PDB-6oao: Structure of DBP in complex with human neutralizing antibody 092096

ID or keywords:

Entry

Database: PDB / ID: 6oao

Title

Structure of DBP in complex with human neutralizing antibody 092096

Components

Antibody 092096 single chain variable fragment
Duffy binding surface protein region II

Keywords

CELL INVASION /

Plasmodium / vivax / Duffy Binding Protein / DBP / PvDBP /

antibody /

neutralizing /

inhibition /

malaria / invasion / blocking /

vaccine / structural vaccinology

Function / homology

Function and homology information

host cell surface receptor binding /

membrane / identical protein binding
Similarity search - Function

Biological species

Plasmodium vivax (malaria parasite P. vivax)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.497 Å

Authors

Urusova, D. / Tolia, N.H.

Funding support

United States, 4items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	Intramural Research Program	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R56 AI080792	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201400018C	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01 AI064478	United States

Citation

Journal: Nat Microbiol / Year: 2019
Title: Structural basis for neutralization of Plasmodium vivax by naturally acquired human antibodies that target DBP.
Authors: Urusova, D. / Carias, L. / Huang, Y. / Nicolete, V.C. / Popovici, J. / Roesch, C. / Salinas, N.D. / Witkowski, B. / Ferreira, M.U. / Adams, J.H. / Gross, M.L. / King, C.L. / Tolia, N.H.

History

Deposition	Mar 18, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2019	Provider: repository / Type: Initial release
Revision 1.1	Sep 4, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6oao.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb6oao.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	6oao.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oa/6oao ftp://data.pdbj.org/pub/pdb/validation_reports/oa/6oao	HTTPS FTP

-
Related structure data

Related structure data	6oanC 4nuvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1t5o-2 4h1l-1 1t5o-1 6p8s-d 6iid-2 3wdi-d 5sy5-3 6m4w-1 5lkb-d 5sy5-1 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) 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

6oanC

4nuvS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
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) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1)

Deposited unit

A: Duffy binding surface protein region II

B: Antibody 092096 single chain variable fragment

C: Duffy binding surface protein region II

D: Antibody 092096 single chain variable fragment

E: Duffy binding surface protein region II

F: Antibody 092096 single chain variable fragment

G: Duffy binding surface protein region II

H: Antibody 092096 single chain variable fragment

I: Duffy binding surface protein region II

J: Antibody 092096 single chain variable fragment

K: Duffy binding surface protein region II

L: Antibody 092096 single chain variable fragment

hetero molecules

382 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Duffy binding surface protein region II

B: Antibody 092096 single chain variable fragment

defined by author
Evidence: gel filtration
63.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Duffy binding surface protein region II

D: Antibody 092096 single chain variable fragment

defined by author
Evidence: gel filtration
63.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Duffy binding surface protein region II

F: Antibody 092096 single chain variable fragment

hetero molecules

defined by author
Evidence: gel filtration
63.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Duffy binding surface protein region II

H: Antibody 092096 single chain variable fragment

defined by author
Evidence: gel filtration
63.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Duffy binding surface protein region II

J: Antibody 092096 single chain variable fragment

defined by author
Evidence: gel filtration
63.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Duffy binding surface protein region II

L: Antibody 092096 single chain variable fragment

defined by author
Evidence: gel filtration
63.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	130.658, 89.563, 193.705
Angle α, β, γ (deg.)	90.00, 108.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Duffy binding surface protein region II Mass: 37451.898 Da / Num. of mol.: 6 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Production host: Escherichia coli (E. coli) / References: UniProt: B7T089, UniProt: P22290*PLUS
#2: Antibody	Antibody 092096 single chain variable fragment Mass: 26245.713 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.07 Å³/Da / Density % sol: 59.92 %
Crystal grow	Temperature: 290 K / Method: evaporation / pH: 6 / Details: 12% w/v PEG 6,000, 0.1 M MES, pH 6.0

-
Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 3.497→19.971 Å / Num. obs: 53871 / % possible obs: 92.6 % / Redundancy: 1.66 % / R_merge(I) obs: 0.132 / Net I/σ(I): 4.91
Reflection shell	Resolution: 3.497→3.7 Å / R_merge(I) obs: 0.63 / Num. unique obs: 11515

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4NUV

4nuv

Resolution: 3.497→19.971 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.32

	R_factor	Num. reflection	% reflection
R_free	0.2789	2787	5.18 %
R_work	0.2375	-	-
obs	0.2396	53786	99.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.497→19.971 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24623	0	5	20	24648

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	25173
X-RAY DIFFRACTION	f_angle_d	0.777	33995
X-RAY DIFFRACTION	f_dihedral_angle_d	13.232	15177
X-RAY DIFFRACTION	f_chiral_restr	0.045	3599
X-RAY DIFFRACTION	f_plane_restr	0.005	4357

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 (%)
3.4975-3.5575	0.3636	123	0.3134	2454	X-RAY DIFFRACTION	96
3.5575-3.6218	0.3412	156	0.2981	2519	X-RAY DIFFRACTION	100
3.6218-3.691	0.3102	141	0.299	2534	X-RAY DIFFRACTION	100
3.691-3.7659	0.2963	131	0.2788	2529	X-RAY DIFFRACTION	100
3.7659-3.8472	0.3124	139	0.2719	2544	X-RAY DIFFRACTION	100
3.8472-3.936	0.2912	136	0.2827	2552	X-RAY DIFFRACTION	100
3.936-4.0337	0.3287	137	0.2639	2532	X-RAY DIFFRACTION	100
4.0337-4.1418	0.3123	125	0.2597	2535	X-RAY DIFFRACTION	100
4.1418-4.2625	0.2358	148	0.2385	2578	X-RAY DIFFRACTION	100
4.2625-4.3987	0.2806	163	0.2415	2500	X-RAY DIFFRACTION	100
4.3987-4.5541	0.2779	165	0.2218	2510	X-RAY DIFFRACTION	100
4.5541-4.7341	0.2949	127	0.2155	2585	X-RAY DIFFRACTION	100
4.7341-4.9465	0.2541	139	0.2053	2559	X-RAY DIFFRACTION	100
4.9465-5.2029	0.2616	142	0.213	2537	X-RAY DIFFRACTION	100
5.2029-5.5224	0.2433	136	0.2238	2566	X-RAY DIFFRACTION	100
5.5224-5.9384	0.2923	128	0.2253	2577	X-RAY DIFFRACTION	100
5.9384-6.5171	0.2916	150	0.2449	2559	X-RAY DIFFRACTION	100
6.5171-7.4175	0.2518	122	0.2373	2597	X-RAY DIFFRACTION	100
7.4175-9.1911	0.2375	132	0.2039	2588	X-RAY DIFFRACTION	99
9.1911-19.9712	0.2623	147	0.2071	2644	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	2.3766	-0.8491	-0.1963	2.6868	-0.5549	2.631	-0.5318	0.8532	0.0711	-0.9849	0.0012	-0.558	0.8978	-0.979	0.2521	1.3539	-0.2248	0.1855	1.204	-0.1384	0.5844	-6.3329	-15.9484	17.0348
2	1.9477	-1.498	-1.0924	3.1032	-1.0257	1.4604	0.02	0.7377	0.4099	-0.5113	-0.2034	-0.3495	0.2252	0.0169	0.2339	0.9643	-0.0582	0.14	0.8082	0.0551	0.5392	6.0945	-4.5868	20.5876
3	3.4641	-1.154	-0.5269	3.0064	-0.1004	1.5131	0.3656	-0.1523	-0.0739	-1.1017	0.1961	0.2915	0.5578	-0.6468	0.0716	1.0103	-0.0165	0.1409	0.8188	0.0452	0.3891	-7.1853	-3.24	24.2541
4	2.6772	-0.9169	0.5004	4.113	-1.1547	1.4491	0.0782	0.5086	-0.289	-0.371	-0.1617	0.0673	0.112	0.0493	0.1995	0.9082	-0.0833	0.1505	0.782	0.0223	0.5191	4.4545	-3.4577	28.705
5	4.8237	0.0229	0.72	2.2062	0.389	0.2692	-0.4515	1.3275	1.018	-0.5065	-0.0148	0.3532	0.0448	0.2287	0.1645	0.9837	-0.1436	-0.0425	0.8165	0.1245	0.6509	-19.2538	-15.5363	24.2452
6	5.2544	-0.2523	0.4656	1.1422	0.2116	0.5566	0.4696	1.0465	-1.1935	-1.1152	0.3657	1.7159	0.8414	0.0466	0.0662	1.1057	0.0507	-0.0747	1.4283	-0.0411	1.2789	-43.1729	-28.6125	16.2523
7	4.6207	0.672	0.4258	1.4248	0.0116	0.0369	-0.2548	0.3857	-0.1531	0.0153	0.0841	0.1416	-0.0676	-0.1049	0.0549	0.9924	-0.0993	0.0377	0.6494	0.1061	0.52	-15.4834	-20.5867	31.3392
8	5.4145	-1.186	-0.1241	2.8159	-0.0478	2.4923	0.0188	-0.2912	-0.4913	-0.6693	0.0461	-0.261	0.1481	-0.9931	0.0242	1.0147	-0.172	0.1484	0.7573	0.1432	0.6439	-29.1697	-25.6122	28.5264
9	7.4397	4.4735	-3.183	4.6313	-1.3598	2.6143	-0.8529	0.4883	2.2466	-1.8058	0.5671	0.5751	-0.7212	0.2974	0.2569	1.5378	-0.0095	0.1597	0.8493	0.3873	1.1408	7.9796	35.3135	19.6153
10	2.845	-0.0767	-0.6211	2.7604	0.5219	4.842	0.1414	0.1705	-0.153	0.547	-0.4859	-0.4776	-1.2872	0.8329	0.0568	1.1078	-0.5111	0.0021	1.1283	0.2866	0.6634	4.3897	25.0927	22.851
11	2.8424	0.3034	0.791	1.9618	1.2691	0.8122	0.3272	0.3861	0.9989	0.1545	0.6126	0.075	0.4133	1.0615	-0.4177	1.1502	-0.3543	0.1831	1.2069	0.1627	0.8884	16.0873	21.2499	20.6852
12	1.4923	0.4827	0.3358	1.8831	0.1607	3.474	0.2314	0.5439	0.3272	0.2229	0.0149	-0.3348	-1.0478	0.7169	-0.0993	1.2728	-0.1733	0.0533	0.9884	0.1454	0.6966	9.2787	26.2434	20.5564
13	0.5887	1.6004	0.9323	4.1823	-1.3748	3.3426	0.1396	0.9181	0.3308	-1.3637	-0.1766	-0.4683	0.2401	0.5534	0.0457	1.3735	-0.1659	0.2003	1.3982	0.1697	0.6048	7.9155	13.6881	3.3887
14	-0.0998	-0.6799	0.1305	6.405	0.1764	0.0394	-0.2861	1.1872	0.4424	-0.228	-0.2122	-0.1394	-0.3176	0.1517	0.2042	1.8509	-0.0257	0.0721	1.3565	0.3351	0.7304	2.6596	16.4687	-4.2061
15	1.7878	-0.4824	0.4456	0.73	0.6202	1.7084	-0.17	0.1698	0.451	-0.4909	-0.0756	-0.1523	-0.1243	0.0062	0.0573	1.1141	-0.2339	0.2059	1.4001	0.2517	0.8271	13.9275	15.9985	8.1272
16	3.8329	1.8445	0.4048	1.5077	0.0987	3.1486	-0.2105	-0.0315	0.4256	0.4096	-0.1633	-0.1334	-0.7143	0.4367	0.3664	1.0837	0.0709	-0.1064	0.4666	0.0762	0.9708	-10.2858	29.8122	52.5331
17	5.0948	1.6946	-3.6133	2.3881	-1.023	7.3261	0.0852	0.299	0.4718	-0.0284	-0.0594	0.0295	-0.3394	0.0546	-0.0695	0.5064	0.0323	-0.0373	0.3353	0.0383	0.6197	-6.4467	20.6567	56.2915
18	6.2422	0.2578	-0.6389	1.6388	-0.6356	0.6571	0.1725	0.2092	-0.1591	0.0948	-0.2295	0.5597	0.026	-0.1278	0.0654	0.9116	0.0009	-0.0867	0.5599	-0.0971	0.7496	-33.9687	15.8785	45.9732
19	1.9895	-0.0522	4.7667	3.6453	1.1272	7.7578	-0.398	-0.4655	0.4245	1.2388	0.2165	-0.2999	-0.1347	0.89	-0.0862	1.0171	0.0306	-0.0061	0.8537	0.0123	0.4824	14.2203	16.455	89.1399
20	9.806	-1.2233	3.4943	5.4666	0.2521	7.8771	0.1696	0.4455	-0.7384	0.8019	-0.0164	0.1553	-0.0756	0.6589	-0.0426	0.6739	0.0627	0.0304	0.4688	-0.043	0.3762	7.2541	15.3406	80.2321
21	3.715	-2.1461	-0.1431	1.9368	1.0005	2.7883	-0.2344	0.1688	0.4483	-0.089	0.3882	-0.3504	-0.2242	0.7095	-0.2057	0.6554	-0.0889	0.0384	0.6548	-0.0007	0.6773	12.4712	20.7159	78.7011
22	1.447	-0.8698	0.5988	-0.0183	0.3777	4.0953	-0.5149	-0.3544	0.3736	-0.4323	0.6477	-0.0279	-1.0041	0.7067	-0.2265	1.126	-0.1228	-0.0066	0.6758	-0.1339	0.8272	2.8098	42.4268	83.7952
23	6.0911	-1.453	0.1612	4.8001	3.1026	4.8366	0.1837	0.3349	0.2745	-0.4498	-0.1584	0.0123	-1.3585	-0.1084	0.013	0.6739	-0.1241	-0.0039	0.4675	0.0149	0.533	-2.867	34.4625	77.5126
24	0.8974	0.6536	1.4675	3.5766	2.5746	4.1176	0.4196	-0.1982	0.5596	0.6833	0.0295	-0.8071	-0.7647	-0.2345	-0.0899	1.1041	-0.0135	-0.0305	0.5236	0.0031	0.6241	-0.9053	36.146	84.1826
25	4.3963	-1.1321	-0.0267	3.6985	2.2214	3.1525	0.0201	0.1065	0.145	-0.1317	0.1818	-1.1611	-1.3111	0.7385	-0.5494	1.0915	-0.1574	-0.0839	0.6226	-0.0599	0.8519	7.8705	35.5701	77.4931
26	4.1919	-2.0935	-0.3998	6.5792	1.5173	6.18	-0.226	-0.6697	-0.7715	-0.1918	0.316	0.4149	1.1151	1.0671	-0.2439	0.8025	0.2401	-0.0886	0.75	0.2235	0.7108	-4.066	-23.1801	76.0848
27	8.196	-1.057	0.2805	2.228	4.0099	5.2179	-0.1263	-0.1467	0.5369	0.1461	0.3502	-0.8541	-0.4364	1.0378	-0.2962	0.6509	0.1112	-0.0493	0.6144	0.16	0.676	8.8436	-14.5932	71.5323
28	5.0541	2.0873	1.7705	5.7475	5.2824	6.127	0.1515	-0.3052	0.1419	0.4976	0.0452	-0.2174	0.2167	0.248	-0.2017	0.5435	0.1148	0.041	0.5348	0.0813	0.477	5.1089	-17.1857	66.8373
29	1.0621	-1.6751	0.4601	0.31	0.3198	1.3917	0.0315	-0.0782	-0.2205	-0.0988	-0.0421	-0.0257	0.197	0.3324	0.0162	0.5299	0.0204	0.0178	0.5052	-0.0167	0.4685	-2.5088	-16.4669	61.9166
30	7.7143	2.5677	4.9918	6.1557	1.7015	4.0395	-0.4272	-0.7586	1.6263	0.455	0.3362	-0.797	0.0982	-0.1418	0.0382	0.8902	-0.2389	-0.0761	1.1641	-0.1172	1.3164	-41.4199	-34.1994	77.0057
31	4.4264	3.0479	-0.2634	3.8553	-0.4366	2.7662	0.2083	0.0287	0.2082	0.0295	0.0728	0.8562	0.1709	-0.3267	-0.3308	0.3548	0.0891	0.0565	0.4695	-0.0204	0.6896	-21.9716	-14.2153	70.9909
32	7.6079	-1.0858	-0.4185	3.0544	0.4152	4.3338	0.3995	0.0913	0.2989	-0.7168	-0.4596	-0.6659	0.2554	1.0508	0.0754	0.7251	0.157	0.2342	0.7372	0.1454	0.8097	25.3636	-27.3539	43.5449
33	6.448	-0.1033	0.1894	4.6663	-1.4116	1.4324	-0.6214	-0.2813	-0.3414	-0.3414	-0.5037	-1.9106	0.6066	0.8919	1.1987	0.9867	0.1749	0.5253	1.3016	0.4447	1.5149	31.6358	-24.4487	42.5621
34	2.1246	-0.8899	1.7863	0.7522	-0.844	1.7695	0.3141	-0.4894	-0.2472	-0.9802	0.094	-1.6747	0.3911	-0.4808	-0.1073	0.6338	0.286	0.497	0.896	0.1232	1.0718	23.0419	-30.2496	48.181
35	2.0335	0.8742	-0.9553	-0.3205	0.1944	1.7616	0.2629	-0.643	-0.754	0.3666	-0.5284	-1.3816	0.5975	0.7526	0.2854	0.961	0.319	-0.1576	0.9024	0.1447	1.1633	28.7946	-36.9976	65.8704
36	4.3279	-2.1217	5.3852	8.8718	-1.964	7.8474	0.1375	-0.1466	-0.651	-0.0591	0.34	-0.2491	0.2169	0.4702	-0.4647	0.4977	0.153	0.1438	0.7747	0.1232	0.7459	19.1663	-38.583	61.0425
37	2.0257	-0.9587	1.5793	0.759	-0.2195	3.4512	-0.1017	0.6442	0.3206	-1.0481	-0.2224	-0.1274	1.0082	0.6154	0.2103	0.8336	0.1384	0.2819	0.9441	0.1648	0.982	24.4031	-41.6501	59.3985
38	3.8333	2.6151	0.9958	2.338	-0.8736	3.0267	-0.5063	-0.6735	0.2325	-0.5431	0.4259	-1.9477	0.0598	0.1465	0.6272	0.5884	0.1614	0.0414	1.0418	0.1972	1.2368	29.9428	-31.9702	59.9715
39	4.9596	-0.8987	2.0733	0.49	1.3722	2.2787	-0.1937	0.2738	-0.4558	-0.013	0.2358	-0.1096	-0.0595	0.5181	-0.0283	1.2225	-0.0503	-0.1992	0.893	0.0595	0.4831	-66.7747	-8.2983	19.5435
40	4.5571	-2.4164	-1.7348	3.8025	1.3675	1.1027	0.2783	0.5757	-0.3178	-0.6242	-0.282	0.1428	-0.2967	0.0342	0.0081	0.9551	-0.0353	-0.0775	0.7068	-0.0153	0.4106	-63.0044	-18.0979	22.0413
41	4.6995	-2.6909	-0.8296	5.2054	1.4214	0.9058	-0.0002	0.2724	0.2358	-0.3665	-0.0846	0.0171	-0.5156	0.177	0.1189	0.8053	-0.1512	-0.173	0.6462	-0.0072	0.4421	-69.9107	-16.4067	28.744
42	6.7785	0.6177	-1.3434	1.0765	-0.0398	0.6799	-0.0725	0.2304	0.2195	0.0103	-0.0512	-0.2126	-0.1335	0.2026	0.0791	0.8495	-0.1557	-0.0209	0.592	-0.005	0.4319	-43.5183	1.1639	27.4409
43	7.2534	0.6978	2.6312	2.3087	-1.8513	1.7392	0.0689	0.912	-1.7797	-0.3812	0.159	-0.25	0.6792	-0.0637	-0.2441	1.441	-0.1661	-0.1351	0.9215	-0.3505	0.7885	-69.094	-50.199	22.1125
44	5.8032	-1.1759	3.0243	0.6621	-1.3364	2.8569	0.1491	1.3238	-1.9945	-0.9472	0.9299	0.0265	0.402	0.0585	-0.1408	1.0496	-0.6177	-0.1327	1.2603	-0.4635	0.8075	-77.927	-44.2457	15.0564
45	2.3948	1.1113	0.1871	1.8945	-2.1011	3.7806	-0.0858	0.181	-0.0719	-0.2184	-0.021	0.4382	0.8562	-0.8064	0.0306	1.1356	-0.1497	-0.0677	0.8136	-0.1343	0.6818	-76.6733	-44.1842	21.8027
46	2.1211	1.3018	0.4579	4.1744	2.7291	5.1537	0.0252	1.4273	-0.277	-1.3926	-0.2652	0.6698	-0.7299	-0.3433	0.1663	1.1911	-0.026	-0.1925	1.1147	-0.1069	0.669	-73.2822	-33.2305	3.1183
47	1.225	1.571	2.1067	4.6953	3.9796	3.4993	-0.483	1.1197	-0.3391	-1.1214	0.2622	0.2155	1.0671	-0.2311	-0.0257	1.4978	0.0291	-0.2198	1.0936	-0.0974	0.8708	-71.7045	-37.7619	1.6775
48	1.6554	0.6344	0.438	3.5241	2.6585	4.6107	0.0016	1.2128	0.3754	-1.2517	-0.6997	1.1987	-0.2977	-1.6008	0.6224	0.8258	-0.1551	-0.0745	1.4089	-0.1848	0.9515	-80.7127	-36.1463	8.0507
49	2.8234	-0.8596	-0.0096	2.557	0.401	6.0178	-0.0365	0.1552	0.0451	-0.4335	-0.4379	-0.2693	0.1907	-0.2935	0.5357	0.8652	0.0787	0.093	0.5171	0.0025	1.0507	-44.0391	-49.626	51.8728
50	3.9493	1.0541	-2.7792	1.5928	0.3798	3.4323	-0.1589	-0.2082	-0.1443	-0.7135	0.2099	0.5145	0.6684	0.2469	0.1833	0.973	0.0926	-0.0085	0.4674	0.0243	0.7419	-52.7545	-49.2165	52.0984
51	4.4626	1.7291	0.7006	3.3646	3.7198	2.149	-0.2014	-0.6327	0.1719	1.7546	-1.402	0.6613	0.8493	-1.2255	1.6868	1.0912	-0.1609	0.1619	1.0829	-0.0881	1.0905	-74.5028	-50.9246	53.7767
52	5.7845	-0.3452	-1.2683	2.3991	1.5911	5.2161	0.2799	-0.1696	-0.7074	0.6392	-0.332	-0.1008	0.1414	0.1107	0.1032	0.6984	-0.0284	-0.0631	0.3421	0.1059	0.6172	-54.8841	-41.8806	60.2454
53	3.2885	2.28	1.2021	0.3925	0.323	3.9715	0.0571	0.534	-0.6115	-0.0971	0.0286	-0.2186	0.2795	0.11	0.0377	0.5517	0.1147	0.0338	0.5195	-0.0608	0.6526	-65.0216	-43.6174	47.5239
54	1.8124	-0.6743	-2.0872	0.0762	0.7884	1.3847	-0.1174	-0.1953	-0.3371	-0.2799	-0.0808	0.0654	0.1463	0.0479	0.178	0.7373	-0.0299	0.0599	0.4873	0.015	0.7279	-45.044	-35.8834	57.7796
55	2.4584	2.3754	1.5705	4.421	3.3621	2.7106	-0.1162	1.2697	1.4816	-0.1712	0.1387	-1.2933	-0.2376	0.7012	-1.0074	0.5969	0.0296	0.1266	0.911	0.2151	1.3314	-7.0367	-38.102	50.7537
56	7.9754	1.5906	1.1531	3.7391	-0.6836	4.8221	-0.042	0.598	0.1913	-0.1339	-0.029	-0.7954	-0.2172	0.1406	-0.0071	0.6188	0.0389	0.0631	0.3666	0.0235	0.5439	-34.4396	-34.7673	42.8653
57	5.3572	-1.382	-0.8657	6.4263	1.9341	6.5577	0.129	-0.6045	0.335	1.3282	0.0028	0.5051	-0.4634	-0.612	-0.0389	0.8568	-0.0597	0.0029	0.6303	0.1087	0.4665	-75.3543	-33.3493	85.2292
58	4.6295	-0.6485	1.1446	6.5025	3.5353	2.3459	-0.2949	-1.0263	-0.3447	0.9574	-0.1911	0.5583	0.793	-0.3216	0.003	0.6155	-0.1553	-0.1118	0.8135	0.1156	0.5667	-76.8478	-45.2612	81.6657
59	7.4595	0.2841	0.4127	5.736	-0.439	4.3248	-0.0169	2.1756	-0.7257	-1.7066	0.2545	-0.5175	0.2255	-0.5289	-0.5414	0.6581	-0.1398	-0.0192	1.109	-0.1074	0.8355	-76.806	-37.2641	68.9732
60	4.7778	-2.1468	1.0891	6.2644	-0.3828	3.5879	0.3268	-0.5514	-0.5967	0.1714	-0.0146	0.7125	0.2112	-1.0367	-0.2434	0.6767	-0.0926	0.043	0.6526	0.0387	0.5234	-78.1572	-39.444	80.9329
61	4.7932	-1.3279	-1.7287	5.3632	-0.4462	2.9366	0.7749	-1.2304	-2.8325	-0.1031	-0.1965	0.4313	2.0795	-0.9706	0.0234	1.2342	-0.2437	-0.0825	0.8928	0.3494	1.1302	-67.8267	-62.8806	83.9504
62	5.3483	0.8564	-0.239	8.411	-1.9354	8.4998	0.6014	-0.4414	-1.0787	-0.1491	-0.3876	-0.6553	1.7332	-0.1634	-0.1701	0.6866	-0.103	-0.1125	0.4963	0.0815	0.8271	-62.8045	-54.2431	77.6993
63	1.555	2.4916	-3.0057	7.0915	-2.615	6.7643	-0.4217	-1.1694	-1.3341	0.955	0.3756	-0.8428	0.5211	-0.1704	-0.1334	0.8659	-0.0956	0.0081	0.5096	0.1097	0.9734	-64.8931	-55.7602	84.4851
64	5.2784	1.0472	-0.3682	7.031	-2.1127	6.0332	0.1052	-0.4042	-0.8245	-0.1916	0.1523	0.5959	1.7735	-1.183	-0.6549	0.7767	-0.2141	0.1096	0.818	0.1882	0.8419	-73.5633	-55.071	77.8358
65	5.2567	-0.7112	-0.6243	6.048	-0.7051	5.7517	-0.1365	-0.7322	0.911	-0.451	0.1653	-0.1359	-1.7708	-0.9137	-0.0685	1.1343	0.3742	0.0384	0.8287	-0.1607	0.6718	-61.7072	3.2457	76.2187
66	5.3369	-2.3967	-1.2357	3.3346	-2.7459	5.8712	-0.03	-0.001	-0.1215	0.2009	0.2012	0.153	-0.3729	-0.6028	-0.1837	0.6308	0.088	-0.05	0.4188	-0.1469	0.4772	-71.1643	-1.3131	66.1686
67	2.7883	-0.0825	-0.6394	3.9601	-2.1706	3.3502	-0.1716	-0.4532	-0.1646	0.329	0.0149	0.0037	-0.1218	0.1552	0.1847	0.4527	0.0417	-0.0681	0.571	-0.0543	0.4676	-72.423	-7.8868	62.9328
68	6.9213	4.1534	0.549	4.5816	0.6956	3.1074	0.1304	-0.0781	0.4195	0.0551	0.0313	-0.4702	-0.197	0.4091	-0.1583	0.427	0.1126	0.004	0.4415	0.0071	0.5843	-42.53	-1.6783	71.1
69	4.7762	-1.8259	-1.2909	3.694	-0.6404	3.9594	0.1188	0.2326	0.1741	-0.8087	-0.4775	0.7812	-0.9529	-1.1077	0.3802	0.7258	0.154	-0.3075	0.8449	-0.1968	0.8889	-91.0463	8.6458	43.0187
70	2.8849	-0.4497	0.932	1.9654	1.3262	3.9314	-0.3117	0.1164	-0.408	-0.6405	-0.3788	1.451	0.0588	-1.3747	0.7926	0.88	0.1511	-0.3978	1.0224	-0.3074	1.1455	-93.0583	5.6368	45.2959
71	4.032	-2.1977	-0.0186	4.2678	-0.3695	3.939	-0.5107	-1.663	1.3705	0.5791	-0.7021	2.0939	0.3246	-0.7437	0.5089	1.002	0.3513	-0.0657	0.9385	-0.2691	1.284	-95.7797	21.9783	63.9014
72	4.2667	-2.7504	-1.0466	8.2372	1.4961	4.5153	-0.2224	-0.2768	0.4025	0.0134	0.1703	0.9035	0.2075	-0.6615	0.2381	0.3741	-0.0415	-0.1345	0.6434	-0.0882	0.7407	-85.971	16.1765	62.3719
73	4.8243	-3.7439	-0.7022	3.0913	0.2027	2.7392	-0.5158	0.5025	0.3318	-1.4113	0.4481	1.4403	-0.5711	-0.6634	0.1898	0.6557	0.0454	-0.229	0.8341	-0.1212	0.7256	-89.9584	21.5199	59.6928
74	3.4475	-1.5605	-0.2625	3.2392	1.5371	2.7991	-0.2276	-0.4671	-0.6641	-0.0917	0.0014	1.7234	0.0239	-0.7615	0.5437	0.5785	-0.0052	-0.0427	0.9307	-0.2073	1.3203	-95.4539	12.0452	60.0397

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 216 through 235 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 236 through 290 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 291 through 314 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 315 through 387 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 388 through 415 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 416 through 429 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 430 through 486 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 487 through 508 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 5 through 21 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 22 through 43 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 44 through 71 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 72 through 121 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 122 through 214 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 215 through 229 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 230 through 252 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 216 through 271 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 272 through 387 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 388 through 508 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 5 through 21 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 22 through 43 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 44 through 121 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 122 through 167 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 168 through 220 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 221 through 237 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 238 through 252 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 215 through 234 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 235 through 270 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 271 through 336 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 337 through 415 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 416 through 429 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 430 through 508 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 5 through 63 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 64 through 101 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 102 through 124 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 125 through 177 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 178 through 220 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 221 through 237 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 238 through 252 )
39	X-RAY DIFFRACTION	39	chain 'G' and (resid 216 through 270 )
40	X-RAY DIFFRACTION	40	chain 'G' and (resid 271 through 314 )
41	X-RAY DIFFRACTION	41	chain 'G' and (resid 315 through 387 )
42	X-RAY DIFFRACTION	42	chain 'G' and (resid 388 through 508 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 3 through 35 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 36 through 53 )
45	X-RAY DIFFRACTION	45	chain 'H' and (resid 54 through 121 )
46	X-RAY DIFFRACTION	46	chain 'H' and (resid 122 through 220 )
47	X-RAY DIFFRACTION	47	chain 'H' and (resid 221 through 237 )
48	X-RAY DIFFRACTION	48	chain 'H' and (resid 238 through 252 )
49	X-RAY DIFFRACTION	49	chain 'I' and (resid 216 through 235 )
50	X-RAY DIFFRACTION	50	chain 'I' and (resid 236 through 251 )
51	X-RAY DIFFRACTION	51	chain 'I' and (resid 252 through 270 )
52	X-RAY DIFFRACTION	52	chain 'I' and (resid 271 through 314 )
53	X-RAY DIFFRACTION	53	chain 'I' and (resid 315 through 361 )
54	X-RAY DIFFRACTION	54	chain 'I' and (resid 362 through 415 )
55	X-RAY DIFFRACTION	55	chain 'I' and (resid 416 through 429 )
56	X-RAY DIFFRACTION	56	chain 'I' and (resid 430 through 508 )
57	X-RAY DIFFRACTION	57	chain 'J' and (resid 5 through 35 )
58	X-RAY DIFFRACTION	58	chain 'J' and (resid 36 through 53 )
59	X-RAY DIFFRACTION	59	chain 'J' and (resid 54 through 65 )
60	X-RAY DIFFRACTION	60	chain 'J' and (resid 66 through 123 )
61	X-RAY DIFFRACTION	61	chain 'J' and (resid 124 through 167 )
62	X-RAY DIFFRACTION	62	chain 'J' and (resid 168 through 220 )
63	X-RAY DIFFRACTION	63	chain 'J' and (resid 221 through 237 )
64	X-RAY DIFFRACTION	64	chain 'J' and (resid 238 through 252 )
65	X-RAY DIFFRACTION	65	chain 'K' and (resid 215 through 234 )
66	X-RAY DIFFRACTION	66	chain 'K' and (resid 235 through 314 )
67	X-RAY DIFFRACTION	67	chain 'K' and (resid 315 through 387 )
68	X-RAY DIFFRACTION	68	chain 'K' and (resid 388 through 508 )
69	X-RAY DIFFRACTION	69	chain 'L' and (resid 5 through 58 )
70	X-RAY DIFFRACTION	70	chain 'L' and (resid 59 through 121 )
71	X-RAY DIFFRACTION	71	chain 'L' and (resid 122 through 167 )
72	X-RAY DIFFRACTION	72	chain 'L' and (resid 168 through 220 )
73	X-RAY DIFFRACTION	73	chain 'L' and (resid 221 through 237 )
74	X-RAY DIFFRACTION	74	chain 'L' and (resid 238 through 252 )

-
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