PDB-7a0j: Crystal structure of the CRINKLY WD40 ectodomain from the Arabido...

ID or keywords:

Entry

Database: PDB / ID: 7a0j

Title

Crystal structure of the CRINKLY WD40 ectodomain from the Arabidopsis thaliana receptor kinase ACR4

Components

Serine/threonine-protein kinase-like protein ACR4

Keywords

SIGNALING PROTEIN / WD40 domain / plant membrane receptor kinase /

disulfide bond /

ligand binding

Function / homology

Function and homology information

flower morphogenesis / root cap development / plant epidermal cell differentiation /

transmembrane receptor protein kinase activity / lateral root formation /

regulation of asymmetric cell division / protein serine/threonine kinase activity => GO:0004674 / root development / embryo development ending in seed dormancy / multivesicular body membrane ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.95 Å

Authors

Hothorn, M. / Okuda, S.

Funding support

Switzerland, 2items

Citation

Journal: To Be Published
Title: Crystal structures of Arabidopsis and Physcomitrella CR4 reveal the molecular architecture of CRINKLY4 receptor kinases.
Authors: Okuda, S. / Hothorn, L.A. / Hothorn, M.

History

Deposition	Aug 9, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 18, 2021	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7a0j.cif.gz	392.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7a0j.ent.gz		Display	PDB format
PDBx/mmJSON format	7a0j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a0/7a0j ftp://data.pdbj.org/pub/pdb/validation_reports/a0/7a0j	HTTPS FTP

-
Related structure data

Related structure data	7a0kC C: citing same article (ref.)
Similar structure data	7a0j-4 3qi0-6 3qi0-2 3qi0-4 3qst-d 7a0j-2 3qi0-1 4zre-d 4o52-d 6zyk-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) 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

7a0kC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#68 - Aug 2005 Neurotrophins similarity (3)

Deposited unit

AAA: Serine/threonine-protein kinase-like protein ACR4

BBB: Serine/threonine-protein kinase-like protein ACR4

CCC: Serine/threonine-protein kinase-like protein ACR4

DDD: Serine/threonine-protein kinase-like protein ACR4

hetero molecules

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

1

AAA: Serine/threonine-protein kinase-like protein ACR4

hetero molecules

defined by author
Evidence: gel filtration
33.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Serine/threonine-protein kinase-like protein ACR4

hetero molecules

defined by author
34.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

CCC: Serine/threonine-protein kinase-like protein ACR4

hetero molecules

defined by author
34.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

DDD: Serine/threonine-protein kinase-like protein ACR4

hetero molecules

defined by author
34 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.991, 87.952, 88.618
Angle α, β, γ (deg.)	90.000, 90.097, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

Serine/threonine-protein kinase-like protein ACR4 / Protein CRINKLY 4 / AtCR4

Mass: 33692.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: ACR4, At3g59420, F25L23.280 / Organ: seedling / Plasmid: pFastBac / Production host:

Trichoplusia ni (cabbage looper) / Variant (production host): Tnao38
References: UniProt: Q9LX29,

non-specific serine/threonine protein kinase

#2: Polysaccharide

alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide

/ Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
LFucpa1-6DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL /

Ethylene glycol

Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: 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 /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆ / Feature type: SUBJECT OF INVESTIGATION

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

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.28 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 16 % PEG 6,000, 0.01 M tri-sodium citrate pH 5.0

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99187 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99187 Å / Relative weight: 1
Reflection	Resolution: 1.95→48.05 Å / Num. obs: 83857 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / B_iso Wilson estimate: 40.2 Å² / CC_1/2: 1 / R_rim(I) all: 0.125 / R_sym value: 0.119 / Net I/σ(I): 8.75
Reflection shell	Resolution: 1.95→2.07 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 0.91 / Num. unique obs: 13541 / CC_1/2: 0.39 / R_rim(I) all: 1.94 / R_sym value: 2.08 / % possible all: 98.3

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XSCALE		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 1.95→48.05 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.945 / SU B: 12.245 / SU ML: 0.159 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2391	4029	4.808 %
R_work	0.22	79774	-
all	0.221	-	-
obs	-	83803	99.856 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 48.462 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.201 Å²	0 Å²	0.754 Å²
2-	-	1.64 Å²	0 Å²
3-	-	-	-0.441 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→48.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7918	0	106	270	8294

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.013	8330
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	7328
X-RAY DIFFRACTION	r_angle_refined_deg	1.187	1.635	11313
X-RAY DIFFRACTION	r_angle_other_deg	1.102	1.58	17018
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	12.834	5.237	1119
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.388	23.01	299
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.841	15	1163
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	18.168	15	2
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.076	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.033	0.2	1051
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	10347
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1763
X-RAY DIFFRACTION	r_nbd_refined	0.148	0.2	1276
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.154	0.2	6843
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	3857
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.07	0.2	3512
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.103	0.2	378
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.082	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.118	0.2	97
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.089	0.2	31
X-RAY DIFFRACTION	r_mcbond_it	0.329	2.783	4371
X-RAY DIFFRACTION	r_mcbond_other	0.329	2.783	4370
X-RAY DIFFRACTION	r_mcangle_it	0.6	4.169	5443
X-RAY DIFFRACTION	r_mcangle_other	0.6	4.17	5444
X-RAY DIFFRACTION	r_scbond_it	0.393	2.883	3959
X-RAY DIFFRACTION	r_scbond_other	0.393	2.883	3960
X-RAY DIFFRACTION	r_scangle_it	0.707	4.295	5859
X-RAY DIFFRACTION	r_scangle_other	0.707	4.295	5860
X-RAY DIFFRACTION	r_lrange_it	3.843	32.674	8676
X-RAY DIFFRACTION	r_lrange_other	3.756	32.389	8616

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.95-2.001	0.384	307	0.378	5840	X-RAY DIFFRACTION	99.4338
2.001-2.056	0.334	277	0.338	5743	X-RAY DIFFRACTION	99.917
2.056-2.115	0.327	320	0.306	5531	X-RAY DIFFRACTION	99.9658
2.115-2.18	0.269	260	0.281	5416	X-RAY DIFFRACTION	99.8944
2.18-2.252	0.271	200	0.258	5297	X-RAY DIFFRACTION	99.9636
2.252-2.331	0.274	257	0.241	5064	X-RAY DIFFRACTION	99.8499
2.331-2.419	0.275	262	0.246	4923	X-RAY DIFFRACTION	99.9229
2.419-2.517	0.266	299	0.245	4670	X-RAY DIFFRACTION	99.9397
2.517-2.629	0.263	270	0.234	4463	X-RAY DIFFRACTION	99.9578
2.629-2.757	0.235	222	0.211	4331	X-RAY DIFFRACTION	99.9342
2.757-2.906	0.233	166	0.203	4182	X-RAY DIFFRACTION	99.954
2.906-3.082	0.224	204	0.206	3849	X-RAY DIFFRACTION	99.8522
3.082-3.295	0.223	199	0.197	3709	X-RAY DIFFRACTION	99.9233
3.295-3.558	0.232	133	0.205	3455	X-RAY DIFFRACTION	99.9721
3.558-3.897	0.214	150	0.196	3154	X-RAY DIFFRACTION	99.9093
3.897-4.356	0.186	119	0.178	2862	X-RAY DIFFRACTION	99.8995
4.356-5.028	0.215	136	0.18	2544	X-RAY DIFFRACTION	99.851
5.028-6.153	0.252	102	0.233	2122	X-RAY DIFFRACTION	99.6416
6.153-8.681	0.237	99	0.231	1660	X-RAY DIFFRACTION	99.9432
8.681-48.05	0.239	47	0.262	959	X-RAY DIFFRACTION	99.5054

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	5.0769	-1.1637	0.0911	1.9802	-0.6863	4.5574	0.0407	-0.0078	0.2526	0.2266	0.0434	-0.0605	-0.1934	0.1044	-0.0842	0.0746	-0.0067	-0.0482	0.0067	0.0096	0.0832	-40.0227	0.5057	-7.2078
2	6.1323	-1.0254	-3.0494	1.829	-1.1163	3.3513	-0.2074	-0.1657	-0.4183	0.1245	0.2187	0.22	0.2807	-0.2556	-0.0113	0.3564	-0.0939	-0.0554	0.1948	0.0969	0.1193	-45.1111	-8.2071	1.0487
3	9.0279	0.8223	3.4165	1.0705	-0.1269	5.9493	-0.0833	-0.3433	0.1222	0.2278	0.1661	-0.0698	0.0415	0.1103	-0.0828	0.2845	0.0489	-0.0159	0.1687	0.0741	0.2099	-38.9891	-10.4419	8.0993
4	4.6035	-1.754	-3.0719	2.644	-0.3763	5.9055	-0.2879	-0.3833	-0.9146	0.4718	0.2196	0.1813	0.7548	-0.0948	0.0684	0.4198	0.0332	-0.1606	0.1946	0.1792	0.3838	-33.0131	-17.5912	4.3401
5	3.3079	0.598	-0.9233	3.7564	-1.713	4.2004	0.0249	0.0996	-0.3967	0.1123	-0.1045	-0.5395	0.3054	0.6081	0.0796	0.186	0.0963	-0.1212	0.1424	-0.0039	0.2893	-20.0841	-13.7402	-6.616
6	8.227	2.1347	-0.1455	3.5055	-4.1527	5.8336	-0.241	0.6682	0.3247	-0.1304	-0.0147	-0.2421	0.021	0.3267	0.2557	0.1728	-0.0073	0.122	0.2585	-0.1348	0.4415	-26.1645	-1.8228	-16.7171
7	5.3715	1.1997	-0.4042	2.0441	-0.1851	4.8407	0.0056	0.0634	0.3272	0.0421	-0.0447	0.1197	-0.2263	-0.2012	0.039	0.0468	0.046	-0.0452	0.1518	-0.0216	0.0822	11.6753	9.1107	-39.6714
8	9.4614	0.5551	0.7009	3.3423	2.5781	2.0942	-0.0509	0.5021	-0.1144	-0.136	0.0873	-0.1193	-0.028	0.1015	-0.0364	0.2147	-0.0007	-0.023	0.3129	0.0221	0.0782	18.3282	9.8716	-52.918
9	5.5774	0.277	0.3991	3.1472	-1.8022	7.3338	-0.213	0.7746	0.0308	-0.5916	0.1474	-0.0375	0.0401	-0.2952	0.0655	0.1783	-0.0229	-0.013	0.3349	-0.0618	0.1222	12.3238	3.5102	-54.7384
10	6.7442	0.4184	0.7041	4.6074	-1.4498	6.449	-0.0948	0.9956	-0.1929	-0.8512	0.0796	0.0616	0.3228	-0.33	0.0153	0.2887	-0.0483	-0.0197	0.4953	-0.1271	0.1371	4.4565	0.8645	-58.6584
11	3.8651	3.7256	-3.6067	3.9102	-2.522	6.5028	-0.2395	0.167	-0.4575	-0.2263	-0.0411	-0.3797	0.4858	-0.5115	0.2806	0.5948	-0.1034	-0.1396	0.8329	-0.3588	0.5358	0.7719	-9.2421	-57.3078
12	8.541	-1.2896	0.334	4.762	-0.0352	5.5442	0.05	0.3592	-0.9629	-0.1731	-0.0755	0.6639	0.3186	-0.5115	0.0255	0.2391	-0.1811	-0.0628	0.5365	-0.1742	0.3619	-7.806	-5.0477	-49.8808
13	6.581	-2.8631	-1.369	5.3406	1.9465	3.8165	-0.2665	0.2662	-0.535	0.263	0.0262	0.365	0.1472	-0.6628	0.2404	0.1212	-0.114	-0.0059	0.434	-0.0463	0.2822	-8.2218	-1.3563	-41.0983
14	0.459	0.3391	-0.9626	0.418	-1.4727	5.4963	0.1348	-0.0688	-0.0019	0.0846	0.0293	0.0372	-0.1598	-0.2618	-0.1641	0.314	-0.0635	0.0146	0.2958	0.0006	0.3513	-6.7355	-8.0044	-36.7067
15	11.3847	-4.7438	-5.2926	4.1657	3.361	5.9835	-0.3036	-0.0486	0.0595	0.2955	0.2218	0.1786	-0.1535	-0.1915	0.0818	0.1098	-0.0257	-0.0321	0.3773	-0.0063	0.1945	-2.6928	4.1146	-35.0452
16	7.2569	-0.7691	-0.4039	11.0165	2.7091	4.6048	-0.3175	-0.1303	0.0619	0.5153	0.4028	0.1656	0.1644	0.0137	-0.0853	0.2105	-0.0269	0.0294	0.4733	0.0229	0.1809	0.1041	-0.0657	-31.4578
17	4.672	-0.4226	-0.3736	2.4405	-0.7288	3.3437	-0.0309	0.1618	-0.4248	-0.0413	-0.0295	0.1206	0.3953	-0.0931	0.0604	0.0754	-0.0264	-0.0182	0.0308	-0.0199	0.0875	12.9161	-0.6946	-10.3198
18	7.1379	-1.48	-0.0531	1.2834	0.0812	3.391	0.0291	-0.4801	-0.1854	0.3396	-0.0425	0.0072	0.2998	0.1695	0.0133	0.2268	-0.0124	0.0189	0.1315	0.0455	0.0954	16.0846	-2.3827	3.8287
19	6.3223	-1.3766	0.993	1.7217	0.2257	2.7649	-0.1467	-0.5647	0.2165	0.3542	0.018	0.3	-0.133	-0.4374	0.1287	0.1814	-0.0493	0.0475	0.2267	-0.0897	0.1576	0.6164	10.5831	3.2481
20	1.3324	-1.4388	1.1749	2.6808	0.552	5.9441	-0.0074	0.1707	0.3118	-0.2069	-0.146	0.0935	-0.445	-0.173	0.1533	0.0484	0.0239	-0.0632	0.2482	0.1394	0.613	-4.4351	14.2786	-13.805
21	5.1145	-0.2362	-0.1654	1.2766	0.1257	6.0193	-0.1402	0.5282	-0.1625	-0.2476	-0.0216	0.3947	0.375	-0.3881	0.1617	0.082	-0.0282	-0.0674	0.1875	-0.0152	0.1805	1.5331	7.1322	-19.7427
22	3.2604	4.6157	-2.1781	9.5301	-2.7313	1.5072	-0.3427	0.0632	-0.0794	0.2452	0.3083	0.1667	0.3253	-0.0312	0.0344	0.3103	-0.0084	-0.0019	0.2949	-0.0054	0.3292	5.8157	-2.3911	-25.4901
23	4.1845	0.6582	1.0277	2.1722	-0.4599	5.5537	-0.0568	0.6364	-0.0956	-0.2787	0.0892	-0.1008	0.0409	0.1934	-0.0324	0.0486	-0.0112	-0.0191	0.1533	0.0374	0.1185	-41.4622	10.0304	-41.7738
24	6.058	2.5477	3.416	5.3638	0.4118	4.6694	-0.0937	1.5027	1.1742	-0.3827	0.1173	-0.0569	-0.8316	0.6051	-0.0236	0.5332	-0.0773	0.1548	0.8015	0.6129	0.6863	-32.2991	23.3512	-48.208
25	1.2415	1.5649	1.1306	1.9767	1.422	1.048	-0.0871	-0.2096	0.3385	-0.126	-0.2206	0.4245	0.0309	-0.2003	0.3077	0.6682	-0.0058	0.0317	0.588	0.0713	0.5656	-25.5828	31.7481	-42.6805
26	7.516	-1.8975	1.5793	5.0931	-1.1123	4.0542	-0.1342	0.0544	0.6808	-0.1329	0.2185	-0.3721	-0.4995	0.7052	-0.0843	0.179	-0.1275	-0.013	0.2599	0.0768	0.2718	-21.65	21.2858	-36.2444
27	6.2616	0.6509	-0.1446	2.7085	-3.1203	4.7882	-0.0019	-0.5328	-0.0022	0.3191	-0.1226	-0.3458	-0.0651	0.5684	0.1246	0.1599	0.0673	-0.1244	0.3462	-0.0611	0.2162	-25.0216	11.8846	-27.1112
28	7.5274	3.6821	0.2518	4.3239	-4.0603	6.9462	-0.0806	0.1716	-0.3639	-0.0247	0.0748	-0.187	-0.0269	0.0328	0.0058	0.022	0.0381	-0.0214	0.1423	0.0253	0.1578	-34.9671	7.2867	-22.2576

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	30 - 104
2	X-RAY DIFFRACTION	2	ALL	AAA	105 - 130
3	X-RAY DIFFRACTION	3	ALL	AAA	131 - 158
4	X-RAY DIFFRACTION	4	ALL	AAA	159 - 202
5	X-RAY DIFFRACTION	5	ALL	AAA	203 - 286
6	X-RAY DIFFRACTION	6	ALL	AAA	287 - 328
7	X-RAY DIFFRACTION	7	ALL	BBB	30 - 105
8	X-RAY DIFFRACTION	8	ALL	BBB	106 - 122
9	X-RAY DIFFRACTION	9	ALL	BBB	123 - 160
10	X-RAY DIFFRACTION	10	ALL	BBB	161 - 188
11	X-RAY DIFFRACTION	11	ALL	BBB	189 - 208
12	X-RAY DIFFRACTION	12	ALL	BBB	209 - 260
13	X-RAY DIFFRACTION	13	ALL	BBB	261 - 284
14	X-RAY DIFFRACTION	14	ALL	BBB	285 - 297
15	X-RAY DIFFRACTION	15	ALL	BBB	298 - 318
16	X-RAY DIFFRACTION	16	ALL	BBB	319 - 331
17	X-RAY DIFFRACTION	17	ALL	CCC	30 - 105
18	X-RAY DIFFRACTION	18	ALL	CCC	106 - 123
19	X-RAY DIFFRACTION	19	ALL	CCC	124 - 260
20	X-RAY DIFFRACTION	20	ALL	CCC	261 - 295
21	X-RAY DIFFRACTION	21	ALL	CCC	296 - 333
22	X-RAY DIFFRACTION	22	ALL	CCC	334 - 338
23	X-RAY DIFFRACTION	23	ALL	DDD	30 - 156
24	X-RAY DIFFRACTION	24	ALL	DDD	157 - 192
25	X-RAY DIFFRACTION	25	ALL	DDD	193 - 208
26	X-RAY DIFFRACTION	26	ALL	DDD	209 - 269
27	X-RAY DIFFRACTION	27	ALL	DDD	270 - 322
28	X-RAY DIFFRACTION	28	ALL	DDD	323 - 336

-
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