PDB-6fuz: Crystal structure of the TPR domain of KLC1 in complex with the C...

ID or keywords:

Entry

Database: PDB / ID: 6fuz

Title

Crystal structure of the TPR domain of KLC1 in complex with the C-terminal peptide of JIP1

Components

Kinesin light chain 1,Kinesin light chain 1,C-Jun-amino-terminal kinase-interacting protein 1
nanobody

Keywords

MOTOR PROTEIN / Protein complex / nanobody / cargo recognition

Function / homology

Function and homology information

RHO GTPases activate KTN1 / membrane-bounded organelle / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / protein localization to synapse / MHC class II antigen presentation / axo-dendritic transport / stress granule disassembly / ciliary rootlet / kinesin complex ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.7 Å

Authors

Pernigo, S. / Dodding, M.P. / Steiner, R.A.

Funding support

United Kingdom, 1items

Citation

Journal: Elife / Year: 2018
Title: Structural basis for isoform-specific kinesin-1 recognition of Y-acidic cargo adaptors.
Authors: Pernigo, S. / Chegkazi, M.S. / Yip, Y.Y. / Treacy, C. / Glorani, G. / Hansen, K. / Politis, A. / Bui, S. / Dodding, M.P. / Steiner, R.A.

History

Deposition	Feb 28, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 2, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 12, 2018	Group: Data collection / Database references / Source and taxonomy Category: citation / entity_src_gen Item: _citation.title / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2	Sep 18, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6fuz.cif.gz	165.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6fuz.ent.gz	139.9 KB	Display	PDB format
PDBx/mmJSON format	6fuz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	6fv0C C: citing same article (ref.)
Similar structure data	6fv0-d 6i2p-2 4m37-d 5wpz-5 4qf5-2 3bca-d 2wtz-3 5ii4-d 1w5d-d 4yzp-d 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	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (6) #141 - Sep 2011 O-GlcNAc Transferase similarity (6) #88 - Apr 2007 Clathrin similarity (1) #176 - Aug 2014 Dynein similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #166 - Oct 2013 Proteasome similarity (3)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#136 - Apr 2011
Nanobodies
similarity (1)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (6)
#141 - Sep 2011
O-GlcNAc Transferase
similarity (6)
#88 - Apr 2007
Clathrin
similarity (1)
#176 - Aug 2014
Dynein
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#166 - Oct 2013
Proteasome
similarity (3)

Deposited unit

A: Kinesin light chain 1,Kinesin light chain 1,C-Jun-amino-terminal kinase-interacting protein 1

N: nanobody

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, isothermal titration calorimetry, assay for oligomerization, Fluorescence polarisation

Unit cell

Length a, b, c (Å)	107.473, 90.364, 51.698
Angle α, β, γ (deg.)	90.00, 99.80, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Kinesin light chain 1,Kinesin light chain 1,C-Jun-amino-terminal kinase-interacting protein 1 / JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / Mitogen- ...JNK-interacting protein 1 / Islet-brain 1 / IB-1 / JNK MAP kinase scaffold protein 1 / Mitogen-activated protein kinase 8-interacting protein 1 Mass: 37301.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Chains A is a chimeric construct of TPR domain of KLC1 and J the C-terminal peptide of JIP1 fused via a (TGS)10 linker.,Chains A is a chimeric construct of TPR domain of KLC1 and J the C- ...Details: Chains A is a chimeric construct of TPR domain of KLC1 and J the C-terminal peptide of JIP1 fused via a (TGS)10 linker.,Chains A is a chimeric construct of TPR domain of KLC1 and J the C-terminal peptide of JIP1 fused via a (TGS)10 linker. Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Gene: Klc1, Kns2, MAPK8IP1, IB1, JIP1, PRKM8IP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5UE59, UniProt: O88447*PLUS
#2: Antibody	nanobody Mass: 13395.817 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Variant (production host): WK6
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.44 Å³/Da / Density % sol: 49.58 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.04 M potassium phosphate monobasic, 16% PEG8000, 20% glycerol

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.7→45.18 Å / Num. obs: 13229 / % possible obs: 98.6 % / Redundancy: 3.8 % / B_iso Wilson estimate: 94.37 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.051 / R_pim(I) all: 0.047 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.7→2.83 Å / R_merge(I) obs: 1.176 / Mean I/σ(I) obs: 1 / Num. unique obs: 1747 / CC_1/2: 0.584 / R_pim(I) all: 1.067 / % possible all: 98.5

-
Processing

Software

Name	Version	Classification
BUSTER	2.10.3	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Resolution: 2.7→45.18 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.933 / R_factor R_free error: 0 / SU R Cruickshank DPI: 1.024 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.822 / SU R_free Blow DPI: 0.32 / SU R_free Cruickshank DPI: 0.333

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.257	669	5.06 %	RANDOM
R_work	0.233	-	-	-
obs	0.234	13228	98.4 %	-

Displacement parameters

B_iso mean: 113.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	11.0292 Å²	0 Å²	-23.036 Å²
2-	-	-3.6355 Å²	0 Å²
3-	-	-	-7.3937 Å²

Refine analyze

Luzzati coordinate error obs: 0.48 Å

Refinement step

Cycle: 1 / Resolution: 2.7→45.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3001	0	6	13	3020

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	3060	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.07	4129	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1091	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		88	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		436	HARMONIC	5
X-RAY DIFFRACTION	t_it		3060	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.45
X-RAY DIFFRACTION	t_other_torsion	19.92
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		386	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		3493	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.7→2.92 Å / R_factor R_free error: 0 / Total num. of bins used: 7

	R_factor	Num. reflection	% reflection
R_free	0.238	152	5.64 %
R_work	0.238	2545	-
all	0.238	2697	-
obs	-	-	98 %

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	-0.3609	2.9876	1.1772	0.0513	1.3179	0.4325	0.0046	-0.0206	-0.1058	0.0105	0.0387	-0.0185	0.0917	-0.1318	-0.0433	-0.4341	-0.313	-0.2126	0.4396	0.0262	-0.5593	47.5862	1.5679	2.8758
2	-0.0499	-2.4903	3.0747	0.475	3.638	2.5648	-0.0536	-0.1548	0.196	0.2074	0.0709	-0.0562	-0.0586	-0.104	-0.0173	-0.2867	-0.2329	0.2323	0.6035	-0.3487	0.1934	47.3924	12.228	-0.7543
3	7.1802	4.6766	-6.3664	9.8144	-5.0572	8.5654	-0.0665	0.0837	-0.1339	-0.1617	-0.0045	-0.4098	0.3344	0.8261	0.071	-0.1837	0.0166	-0.0112	0.3147	0.0333	-0.1931	44.1458	-0.2553	-8.9499
4	11.3382	-4.5442	-2.9252	4.6827	-6.6296	5.3141	-0.0961	0.8269	0.3421	-0.015	-0.0045	0.2288	-0.132	0.0241	0.1006	-0.2281	-0.0229	0.088	0.0964	0.1381	-0.1324	36.5818	4.1298	-11.6006
5	8.5574	-1.2119	-2.1387	0.3203	2.3134	6.7221	-0.1933	0.8585	-0.0611	-0.4944	0.1405	0.0301	0.5006	0.0995	0.0528	-0.0913	-0.1002	0.0405	-0.0759	0.0863	-0.202	31.7752	-3.8179	-7.6994
6	-1.5886	0.3801	4.0186	2.1497	5.0637	6.7135	0.1039	0.6901	-0.2176	-0.0858	0.1087	-0.0203	-0.1526	-0.2233	-0.2126	-0.1778	-0.1007	0.0787	0.3993	0.0251	-0.0874	22.0182	1.99	-10.4728
7	0.7395	2.7315	-1.8794	0.0025	-0.2302	-0.6713	0.0182	-0.0021	-0.1961	-0.0119	0.0429	0.098	0.1742	0.0451	-0.061	-0.1463	0.0343	0.2307	-0.2808	0.1147	-0.0159	25.2209	-8.8966	-2.8823
8	1.2305	-1.0987	-3.5155	3.0183	-0.177	-0.5366	0.0248	-0.0066	-0.3795	0.0009	0.0139	0.0361	0.3897	-0.0499	-0.0387	0.0428	0.1219	0.2729	-0.0237	0.3029	0.312	25.5061	-9.118	3.7772
9	1.7892	-0.7891	0.9738	0.0301	0.8231	3.4337	-0.1058	0.5636	-0.0037	0.1488	-0.1721	0.7954	0.2998	-0.2779	0.278	-0.2601	-0.0469	0.0459	-0.0333	0.2132	0.0826	14.2639	2.3144	-1.3536
10	0.6908	-4.5301	-2.1527	0.2154	1.8813	1.7718	-0.0932	-0.5025	-0.1126	0.7209	-0.1516	0.051	0.1943	0.0198	0.2448	0.0586	0.0074	0.3095	-0.0648	0.2668	-0.1658	20.3104	-3.0155	10.8224
11	1.2888	0.7482	-3.3577	0	2.0979	-0.4766	0.0008	-0.081	0.1686	0.3594	-0.0209	0.0109	-0.0075	0.1814	0.0201	-0.1886	-0.1075	-0.0163	-0.2207	0.2258	-0.1049	22.2161	5.4527	11.3422
12	1.3688	-1.4579	-4.117	6.9711	-0.0272	1.7909	-0.0263	0.4028	0.2187	0.119	0.0694	0.4738	-0.3057	-0.2217	-0.0431	-0.2013	-0.0153	0.088	-0.2579	0.2508	0.1393	11.2838	11.3334	10.9234
13	0.5336	1.655	1.4946	0.1913	-4.014	1.4863	0.0059	-0.1366	0.0387	-0.0285	-0.0525	0.0272	0.0119	0.071	0.0465	0.1533	-0.2277	-0.2652	0.4306	0.254	-0.1448	24.1343	10.7644	25.5831
14	-0.7879	-0.2903	2.2095	0	-2.9304	0.825	-0.0549	-0.1291	0.1733	0.1361	0.1473	-0.1546	-0.0189	0.1514	-0.0924	0.1358	-0.2312	-0.0119	-0.2782	0.0987	-0.0493	16.3021	16.4135	28.6715
15	-0.0825	0.6057	0.1514	0.6966	0.9116	1.0121	-0.0148	-0.0847	0.0222	0.0406	0.0277	0.0405	-0.0098	-0.0448	-0.0129	0.1546	-0.1349	0.1214	-0.0902	0.1364	-0.1217	9.7575	25.0987	24.5893
16	1.877	2.7406	0.0623	3.3385	-0.5203	-0.034	0.0105	0.0732	0.1153	0.0635	0.2095	-0.0041	-0.1355	0.3248	-0.2201	-0.1091	0.0413	-0.035	-0.1558	0.2782	-0.1979	20.3332	18.0083	13.3619
17	0.6908	-0.0072	-1.1011	2.3677	-0.4547	0.5053	-0.0129	0.0778	-0.0008	-0.0179	0.0128	0.1345	-0.0354	0.005	0.0001	-0.0768	0.0422	0.2387	-0.0732	0.2775	0.2379	10.0404	23.5481	11.5781
18	2.0952	1.1794	0.666	1.6879	-4.9158	1.7631	0.0066	-0.0041	0.2246	0.202	0.0447	-0.0836	-0.0398	-0.1392	-0.0514	0.1634	0.1246	0.1226	-0.1989	0.2791	-0.1131	16.0016	26.7438	17.0313
19	0.2376	0.0251	-0.6825	0	0.3347	-0.0598	0.0071	-0.0252	-0.0064	0.0201	0.0371	-0.0034	-0.0203	-0.052	-0.0441	0.044	-0.167	-0.088	-0.0143	-0.1864	0.0848	29.0624	24.0817	15.8698
20	-0.5694	-3.4935	2.1622	2.0607	-6.0709	0.7639	0.0065	-0.0339	0.0234	0.1519	-0.045	-0.0525	-0.0471	0.1165	0.0385	-0.1199	0.1919	0.067	-0.0438	0.3309	0.1294	14.735	-13.5942	26.8034
21	0.0622	-2.6784	2.1328	0	2.609	0.9346	-0.0209	0.0318	-0.0305	-0.0442	0.0049	-0.1774	0.0581	-0.1313	0.016	0.0904	-0.0977	0.2734	-0.4941	0.062	0.3458	-5.6333	-20.5311	21.4725
22	1.6481	-0.3891	-1.9948	0	0.6692	-0.7383	-0.0093	0.0038	-0.0018	-0.043	-0.0459	0.1373	0.1907	-0.0757	0.0552	-0.3498	0.0122	0.2066	-0.4028	0.0714	0.3021	-2.4133	-12.9972	23.091
23	0.4764	-0.8282	-0.6405	0.0445	-0.6141	-0.2014	0.0199	0.0211	-0.0386	-0.0602	-0.0504	-0.1218	-0.1483	0.271	0.0305	-0.0233	0.1353	-0.0398	0.2224	0.1925	-0.012	15.3946	-8.4096	27.8598
24	0.4035	-0.0985	-1.1556	0.1898	-1.1501	-0.1279	-0.03	-0.019	0.1285	-0.052	0.0389	-0.1044	0.0115	0.1753	-0.0089	0.1109	-0.0947	0.159	0.3251	0.286	-0.1305	17.6608	-1.042	24.0066
25	3.3212	3.248	1.3355	0.1162	1.1673	0.3928	-0.0935	0.0641	-0.3488	-0.1367	-0.1701	0.1463	0.2355	0.7635	0.2636	-0.3498	0.0578	0.2282	-0.4285	0.0392	0.1809	10.3061	-10.5383	15.533
26	1.1937	-1.3674	-2.8967	0.4257	2.9532	-0.8623	0.0411	0.1169	-0.19	-0.0771	-0.0253	0.0517	0.0832	-0.0603	-0.0158	0.1337	0.1825	0.2451	-0.4944	-0.0533	0.5464	8.4906	-21.9912	9.1642
27	1.092	-2.2174	3.0023	0	1.7814	1.0121	0.0213	0.0655	-0.1503	0.0749	-0.1086	-0.0707	-0.1273	0.1758	0.0874	-0.4759	-0.0525	0.2022	0.0867	0.2911	0.0921	8.6241	-5.2004	14.1535
28	0.9844	0.6562	-2.7645	3.0781	3.1701	-0.9844	-0.0019	0.0294	0.047	0.2758	-0.0398	-0.1537	-0.2823	-0.0426	0.0417	-0.1675	-0.0825	0.2213	-0.121	0.0621	0.3662	8.0289	2.0745	15.8109
29	1.8825	-3.1644	0.7917	0.9848	2.2771	0.2173	0.0123	0.0162	0.0153	-0.2253	0.0307	0.0125	0.0302	0.0173	-0.043	-0.1031	-0.0521	-0.0604	0.1938	-0.0149	0.0293	1.4742	-7.9686	9.3929
30	-0.5025	1.3839	1.5426	2.5274	-2.6754	1.5475	0.0357	0.1505	0.0418	-0.0101	-0.0286	-0.0775	-0.2433	-0.0148	-0.0071	-0.1796	0.0512	-0.0255	0.0646	-0.096	0.1238	-1.3178	-6.9453	14.6155
31	-0.1891	1.9936	0.5321	0	3.4248	0.1894	0.036	-0.1798	-0.0299	0.1594	-0.0375	0.0015	-0.0929	-0.0647	0.0015	-0.011	-0.1296	0.1706	0.0999	0.0272	0.1587	8.9205	-1.5127	28.3411
32	-0.037	-2.4518	0.1386	3.3739	3.8043	0.5466	0.0047	-0.1034	0.0677	0.139	0.0987	-0.0977	0.0362	-0.014	-0.1034	-0.2409	0.0513	0.125	-0.0927	0.2093	-0.0971	7.4274	-6.4435	25.8862
33	0.6307	-2.6986	3.5419	0.0057	1.5566	1.2048	0.0169	0.3181	-0.2616	-0.1841	-0.0946	0.0211	0.2174	-0.0657	0.0777	-0.2619	-0.0661	0.1067	-0.2105	-0.2359	0.3791	-4.696	-13.4681	16.5802
34	-0.5429	-2.2341	1.5089	0	0.5744	0.7267	-0.0926	0.0577	0.0033	-0.0432	0.103	0.1858	0.2006	0.0097	-0.0104	-0.0971	0.0345	0.225	-0.4992	0.0313	0.4233	2.6529	-18.5136	14.8916
35	2.0729	-0.1077	-1.186	0.7935	-3.2806	-0.4705	-0.0351	0.0055	-0.1417	0.2447	-0.1026	-0.1661	0.0211	0.0266	0.1377	-0.1529	0.0489	0.2672	0.2876	0.1218	0.1271	14.9404	-11.8614	16.0566
36	0.872	-2.6679	-2.4489	1.6849	0.4046	-0.872	-0.0247	0.1572	0.0616	0.0012	-0.0428	0.0262	-0.0858	0.2143	0.0675	-0.2616	0.2739	0.2002	0.0875	0.1516	0.3258	17.9088	-15.7547	20.2058
37	0.5965	-1.383	-1.1223	1.7865	-0.9552	1.0202	-0.0057	-0.089	-0.0816	-0.1385	0.0706	0.0951	0.134	0.1896	-0.0649	-0.0296	0.0187	0.2337	-0.5054	0.0964	0.4638	1.9255	-21.4123	20.4
38	7.8141	5.9676	4.1701	2.1278	-0.3584	6.9881	0.0283	-0.0953	0.3202	0.1889	0.0524	0.0757	-0.2578	0.2204	-0.0807	-0.0689	-0.0654	0.0431	-0.1031	0.076	0.0386	23.8425	9.9897	2.3064

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|214 - A\|222 }
2	X-RAY DIFFRACTION	2	{ A\|223 - A\|236 }
3	X-RAY DIFFRACTION	3	{ A\|245 - A\|266 }
4	X-RAY DIFFRACTION	4	{ A\|267 - A\|286 }
5	X-RAY DIFFRACTION	5	{ A\|287 - A\|309 }
6	X-RAY DIFFRACTION	6	{ A\|310 - A\|322 }
7	X-RAY DIFFRACTION	7	{ A\|323 - A\|327 }
8	X-RAY DIFFRACTION	8	{ A\|328 - A\|341 }
9	X-RAY DIFFRACTION	9	{ A\|342 - A\|360 }
10	X-RAY DIFFRACTION	10	{ A\|361 - A\|375 }
11	X-RAY DIFFRACTION	11	{ A\|376 - A\|387 }
12	X-RAY DIFFRACTION	12	{ A\|388 - A\|409 }
13	X-RAY DIFFRACTION	13	{ A\|410 - A\|417 }
14	X-RAY DIFFRACTION	14	{ A\|418 - A\|430 }
15	X-RAY DIFFRACTION	15	{ A\|431 - A\|435 }
16	X-RAY DIFFRACTION	16	{ A\|436 - A\|473 }
17	X-RAY DIFFRACTION	17	{ A\|474 - A\|478 }
18	X-RAY DIFFRACTION	18	{ A\|479 - A\|490 }
19	X-RAY DIFFRACTION	19	{ A\|491 - A\|495 }
20	X-RAY DIFFRACTION	20	{ N\|2 - N\|7 }
21	X-RAY DIFFRACTION	21	{ N\|8 - N\|14 }
22	X-RAY DIFFRACTION	22	{ N\|15 - N\|20 }
23	X-RAY DIFFRACTION	23	{ N\|21 - N\|27 }
24	X-RAY DIFFRACTION	24	{ N\|28 - N\|32 }
25	X-RAY DIFFRACTION	25	{ N\|33 - N\|40 }
26	X-RAY DIFFRACTION	26	{ N\|41 - N\|46 }
27	X-RAY DIFFRACTION	27	{ N\|47 - N\|52 }
28	X-RAY DIFFRACTION	28	{ N\|53 - N\|59 }
29	X-RAY DIFFRACTION	29	{ N\|60 - N\|64 }
30	X-RAY DIFFRACTION	30	{ N\|65 - N\|70 }
31	X-RAY DIFFRACTION	31	{ N\|71 - N\|76 }
32	X-RAY DIFFRACTION	32	{ N\|77 - N\|81 }
33	X-RAY DIFFRACTION	33	{ N\|82 - N\|88 }
34	X-RAY DIFFRACTION	34	{ N\|89 - N\|94 }
35	X-RAY DIFFRACTION	35	{ N\|95 - N\|102 }
36	X-RAY DIFFRACTION	36	{ N\|103 - N\|107 }
37	X-RAY DIFFRACTION	37	{ N\|108 - N\|113 }
38	X-RAY DIFFRACTION	38	{ A\|704 - A\|711 }

-
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://pdbjlc1.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