PDB-6yz7: H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex

ID or keywords:

Entry

Database: PDB / ID: 6yz7

Title

H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex

Components

Antibody Cr3022
Antibody light chain
Nanobody
Spike glycoprotein

Keywords

VIRAL PROTEIN / Antibody / nanobody complex / rbd

Function / homology

Function and homology information

symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...
Similarity search - Function

Biological species

Severe acute respiratory syndrome coronavirus 2

Homo sapiens (human)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Naismith, J.H. / Ren, J. / Zhou, D. / Zhao, Y. / Stuart, D.I.

Funding support

United Kingdom, 2items

Citation

Journal: To Be Published / Year: 2020
Title: Structural characterisation of a nanobody derived from a naive library that neutralises SARS-CoV-2
Authors: Naismith, J.H.

History

Deposition	May 6, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 3, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6yz7.cif.gz	573.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6yz7.ent.gz		Display	PDB format
PDBx/mmJSON format	6yz7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6yz7_validation.pdf.gz	522.7 KB	Display	wwPDB validaton report
Full document	6yz7_full_validation.pdf.gz	559.1 KB	Display
Data in XML	6yz7_validation.xml.gz	52.3 KB	Display
Data in CIF	6yz7_validation.cif.gz	70.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yz/6yz7 ftp://data.pdbj.org/pub/pdb/validation_reports/yz/6yz7	HTTPS FTP

-
Related structure data

Related structure data	6z2mC 6ylaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6z2m-1 6z2m-2 6zh9-d 6cw6-d 6miy-1 4y4f-2 4y4k-d 3to4-d 3quz-d 5w08-4 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (2) #264 - Dec 2021 SARS-CoV-2 Spike Variants similarity (1) #246 - Jun 2020 SARS-CoV-2 Spike similarity (1) #21 - Sep 2001 Antibodies similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

AAA: Spike glycoprotein

BBB: Antibody Cr3022

CCC: Antibody light chain

DDD: Nanobody

EEE: Spike glycoprotein

FFF: Nanobody

HHH: Antibody Cr3022

LLL: Antibody light chain

hetero molecules

175 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Spike glycoprotein

BBB: Antibody Cr3022

CCC: Antibody light chain

DDD: Nanobody

hetero molecules

defined by author
Evidence: gel filtration
87.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

EEE: Spike glycoprotein

FFF: Nanobody

HHH: Antibody Cr3022

LLL: Antibody light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	154.598, 154.598, 229.312
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	91
Space group name H-M	P4₁22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains AAA EEE
2	2	Chains BBB HHH
3	3	Chains CCC LLL
4	4	Chains DDD FFF

NCS ensembles :

ID
1
2
3
4

#1: Protein

Spike glycoprotein / S glycoprotein / E2 / Peplomer protein

Mass: 23716.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): HEK293S GnTI- / Production host:

Homo sapiens (human) / References: UniProt: P0DTC2

#2: Antibody

Antibody Cr3022

Mass: 24455.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Cell line (production host): HEK293T / Production host:

Homo sapiens (human)

#3: Antibody

Antibody light chain

Mass: 24289.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Homo sapiens (human)

#4: Antibody

Nanobody

Mass: 15010.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: His tag / Source: (gene. exp.)

Lama glama (llama) / Production host:

Escherichia coli (E. coli)

#5: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

Has ligand of interest

N

Has protein modification

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.92 Å³/Da / Density % sol: 68.59 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion Details: The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.

-
Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 3.29→128.187 Å / Num. obs: 40954 / % possible obs: 98 % / Redundancy: 78 % / CC_1/2: 0.994 / R_pim(I) all: 0.094 / Net I/σ(I): 4.9
Reflection shell	Resolution: 3.29→3.35 Å / Num. unique obs: 1538 / CC_1/2: 0.369 / R_pim(I) all: 4.094

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6YLA

6yla

Resolution: 3.3→128.187 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.93 / SU B: 94.993 / SU ML: 0.571 / Cross valid method: FREE R-VALUE / ESU R Free: 0.5
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2688	1939	4.735 %
R_work	0.2377	-	-
all	0.239	-	-
obs	-	40954	96.292 %

Solvent computation

Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å

Displacement parameters

B_iso mean: 144.159 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.97 Å²	0 Å²	0 Å²
2-	-	-1.97 Å²	0 Å²
3-	-	-	3.94 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→128.187 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11686	0	28	0	11714

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	12028
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	10650
X-RAY DIFFRACTION	r_angle_refined_deg	1.39	1.649	16366
X-RAY DIFFRACTION	r_angle_other_deg	1.126	1.574	24822
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.668	5	1504
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.684	22.796	558
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.533	15	1886
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.96	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.049	0.2	1560
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	13512
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2568
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	1894
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	10037
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	5567
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	5591
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	237
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.32	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.236	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.237	0.2	62
X-RAY DIFFRACTION	r_mcbond_it	1.678	9.809	6045
X-RAY DIFFRACTION	r_mcbond_other	1.679	9.808	6044
X-RAY DIFFRACTION	r_mcangle_it	2.879	14.712	7540
X-RAY DIFFRACTION	r_mcangle_other	2.879	14.713	7541
X-RAY DIFFRACTION	r_scbond_it	1.6	9.993	5982
X-RAY DIFFRACTION	r_scbond_other	1.6	9.994	5983
X-RAY DIFFRACTION	r_scangle_it	2.857	14.928	8826
X-RAY DIFFRACTION	r_scangle_other	2.857	14.929	8827
X-RAY DIFFRACTION	r_lrange_it	4.952	109.116	12487
X-RAY DIFFRACTION	r_lrange_other	4.951	109.116	12488
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.046	0.05	6051
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.063	0.05	6154
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.042	0.05	6556
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.014	0.05	3842

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
3.3-3.386	0.379	66	0.415	1472	0.413	3094	0.582	0.55	49.7091	0.413
3.386-3.478	0.467	141	0.436	2818	0.438	2979	0.494	0.536	99.3286	0.432
3.478-3.579	0.422	151	0.383	2795	0.385	2946	0.466	0.469	100	0.387
3.579-3.689	0.419	152	0.394	2703	0.396	2855	0.499	0.506	100	0.394
3.689-3.81	0.301	117	0.337	2638	0.335	2755	0.623	0.633	100	0.338
3.81-3.944	0.415	131	0.346	2556	0.349	2687	0.674	0.717	100	0.337
3.944-4.092	0.298	116	0.28	2462	0.281	2578	0.855	0.834	100	0.265
4.092-4.259	0.24	120	0.238	2375	0.238	2495	0.903	0.901	100	0.217
4.259-4.449	0.25	101	0.212	2304	0.213	2405	0.9	0.929	100	0.183
4.449-4.665	0.207	110	0.187	2198	0.188	2308	0.945	0.94	100	0.158
4.665-4.917	0.214	106	0.167	2062	0.169	2168	0.938	0.956	100	0.138
4.917-5.215	0.257	105	0.2	2001	0.203	2106	0.921	0.936	100	0.163
5.215-5.575	0.239	92	0.2	1862	0.202	1954	0.913	0.938	100	0.166
5.575-6.02	0.266	100	0.214	1740	0.216	1840	0.921	0.939	100	0.178
6.02-6.593	0.264	77	0.235	1630	0.236	1707	0.929	0.931	100	0.201
6.593-7.369	0.285	66	0.216	1495	0.219	1561	0.909	0.934	100	0.183
7.369-8.505	0.199	67	0.168	1301	0.169	1368	0.95	0.958	100	0.142
8.505-10.405	0.167	49	0.148	1148	0.149	1197	0.974	0.975	100	0.136
10.405-14.666	0.222	46	0.177	895	0.179	941	0.97	0.974	100	0.167
14.666-128.187	0.356	26	0.414	560	0.411	586	0.944	0.906	100	0.397

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	7.3659	-2.6568	-4.4313	6.6534	3.0509	4.7085	0.1805	-0.3527	1.6956	-0.8589	0.3432	-0.5248	-0.6016	-0.3872	-0.5238	0.4631	0.2067	0.1472	0.9313	0.0554	0.7458	-55.377	-30.562	42.165
2	3.5821	0.9232	-2.6271	3.7845	0.3642	4.4103	-0.1016	-1.0358	-0.1034	1.0771	0.2374	-0.1497	0.6998	-0.0586	-0.1358	0.5946	0.1167	0.1039	1.1689	0.0617	0.3966	-60.408	-42.216	59.566
3	6.5974	-0.4703	4.9164	5.7711	-1.0515	10.3103	0.2222	0.0143	0.8048	-0.2827	-0.3062	-0.1503	-0.0172	0.0335	0.084	0.2106	0.1083	0.243	0.8388	-0.0669	0.4238	-54.267	-34.478	47.605
4	2.7805	-0.6427	-2.0569	2.8859	1.881	5.0671	-0.0843	-0.339	-0.3405	0.0482	0.4072	0.2592	0.5864	0.154	-0.3229	0.2356	-0.0382	-0.1112	0.3703	0.0795	0.2196	-35.967	-55.005	28.11
5	4.8	0.1641	-0.2146	4.518	-1.688	5.4693	-0.4964	-0.2188	0.4779	-0.1836	-0.0324	-0.5064	-0.4729	0.5245	0.5288	1.0624	0.0089	-0.2575	0.4927	-0.2275	0.5663	-21.326	-62.31	3.894
6	3.3937	-1.1327	-0.856	5.2558	0.1408	8.6397	0.3145	0.061	-0.5631	-0.4611	-0.0364	0.9338	0.0898	-0.8631	-0.278	0.1903	-0.071	-0.1512	0.4044	0.0478	0.3306	-54.466	-49.469	16.877
7	3.6834	-3.9389	0.046	8.8523	1.0055	3.9715	-0.0797	-0.1292	-0.172	-0.4094	0.045	-0.3587	0.0797	-0.0509	0.0347	0.7983	-0.1589	-0.0858	0.3851	-0.2053	0.318	-32.29	-71.275	-5.219
8	1.5746	-2.4941	-1.1441	4.0038	1.843	0.8572	-0.4197	-0.1082	-0.0806	0.9266	0.0308	0.2628	0.5461	-0.1624	0.3889	2.6458	-0.3482	0.0915	2.9929	-0.497	1.2371	-60.195	-27.209	88.518
9	1.0142	0.5009	0.6158	0.3498	0.1893	0.5202	0.511	-0.7812	0.5297	0.7008	-0.5872	0.3174	-0.0245	-0.2516	0.0762	2.5035	-0.0195	0.2266	2.9429	-0.4292	1.1242	-62.546	-34.832	88.122
10	1.4054	0.8449	-0.1904	2.0189	-0.3175	0.0658	0.3227	-0.179	0.3625	0.2958	-0.2347	0.4205	-0.2141	0.0647	-0.088	2.0234	-0.1349	0.1048	2.1143	-0.133	0.7944	-56.723	-34.568	87.228
11	2.0964	-0.3363	0.85	6.6741	-1.4968	7.9488	0.4019	-0.154	-0.3645	0.0206	-0.0904	1.2801	-0.6056	-0.6456	-0.3115	0.3292	0.1961	0.0743	0.3256	0.1293	0.3974	-46.61	-22.848	2.4
12	4.2888	0.457	0.9881	6.0627	0.3154	8.1297	-0.078	-0.196	-0.2323	-0.0264	0.3723	-0.0029	0.2347	0.5514	-0.2943	0.2733	0.1162	0.0828	0.2509	0.0185	0.2271	-36.195	-19.977	-1.103
13	2.6087	0.1828	-0.1091	3.9155	-2.3449	5.5265	0.0102	0.2476	-0.0933	-0.4895	0.259	0.0212	-0.5938	0.5329	-0.2691	0.4506	0.0289	0.078	0.3837	-0.0299	0.0263	-34.976	-17.44	-12.978
14	4.9019	-5.4758	7.5365	8.4776	-10.0419	13.3374	-0.479	-0.9285	0.4616	0.3924	0.3693	0.7057	0.1901	-0.8893	0.1097	1.0633	0.1367	0.2143	0.9298	-0.1111	0.9123	-48.037	-14.276	15.554
15	4.2686	-0.9124	0.001	2.6393	1.1319	9.1706	0.0604	-0.2508	-0.3141	0.0407	0.1145	0.4671	-0.4515	-0.3597	-0.1749	0.5324	0.0706	0.0312	0.3326	0.0357	0.3196	-39.273	-13.419	-41.648
16	1.4734	-0.1329	1.264	3.1358	0.899	10.1624	0.1378	-0.1427	-0.1111	-0.0738	0.0305	0.2805	-0.6603	0.0394	-0.1683	0.4776	0.1206	0.07	0.3789	-0.0397	0.2466	-38.275	-13.571	-41.165
17	2.9787	-0.8579	2.0651	3.8086	-2.9297	4.4577	0.6177	0.0563	-0.0042	-0.3061	-0.477	-0.1607	0.2232	0.4146	-0.1407	0.2476	0.0343	0.0468	0.296	-0.056	0.0637	-22.81	-40.453	16.847
18	3.6002	-2.2155	0.7137	3.5959	-0.6495	6.1543	0.4697	-0.8352	-0.8912	0.2945	0.031	0.4851	0.6584	-0.4535	-0.5007	0.5251	-0.3069	-0.2098	0.9176	0.2721	0.5202	-16.187	-54.29	45.253
19	5.072	-1.2448	0.9174	4.1141	-1.7829	6.8563	0.0089	-0.4313	0.6287	0.3993	0.0257	-0.3094	-0.8755	-0.2193	-0.0346	0.3051	-0.0521	0.0793	0.3366	-0.136	0.1354	-28.029	-22.526	30.239
20	8.7459	-4.3604	3.5194	6.7445	-1.1786	4.1406	0.3969	-1.0501	-0.5119	0.0148	-0.1924	-0.4298	-0.0925	-0.3568	-0.2045	0.3336	-0.3074	-0.0433	0.8456	0.2187	0.1468	-6.322	-44.113	52.716
21	4.7078	0.3466	-2.392	4.065	1.0891	4.0617	0.1268	-0.5662	0.5436	0.2249	0.1237	-0.0942	0.127	-0.2138	-0.2504	0.2855	0.1148	0.1049	0.8624	0.0182	0.3317	-57.638	-36.975	51.66
22	1.7108	-0.6951	-1.7744	2.1849	1.0097	3.8773	-0.0257	-0.0629	-0.2108	-0.362	0.3609	0.0548	0.5117	0.2721	-0.3353	0.3675	-0.069	-0.1564	0.3769	-0.011	0.261	-30.765	-57.608	19.541
23	1.1542	-1.341	-1.7021	4.1209	2.0552	3.577	0.1349	0.1066	-0.2961	-0.6863	-0.017	0.4178	0.0837	-0.3604	-0.1179	0.4513	-0.1425	-0.2283	0.4469	-0.0298	0.4392	-43.778	-59.982	6.238
24	0.0566	0.0455	-0.0057	0.0703	-0.0004	0.0012	0.228	-0.2058	0.1683	0.3428	-0.1965	0.0112	0.0024	0.0283	-0.0316	2.0844	-0.1756	0.1618	2.4586	-0.3516	0.9956	-60.706	-32.448	88.038
25	2.2998	0.671	0.6093	4.3479	-1.1858	4.351	0.0313	-0.0765	-0.1351	-0.098	0.2405	0.348	-0.5283	0.0845	-0.2718	0.2926	0.1196	0.051	0.2681	0.0147	0.1165	-39.179	-19.193	-4.733
26	2.8021	-0.8709	0.677	1.9016	0.5956	9.3262	0.0465	-0.1719	-0.2281	0	0.1547	0.4082	-0.5881	-0.2245	-0.2012	0.4215	0.0809	0.0489	0.2279	-0.0113	0.2249	-38.829	-13.464	-41.38
27	2.8475	-1.099	2.0925	2.4235	-1.822	3.9703	0.5415	-0.4402	-0.4394	0.0189	-0.2055	-0.0275	0.304	0.1328	-0.336	0.2533	-0.1243	-0.0507	0.3833	0.0356	0.1665	-20.218	-45.858	27.896
28	5.2998	-2.1719	3.0614	2.2289	-2.3104	4.0605	-0.0055	-0.8523	0.0684	0.3194	-0.0243	-0.1608	-0.4402	-0.2494	0.0298	0.2938	-0.2047	0.0419	0.4824	-0.0501	0.0794	-17.73	-32.762	40.901

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	334 - 398
2	X-RAY DIFFRACTION	2	ALL	AAA	399 - 493
3	X-RAY DIFFRACTION	3	ALL	AAA	494 - 528
4	X-RAY DIFFRACTION	4	ALL	BBB	0 - 143
5	X-RAY DIFFRACTION	5	ALL	BBB	144 - 219
6	X-RAY DIFFRACTION	6	ALL	CCC	1 - 113
7	X-RAY DIFFRACTION	7	ALL	CCC	114 - 219
8	X-RAY DIFFRACTION	8	ALL	DDD	1 - 42
9	X-RAY DIFFRACTION	9	ALL	DDD	43 - 103
10	X-RAY DIFFRACTION	10	ALL	DDD	104 - 128
11	X-RAY DIFFRACTION	11	ALL	EEE	334 - 386
12	X-RAY DIFFRACTION	12	ALL	EEE	387 - 423
13	X-RAY DIFFRACTION	13	ALL	EEE	424 - 515
14	X-RAY DIFFRACTION	14	ALL	EEE	516 - 528
15	X-RAY DIFFRACTION	15	ALL	FFF	1 - 67
16	X-RAY DIFFRACTION	16	ALL	FFF	68 - 128
17	X-RAY DIFFRACTION	17	ALL	HHH	0 - 129
18	X-RAY DIFFRACTION	18	ALL	HHH	130 - 219
19	X-RAY DIFFRACTION	19	ALL	LLL	1 - 114
20	X-RAY DIFFRACTION	20	ALL	LLL	115 - 219
21	X-RAY DIFFRACTION	21	ALL	AAA	334 - 528
22	X-RAY DIFFRACTION	22	ALL	BBB	0 - 219
23	X-RAY DIFFRACTION	23	ALL	CCC	1 - 219
24	X-RAY DIFFRACTION	24	ALL	DDD	1 - 128
25	X-RAY DIFFRACTION	25	ALL	EEE	334 - 528
26	X-RAY DIFFRACTION	26	ALL	FFF	1 - 128
27	X-RAY DIFFRACTION	27	ALL	HHH	0 - 219
28	X-RAY DIFFRACTION	28	ALL	LLL	1 - 219

-
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