	3.755	0.1131	-0.2717	0.2717	0.1008	-0.1439	0.0907	-0.0376	0.2357	0.0192	0.1391	0.0489	-0.0007	0.1455	-0.0203	0.1489	8.368	55.5356	35.9448
23	2.0461	1.2342	0.9793	3.7837	2.7526	4.9969	-0.0053	-0.0828	-0.0385	0.037	0.1544	-0.1972	0.0025	0.4429	-0.2462	0.1358	0.0034	0.0265	0.2148	-0.0055	0.114	15.8387	49.4747	-4.7252
24	2.8383	0.5546	0.1889	1.8516	0.0358	1.6991	0.0552	-0.3248	-0.006	0.1646	-0.099	-0.0197	-0.0069	0.0963	0.0064	0.1342	-0.014	0.0174	0.1448	-0.0009	0.093	7.3896	47.6337	-10.4057
25	3.0714	-0.5039	-1.9855	1.9012	-0.5865	6.0785	0.1022	0.0159	0.2569	-0.0453	-0.0082	0.054	-0.2128	-0.0948	-0.0919	0.1359	-0.0141	0.0116	0.1194	-0.0083	0.1552	2.7964	54.2508	-15.0054
26	3.3667	-0.9599	-2.8537	6.3826	4.6945	7.5896	0.0799	-0.1356	0.2766	-0.1091	0.0138	0.0249	-0.3943	0.1702	-0.1633	0.1747	-0.0298	0.0095	0.1452	0.007	0.1255	10.0965	56.0702	-12.7905
27	4.0712	2.8896	2.9061	2.2059	1.8877	6.2373	0.0105	-0.2864	0.228	-0.0408	-0.127	-0.0127	-0.4201	0.0321	0.1847	0.1554	-0.009	0.0174	0.1913	-0.0278	0.1168	9.5963	55.2431	-2.1461
28	1.263	0.0791	1.2604	0.5493	0.5016	2.1215	0.0192	-0.2283	-0.031	0.1217	0.046	-0.0552	0.1338	0.0029	-0.0588	0.1687	0.0035	0.0117	0.213	-0.0093	0.1141	11.4072	46.9964	10.1574
29	0.8789	1.2042	0.0445	3.2374	-2.0172	2.9181	-0.0299	0.0721	-0.0623	-0.0221	0.0361	-0.0982	0.0783	0.0325	-0.0004	0.1954	0.0309	0.0237	0.325	-0.0186	0.1737	17.3579	44.311	23.0948
30	1.8791	2.1546	-2.0953	6.8896	-1.5803	4.7204	-0.0852	-0.0853	-0.1357	0.0881	-0.1373	-0.2862	0.4103	0.3812	0.2188	0.1466	0.079	0.0241	0.3754	-0.0081	0.2159	24.9398	39.8271	25.0123
31	5.052	1.2624	-0.3789	3.6414	-2.1871	8.429	0.1771	-0.4791	-0.0462	0.4556	-0.2462	-0.3383	0.1085	0.2883	0.2342	0.2791	0.0306	-0.0887	0.4841	0.0578	0.273	27.1741	43.7753	29.1588
32	6.34	0.4251	6.6557	6.4754	4.121	9.0968	-0.1939	1.1142	0.0649	-0.5504	0.3532	-0.5256	-0.3065	-0.0625	-0.0241	0.3446	-0.1157	0.0554	0.4341	-0.0013	0.1802	-14.5924	43.4379	-33.3082
33	0.7086	1.3607	0.3839	3.8744	1.105	0.3168	0.124	0.2234	-0.5597	0.3253	-0.0773	0.2347	0.7539	-0.649	-0.2069	0.4516	-0.3087	-0.0171	0.7757	-0.0645	0.3393	-27.2658	32.351	-32.7569
34	6.5121	-0.1266	4.781	2.3662	-1.7091	9.8938	-0.2743	1.4253	-0.444	-0.2153	-0.2669	-0.0529	0.3264	0.71	0.3025	0.3141	-0.0356	0.0082	0.4033	-0.0992	0.2746	-5.0337	39.9865	-24.9031
35	2.1578	-0.0342	4.0102	3.9157	-1.3153	7.9898	-0.0481	-0.2321	-0.1204	0.0748	0.1018	0.3029	-0.0671	-0.7958	-0.0223	0.2617	-0.0835	-0.0281	0.3371	-0.0059	0.1875	-21.9635	40.9335	-21.8596
36	4.8898	-2.9783	2.1962	1.7685	-1.3309	0.958	0.093	-0.6103	-0.7609	0.6091	0.1984	0.7301	0.6867	-1.1718	-0.2596	0.6204	-0.2696	0.0194	0.5653	0.0977	0.4041	-20.8577	30.932	-13.2026
37	6.4603	-3.255	-3.491	7.898	0.7971	5.8939	-0.192	0.2292	-0.5746	0.1296	0.263	0.0156	1.2989	-0.1648	0.0003	0.4796	-0.107	-0.0474	0.3305	-0.0615	0.2423	-15.7215	31.6057	-27.4025
38	1.245	0.9697	-1.4269	6.9727	-1.5372	1.6613	0.2091	-0.4051	-0.3021	0.1444	0.0078	0.7586	0.3551	-0.5734	-0.2045	0.227	-0.8229	-0.1857	1.2458	0.1141	0.4465	-34.7205	32.5689	-26.1232
39	8.1398	4.448	7.9492	2.7874	4.3939	8.142	-0.0984	0.1427	0.0833	-0.1232	0.0931	0.0588	-0.0787	-0.2408	0.0855	0.1563	-0.0367	-0.0045	0.2607	0.0218	0.1395	-15.0957	47.1622	-23.2451
40	3.8162	4.6875	0.6744	7.2892	0.5538	0.1631	-0.1852	0.4364	0.6488	-0.2077	0.0699	1.0919	0.1426	-1.2061	0.1408	0.3669	-0.3707	-0.0231	1.0351	-0.0319	0.3636	-32.577	36.6736	-33.8934
41	2.8269	1.2628	-0.3247	3.4696	-2.4859	5.8399	-0.2518	-0.1101	0.0535	0.1968	0.1669	-0.0145	-0.4664	-0.182	0.1015	0.3288	0.0043	-0.0686	0.2596	-0.0257	0.1529	5.935	59.5552	88.704
42	4.3352	-4.2567	5.6003	5.0558	-5.3479	7.2527	-0.7433	-0.7009	1.0511	0.6766	0.3063	0.5282	-0.8585	-0.1313	0.3489	0.8737	0.0993	-0.0521	0.4005	-0.0179	0.3647	-1.8089	73.2252	73.9618
43	4.3447	-4.0958	4.498	8.5005	-4.733	4.6721	-0.0098	0.3098	0.0355	-0.3642	-0.0419	-0.4285	0.2211	0.5329	0.0587	0.2885	-0.0009	-0.0194	0.2881	-0.0187	0.1494	6.0477	58.299	75.9023
44	7.413	-1.7363	7.2901	0.3552	-1.6579	6.999	0.5794	-0.3916	-0.8367	-0.2582	0.1323	0.2511	1.2794	-0.4315	-0.5251	0.4288	-0.0469	-0.0422	0.253	0.0336	0.2529	-5.5847	51.3974	73.4632
45	5.0933	-5.3907	-1.2098	8.4265	0.2124	7.6309	0.1488	-0.4306	0.2006	0.3538	-0.3694	0.2469	-0.7613	-0.5522	0.1644	0.2828	0.0435	-0.0573	0.357	-0.0723	0.1969	-2.6495	63.7243	83.3233
46	3.9367	-0.9237	-5.9285	2.0643	1.5764	8.9513	-0.0897	0.1709	-0.7078	-0.2209	-0.0655	-0.019	0.6372	-0.1285	0.086	0.331	0.0137	0.0021	0.2421	0.0138	0.2779	6.2797	46.8695	86.6486
47	2.1325	-3.3346	4.3195	5.5536	-6.841	8.6284	-0.3824	-0.1322	0.158	0.3153	0.0013	-0.3174	-0.6478	-0.1975	0.3871	0.3075	0.0128	-0.0631	0.2029	0.0101	0.2168	7.844	63.3569	75.9983
48	2.6021	-1.5879	2.314	4.6298	-4.6221	7.6039	-0.064	-0.05	-0.073	0.6041	-0.4023	-0.139	-0.5723	0.7865	0.5921	0.3117	0.02	-0.059	0.1991	-0.0181	0.2093	10.6483	60.7438	80.7903

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 52 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 53 through 94 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 95 through 117 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 118 through 132 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 133 through 167 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 168 through 201 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 202 through 216 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 17 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 18 through 52 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 53 through 67 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 68 through 91 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 92 through 140 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 141 through 181 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 182 through 209 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 210 through 221 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 36 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 37 through 52 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 53 through 117 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 118 through 132 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 133 through 178 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 179 through 216 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 1 through 17 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 18 through 44 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 45 through 60 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 61 through 83 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 84 through 98 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 99 through 140 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 141 through 194 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 195 through 209 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 210 through 221 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 32 through 40 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 41 through 55 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 56 through 63 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 64 through 82 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 83 through 94 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 95 through 110 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 111 through 118 )
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 119 through 136 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 137 through 148 )
41	X-RAY DIFFRACTION	41	chain 'J' and (resid 34 through 55 )
42	X-RAY DIFFRACTION	42	chain 'J' and (resid 56 through 63 )
43	X-RAY DIFFRACTION	43	chain 'J' and (resid 64 through 82 )
44	X-RAY DIFFRACTION	44	chain 'J' and (resid 83 through 94 )
45	X-RAY DIFFRACTION	45	chain 'J' and (resid 95 through 110 )
46	X-RAY DIFFRACTION	46	chain 'J' and (resid 111 through 118 )
47	X-RAY DIFFRACTION	47	chain 'J' and (resid 119 through 128 )
48	X-RAY DIFFRACTION	48	chain 'J' and (resid 129 through 147 )

-
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