PDB-4nrz: Crystal Structure of HIV-1 Neutralizing Antibody m66.6

ID or keywords:

Entry

Database: PDB / ID: 4nrz

Title

Crystal Structure of HIV-1 Neutralizing Antibody m66.6

Components

M66.6 HEAVY CHAIN
M66.6 LIGHT CHAIN

Keywords

IMMUNE SYSTEM / Immunoglobulin / Neutralizing Antibody / HIV-1 gp41 / Membrane Proximal External Region / MPER

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.42 Å

Authors

Ofek, G. / Yang, Y. / Kwong, P.D.

Citation

Journal: J.Virol. / Year: 2014
Title: Structural Basis for HIV-1 Neutralization by 2F5-Like Antibodies m66 and m66.6.
Authors: Ofek, G. / Zirkle, B. / Yang, Y. / Zhu, Z. / McKee, K. / Zhang, B. / Chuang, G.Y. / Georgiev, I.S. / O'Dell, S. / Doria-Rose, N. / Mascola, J.R. / Dimitrov, D.S. / Kwong, P.D.

History

Deposition	Nov 27, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 5, 2014	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_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	4nrz.cif.gz	339.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4nrz.ent.gz	278.1 KB	Display	PDB format
PDBx/mmJSON format	4nrz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nr/4nrz ftp://data.pdbj.org/pub/pdb/validation_reports/nr/4nrz	HTTPS FTP

-
Related structure data

Related structure data	4nrxC 4nryC C: citing same article (ref.)
Similar structure data	4ydv-2 4xxd-2 5ibu-1 1ggi-2 5jue-d 6vor-1 2a6i-d 4xce-3 6vl9-1 5myk-d 4hha-d 6wkl-d 4xc3-d 4hkb-5 2iqa-1 4c83-1 3ifo-1 4h20-d 4r96-3 2hkf-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

4nrxC

4nryC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#170 - Feb 2014 Broadly Neutralizing Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: M66.6 HEAVY CHAIN

A: M66.6 HEAVY CHAIN

L: M66.6 LIGHT CHAIN

B: M66.6 LIGHT CHAIN

hetero molecules

97.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: M66.6 HEAVY CHAIN

L: M66.6 LIGHT CHAIN

hetero molecules

defined by author
48.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: M66.6 HEAVY CHAIN

B: M66.6 LIGHT CHAIN

hetero molecules

defined by author
48.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.160, 118.873, 80.033
Angle α, β, γ (deg.)	90.00, 96.80, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	M66.6 HEAVY CHAIN Mass: 25183.219 Da / Num. of mol.: 2 / Fragment: Fab Heavy Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: homo sapiens (human)
#2: Antibody	M66.6 LIGHT CHAIN Mass: 23398.088 Da / Num. of mol.: 2 / Fragment: Fab Light Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: homo sapiens (human)
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.92 Å³/Da / Density % sol: 57.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 11% polyethylene glycol 8000, 0.05 M zinc acetate, 0.05 M sodium cacaodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2011
Radiation	Monochromator: SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.43→50 Å / Num. obs: 35882 / % possible obs: 85.7 % / Redundancy: 4 % / R_merge(I) obs: 0.177 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.43→2.47 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.315 / % possible all: 50.7

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.42→30.19 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.38 / Phase error: 24.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.216	1543	4.31 %
R_work	0.177	-	-
obs	0.178	35840	84.2 %

Solvent computation

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

Displacement parameters

B_iso mean: 42.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.42→30.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6719	0	7	173	6899

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6894
X-RAY DIFFRACTION	f_angle_d	1.173	9364
X-RAY DIFFRACTION	f_dihedral_angle_d	13.696	2468
X-RAY DIFFRACTION	f_chiral_restr	0.066	1040
X-RAY DIFFRACTION	f_plane_restr	0.006	1187

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 (%)
2.4205-2.4986	0.3063	71	0.2342	1555	X-RAY DIFFRACTION	43
2.4986-2.5878	0.3274	107	0.2352	2038	X-RAY DIFFRACTION	56
2.5878-2.6914	0.2914	105	0.2343	2392	X-RAY DIFFRACTION	65
2.6914-2.8138	0.2863	126	0.2369	2798	X-RAY DIFFRACTION	76
2.8138-2.962	0.285	142	0.2288	3364	X-RAY DIFFRACTION	90
2.962-3.1474	0.2838	157	0.2187	3593	X-RAY DIFFRACTION	98
3.1474-3.3901	0.2467	168	0.1877	3701	X-RAY DIFFRACTION	100
3.3901-3.7307	0.213	167	0.1668	3674	X-RAY DIFFRACTION	100
3.7307-4.2693	0.1878	168	0.154	3713	X-RAY DIFFRACTION	100
4.2693-5.3739	0.1531	177	0.1287	3702	X-RAY DIFFRACTION	100
5.3739-30.1967	0.185	155	0.1728	3767	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	0.0063	-0.0035	0.0054	0.0007	0.0005	-0.002	0.0876	-0.0245	0.0045	-0.0404	0.066	-0.0129	-0.0076	0.0714	-0	0.1619	0.0045	0.0082	0.1622	-0.0415	0.1988	17.9417	-42.8172	-1.3373
2	-0.0053	-0	0.0057	0.003	0.0115	-0.0101	0.0989	-0.0001	-0.0424	-0.0389	0.0723	0.0157	0.0213	-0.0361	-0	-0.5578	-0.2004	-0.4904	-0.369	-0.2933	-0.3692	12.6065	-43.1602	7.1813
3	-0.069	0.0035	0.1013	-0.03	0.0331	-0.0554	0.0937	-0.0765	-0.0539	0.0543	0.0833	0.0891	-0.1205	0.1005	0	-0.6261	-0.1912	-0.7528	-0.3888	-0.4106	-0.8256	7.4555	-37.7557	-1.1763
4	-0.0036	-0.0049	0.002	0.0074	0.0052	0.0008	0.0646	0.0129	0.0115	-0.0423	0.0522	-0.0733	-0.0288	-0.0298	0	0.1766	0.0609	-0.0703	0.0407	-0.0811	0.2101	-6.0288	-51.2545	-21.809
5	0.0016	-0.0024	0.002	0.0097	0.0088	0.0016	0.0864	0.0244	0.0014	0.0346	0.0098	-0.0488	0.0134	-0.0368	-0	0.1427	0.145	-0.1507	0.1162	-0.0212	0.1243	-10.2172	-47.8497	-20.7743
6	-0.0015	-0.0043	0.0043	0.0062	0.0015	-0.0029	0.0429	0.0352	0.0003	-0.0051	0.0482	-0.0551	-0.0173	-0.0418	0	0.1584	0.1019	-0.0396	0.0413	-0.1279	0.2284	-6.5732	-54.2431	-29.3223
7	0.002	-0.003	0.0033	0.0039	0.0036	0.002	-0.0262	0.0194	-0.0229	-0.0226	-0.0205	0.0216	-0.0273	0.0358	0	0.0433	-0.0335	0.0041	0.1025	0.0006	0.1768	-2.2305	-21.3884	-55.9983
8	0.0046	0.0057	-0.0041	-0.002	0.0014	-0.0004	0.0259	-0.0037	-0.0487	-0.0091	0.0218	-0.0074	0.0148	0.0226	-0	-0.3423	-0.1013	-0.0995	-0.083	-0.2481	-0.4189	-13.6226	-22.5715	-56.2831
9	0.0009	-0.0007	0.0001	0.0009	-0.0011	0.0013	0.0031	0.0249	0.0238	-0.0054	0.0048	0.0003	0.0005	-0.014	0	0.1391	0.0018	-0.0045	0.1703	-0.0016	0.1921	-18.2315	-15.8515	-63.3475
10	0.0021	0.0233	0.0068	-0.032	-0.0005	0.0029	0.1394	0.005	-0.0109	-0.1482	0.0984	0.0226	-0.0832	-0.0389	0	-0.4125	-0.0961	0.1752	0.0673	-0.0218	-0.1002	-16.6129	-22.799	-58.5991
11	-0.0041	0.0184	-0.0019	-0.0228	0.0017	0.0037	0.164	0.035	0.0395	-0.0606	-0.0246	-0.0233	-0.1304	-0.0036	0	-0.254	-0.2431	-0.2265	-0.1112	-0.2122	-0.0933	-1.8096	-15.7958	-45.1136
12	0.01	0.0029	-0.0054	-0.0027	0.0003	0.0007	0.0008	-0.0348	-0.0179	-0.0222	-0.0384	0.0037	-0.0095	0.0131	-0	-0.0849	-0.0511	-0.0731	0.2528	0.003	0.0091	11.267	-12.3143	-34.1794
13	0.0208	0.0016	-0.01	-0.0042	-0.0018	0.0048	0.0407	0.0041	-0.0026	0.032	0.0267	0.0087	-0.043	0.0529	-0	-0.1119	0.0291	-0.0256	0.4061	0.0337	0.0377	12.8889	-12.2654	-30.8076
14	0.003	-0.005	-0.0064	-0.0003	0.0035	0.0037	-0.0595	-0.0165	0.0115	-0.0616	-0.0244	0.0754	-0.0131	-0.0054	-0	0.0706	0.0611	-0.0029	0.1803	-0.0427	0.1035	-8.0656	-25.6511	1.615
15	0.0067	-0.0008	0.0028	0.004	-0.0062	0.0045	-0.0182	0.088	-0.0094	-0.0096	0.0014	-0.01	-0.0265	0.0333	0	0.1335	-0.0194	0.0896	-0.0986	-0.2443	-0.227	2.9938	-23.3173	3.1287
16	0.001	0.0007	0.0004	0.001	-0.0012	0.0018	-0.0345	0.0119	0.0088	-0.0263	0.0348	0.0088	-0.0082	0.0009	0	0.1016	-0.0145	-0.0075	0.0847	-0.0102	0.0676	-2.1251	-18.0898	5.7699
17	-0.0013	-0.0021	0.005	-0.0014	-0.0036	-0.0027	-0.0248	0.0354	-0.0039	0.0438	0.0003	0.0293	0.0192	0.0071	-0	-0.118	-0.0579	-0.2502	-0.0276	0.0308	-0.2981	0.6525	-27.2112	1.8069
18	-0	0.0024	0.0013	0.0002	-0.0009	0.0004	-0.0011	-0.0078	0.0028	0.0141	-0.0131	0.0107	-0.0178	0.0151	-0	0.0458	-0.0899	-0.0644	0.0756	0.0159	0.0954	-15.3186	-28.7548	-11.7265
19	0.0031	0.003	-0.0018	0.0012	-0.0011	0.0018	-0.0043	0.0003	-0.0111	-0.004	-0.0098	-0.0074	-0.0185	-0.0024	0	0.1929	-0.028	-0.0395	0.0947	-0.1244	0.237	-18.1828	-57.8795	-20.1946
20	-0.0051	0.0021	0.0035	0.0012	0.0035	0.003	0.0608	-0.0105	-0.023	-0.0063	0.0573	0.0061	-0.0271	-0.0027	-0	0.2373	-0.0553	0.078	-0.0768	-0.1767	-0.0854	-20.2529	-45.0322	-11.9727
21	-0.0012	0.0023	-0.0009	-0.0011	0.0001	0.0008	-0.0273	-0.0013	-0.0083	0.0222	-0.0111	0.0202	-0.0014	-0.0104	0	0.2257	-0.0867	0.0297	0.2334	-0.04	0.1053	-21.2297	-52.5162	-6.4268
22	-0.001	0.008	0.0249	0.004	-0.0096	0.0004	-0.0038	0.0163	-0.0484	0.0714	-0.0314	0.0814	0.0018	0.0413	0	0.2173	-0.0651	0.0303	-0.0334	0.051	0.132	-19.2588	-49.5318	-13.4715
23	0.0036	0.0011	-0.0025	0	0.0016	-0.0003	0.0885	0.0078	-0.0031	-0.0021	0.054	0.0147	0.0069	-0.0279	-0	0.2911	-0.0422	0.1349	0.3039	-0.0785	0.4419	-29.3414	-47.0496	-15.2836
24	0.004	0.0008	-0.0045	-0.0025	-0.0035	-0.0001	-0.0435	0.0169	0.0252	0.0232	0.0055	0.0428	-0.0017	0.0132	-0	0.1152	0.0282	-0.0263	0.2004	0.003	0.1322	-22.9881	-13.9846	-34.0229
25	0.0015	-0.0013	-0.0031	-0	0.0026	0.0083	-0.0009	0.0216	0.0017	-0.0004	-0.0081	-0.016	0.0201	-0.013	0	0.0245	0.0304	0.0695	0.0646	-0.072	0.0612	-24.3443	-19.6001	-42.036
26	0.0014	0.002	-0.0001	0.0014	-0.0006	0.0016	0.0029	-0.01	-0.012	0.0149	-0.006	-0.0205	0.0129	-0.0009	-0	0.0782	-0.0254	-0.015	0.174	-0.0301	0.0692	-28.513	-26.9718	-38.8768
27	-0.0014	-0.0048	-0.0013	-0.0031	-0.0026	0.0016	-0.0049	-0.0092	-0.0272	0.0182	-0.0309	-0.037	0.018	0.0123	-0	0.0862	-0.0109	0.0142	0.1158	0.0314	0.039	-22.9178	-23.1928	-31.0998
28	-0.0001	-0.0011	-0	-0.0038	-0	0.0005	0.0322	0.0277	0.0174	0.0198	-0.0028	-0.0112	-0.0097	-0.0225	0	-0.0248	0.0405	0.0641	0.0026	-0.0589	-0.0577	-23.0129	-16.5007	-46.769
29	0.0008	0.0012	-0.0009	-0.0017	0.0011	-0	0.0145	-0.0124	0.0101	0.0068	0.0275	0.0012	0.0079	-0.0004	0	0.1162	-0.0206	0.0024	0.1282	-0.0389	0.1389	-12.2967	-13.3062	-22.8417
30	-0.0005	0.0012	-0.0057	0.0014	-0.0031	-0.0076	0.0545	-0.0352	-0.0155	0.012	0.0952	0.0318	-0.0633	0.023	-0	0.1116	-0.2337	0.2478	0.0063	0.0354	0.1509	4.8784	-0.4988	-27.4982
31	-0.0007	0.0004	-0.0019	0.0002	0.0002	0.0014	-0.0135	-0.0094	0.0024	-0.0104	-0.0047	-0.0028	0.0277	-0.0025	-0	0.2204	0.0177	0.0885	0.083	-0.0226	0.1587	0.2942	6.167	-32.3463
32	0.0005	0.0001	-0.0001	0.0008	0.0002	0.0006	0.0013	-0.0008	0.0025	0.0053	0.0164	-0.0003	0.0018	0.0154	-0	0.1469	-0.0044	0.0417	0.0769	0.1078	0.0754	-4.7598	-16.1804	-25.0626
33	0.0005	-0.0006	-0.0042	0.0011	0.0018	0.0002	-0.0223	-0.0053	0.0088	0.016	-0.005	-0.0082	0.0083	0.0053	-0	0.2726	-0.05	0.1474	0.0759	-0.0134	0.1558	9.5355	7.1083	-33.4098
34	0.0021	-0.0032	-0.005	0.0035	0.0035	-0.0005	-0.0027	-0.0106	-0.0092	0.0153	0.0134	0.0099	0.0114	0.001	0	0.2285	-0.0471	0.2267	0.1035	-0.0077	0.2759	2.5788	7.5284	-24.2455
35	0.0009	-0.0003	-0.0036	0.003	0.0053	-0.0043	0.013	-0.0116	-0.0104	0.0008	0.034	0.0265	-0.0177	0.0036	-0	0.3609	-0.0982	0.1441	0.3028	-0.1392	0.4827	1.5637	4.8922	-19.1777

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN H AND RESID 1:32 )	H	1 - 32
2	X-RAY DIFFRACTION	2	( CHAIN H AND RESID 33:87 )	H	33 - 87
3	X-RAY DIFFRACTION	3	( CHAIN H AND RESID 88:134 )	H	88 - 134
4	X-RAY DIFFRACTION	4	( CHAIN H AND RESID 135:157 )	H	135 - 157
5	X-RAY DIFFRACTION	5	( CHAIN H AND RESID 158:189 )	H	158 - 189
6	X-RAY DIFFRACTION	6	( CHAIN H AND RESID 190:214 )	H	190 - 214
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 1:17 )	A	1 - 17
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 18:52 )	A	18 - 52
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 53:66 )	A	53 - 66
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 67:100 )	A	67 - 100
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 101:134 )	A	101 - 134
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 135:157 )	A	135 - 157
13	X-RAY DIFFRACTION	13	( CHAIN A AND RESID 158:214 )	A	158 - 214
14	X-RAY DIFFRACTION	14	( CHAIN L AND RESID 1:18 )	L	1 - 18
15	X-RAY DIFFRACTION	15	( CHAIN L AND RESID 19:61 )	L	19 - 61
16	X-RAY DIFFRACTION	16	( CHAIN L AND RESID 62:75 )	L	62 - 75
17	X-RAY DIFFRACTION	17	( CHAIN L AND RESID 76:101 )	L	76 - 101
18	X-RAY DIFFRACTION	18	( CHAIN L AND RESID 102:113 )	L	102 - 113
19	X-RAY DIFFRACTION	19	( CHAIN L AND RESID 114:128 )	L	114 - 128
20	X-RAY DIFFRACTION	20	( CHAIN L AND RESID 129:150 )	L	129 - 150
21	X-RAY DIFFRACTION	21	( CHAIN L AND RESID 151:163 )	L	151 - 163
22	X-RAY DIFFRACTION	22	( CHAIN L AND RESID 164:197 )	L	164 - 197
23	X-RAY DIFFRACTION	23	( CHAIN L AND RESID 198:213 )	L	198 - 213
24	X-RAY DIFFRACTION	24	( CHAIN B AND RESID 1:18 )	B	1 - 18
25	X-RAY DIFFRACTION	25	( CHAIN B AND RESID 19:48 )	B	19 - 48
26	X-RAY DIFFRACTION	26	( CHAIN B AND RESID 49:69 )	B	49 - 69
27	X-RAY DIFFRACTION	27	( CHAIN B AND RESID 70:83 )	B	70 - 83
28	X-RAY DIFFRACTION	28	( CHAIN B AND RESID 84:101 )	B	84 - 101
29	X-RAY DIFFRACTION	29	( CHAIN B AND RESID 102:113 )	B	102 - 113
30	X-RAY DIFFRACTION	30	( CHAIN B AND RESID 114:150 )	B	114 - 150
31	X-RAY DIFFRACTION	31	( CHAIN B AND RESID 151:163 )	B	151 - 163
32	X-RAY DIFFRACTION	32	( CHAIN B AND RESID 164:174 )	B	164 - 174
33	X-RAY DIFFRACTION	33	( CHAIN B AND RESID 175:188 )	B	175 - 188
34	X-RAY DIFFRACTION	34	( CHAIN B AND RESID 189:198 )	B	189 - 198
35	X-RAY DIFFRACTION	35	( CHAIN B AND RESID 199:212 )	B	199 - 212

-
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