PDB-7qqh: Crystal structure of MYORG (D520N) in complex with Gal-a1,4-Glc

ID or keywords:

Entry

Database: PDB / ID: 7qqh

Title

Crystal structure of MYORG (D520N) in complex with Gal-a1,4-Glc

Components

Myogenesis-regulating glycosidase

Keywords

HYDROLASE / GH31 / Glycoside hydrolase / MYORG / NET37 / galactosidase

Function / homology

Function and homology information

Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / positive regulation of insulin-like growth factor receptor signaling pathway / hydrolase activity, hydrolyzing O-glycosyl compounds / skeletal muscle fiber development / nuclear membrane / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Meek, R.W. / Davies, G.J.

Funding support

United Kingdom, 1items

Citation

Journal: Plos Biol. / Year: 2022
Title: The primary familial brain calcification-associated protein MYORG is an alpha-galactosidase with restricted substrate specificity.
Authors: Meek, R.W. / Brockerman, J. / Fordwour, O.B. / Zandberg, W.F. / Davies, G.J. / Vocadlo, D.J.

History

Deposition	Jan 7, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 31, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 18, 2023	Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3	Oct 16, 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	7qqh.cif.gz	941.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7qqh.ent.gz	764 KB	Display	PDB format
PDBx/mmJSON format	7qqh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	7qqfC 7qqgC 2f2hS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Myogenesis-regulating glycosidase

B: Myogenesis-regulating glycosidase

C: Myogenesis-regulating glycosidase

D: Myogenesis-regulating glycosidase

hetero molecules

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

1

A: Myogenesis-regulating glycosidase

D: Myogenesis-regulating glycosidase

hetero molecules

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

2

B: Myogenesis-regulating glycosidase

C: Myogenesis-regulating glycosidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.286, 79.099, 178.016
Angle α, β, γ (deg.)	80.909, 79.112, 62.667
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLU	GLU	TRP	TRP	A	A	91 - 712	13 - 634
2	2	1	GLU	GLU	TRP	TRP	B	B	91 - 712	13 - 634
3	3	2	GLU	GLU	TRP	TRP	A	A	91 - 712	13 - 634
4	4	2	GLU	GLU	TRP	TRP	C	C	91 - 712	13 - 634
5	5	3	GLU	GLU	TRP	TRP	A	A	91 - 712	13 - 634
6	6	3	GLU	GLU	TRP	TRP	D	D	91 - 712	13 - 634
7	7	4	ARG	ARG	TRP	TRP	B	B	89 - 712	11 - 634
8	8	4	ARG	ARG	TRP	TRP	C	C	89 - 712	11 - 634
9	9	5	LEU	LEU	ALA	ALA	B	B	88 - 713	10 - 635
10	10	5	LEU	LEU	ALA	ALA	D	D	88 - 713	10 - 635
11	11	6	ARG	ARG	TRP	TRP	C	C	89 - 712	11 - 634
12	12	6	ARG	ARG	TRP	TRP	D	D	89 - 712	11 - 634

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Myogenesis-regulating glycosidase / Uncharacterized family 31 glucosidase KIAA1161 Mass: 72462.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MYORG, KIAA1161 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q6NSJ0, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

#1: Protein

Myogenesis-regulating glycosidase / Uncharacterized family 31 glucosidase KIAA1161

Mass: 72462.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: MYORG, KIAA1161 / Production host:

Trichoplusia ni (cabbage looper)
References: UniProt: Q6NSJ0, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

-
Sugars , 3 types, 22 molecules

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#3: Polysaccharide

alpha-D-galactopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source

#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

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / 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

-
Non-polymers , 3 types, 499 molecules

#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₂O₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.1 Å³/Da / Density % sol: 60.26 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM HEPES 7.0, 10% PEG MME5000 and 5% tasimate pH7.0

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.97627 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 27, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97627 Å / Relative weight: 1

Reflection

Resolution: 2.25→64.53 Å / Num. obs: 161989 / % possible obs: 98.2 % / Redundancy: 3.1 % / CC_1/2: 0.99 / R_merge(I) obs: 0.073 / R_pim(I) all: 0.073 / R_rim(I) all: 0.103 / Net I/σ(I): 7.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
12.32-64.53	3.6	0.019	31.7	999	0.985	0.019	0.026
2.25-2.29	3.1	0.8	1	7923	0.962	0.8	1.131

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2F2H

2f2h

Resolution: 2.25→64.53 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.938 / SU B: 18.571 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.192
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2266	8099	5 %
R_work	0.2122	153878	-
all	0.213	-	-
obs	-	161977	98.198 %

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: 50.45 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.466 Å²	-0.418 Å²	2.387 Å²
2-	-	0.442 Å²	-0.397 Å²
3-	-	-	0.051 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→64.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19783	0	520	486	20789

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	20991
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	19056
X-RAY DIFFRACTION	r_angle_refined_deg	1.311	1.679	28649
X-RAY DIFFRACTION	r_angle_other_deg	1.111	1.603	43769
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.042	5	2598
X-RAY DIFFRACTION	r_dihedral_angle_other_1_deg	2.921	20	26
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.099	20.176	1193
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.515	15.125	3131
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.618	15	197
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	2644
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	23552
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5266
X-RAY DIFFRACTION	r_nbd_refined	0.177	0.2	3468
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.173	0.2	18098
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	9853
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	9780
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	741
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.106	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.112	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	62
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.145	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	0.795	3.137	9884
X-RAY DIFFRACTION	r_mcbond_other	0.795	3.137	9883
X-RAY DIFFRACTION	r_mcangle_it	1.357	4.703	12342
X-RAY DIFFRACTION	r_mcangle_other	1.357	4.703	12343
X-RAY DIFFRACTION	r_scbond_it	0.787	3.235	11107
X-RAY DIFFRACTION	r_scbond_other	0.787	3.235	11107
X-RAY DIFFRACTION	r_scangle_it	1.343	4.819	16305
X-RAY DIFFRACTION	r_scangle_other	1.343	4.819	16306
X-RAY DIFFRACTION	r_lrange_it	3.255	35.219	22498
X-RAY DIFFRACTION	r_lrange_other	3.235	35.145	22449
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.054	0.05	20844
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.046	0.05	20776
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.051	0.05	20814
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.046	0.05	21006
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.051	0.05	21019
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.047	0.05	20882

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.05393	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.05393	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.0461	0.0501
2	4	C	X-RAY DIFFRACTION	Local ncs	0.0461	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05097	0.0501
3	6	D	X-RAY DIFFRACTION	Local ncs	0.05097	0.0501
4	7	B	X-RAY DIFFRACTION	Local ncs	0.04568	0.0501
4	8	C	X-RAY DIFFRACTION	Local ncs	0.04568	0.0501
5	9	B	X-RAY DIFFRACTION	Local ncs	0.05069	0.0501
5	10	D	X-RAY DIFFRACTION	Local ncs	0.05069	0.0501
6	11	C	X-RAY DIFFRACTION	Local ncs	0.047	0.0501
6	12	D	X-RAY DIFFRACTION	Local ncs	0.047	0.0501

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 (%)
2.25-2.308	0.383	550	0.374	11265	X-RAY DIFFRACTION	97.0351
2.308-2.372	0.304	607	0.314	11022	X-RAY DIFFRACTION	97.5669
2.372-2.44	0.295	543	0.292	10776	X-RAY DIFFRACTION	97.7208
2.44-2.516	0.279	570	0.268	10362	X-RAY DIFFRACTION	97.3464
2.516-2.598	0.284	474	0.261	10182	X-RAY DIFFRACTION	98.1216
2.598-2.689	0.301	490	0.283	9839	X-RAY DIFFRACTION	98.1191
2.689-2.791	0.279	496	0.242	9479	X-RAY DIFFRACTION	98.1212
2.791-2.905	0.259	454	0.223	9191	X-RAY DIFFRACTION	98.3281
2.905-3.034	0.222	457	0.214	8792	X-RAY DIFFRACTION	98.4984
3.034-3.182	0.23	427	0.195	8381	X-RAY DIFFRACTION	97.9646
3.182-3.354	0.218	429	0.19	7889	X-RAY DIFFRACTION	98.0087
3.354-3.557	0.238	427	0.22	7516	X-RAY DIFFRACTION	98.6708
3.557-3.803	0.233	360	0.207	7165	X-RAY DIFFRACTION	99.0392
3.803-4.107	0.191	381	0.195	6595	X-RAY DIFFRACTION	98.9644
4.107-4.499	0.184	360	0.168	6044	X-RAY DIFFRACTION	99.1485
4.499-5.03	0.166	305	0.149	5533	X-RAY DIFFRACTION	99.2688
5.03-5.807	0.202	256	0.187	4867	X-RAY DIFFRACTION	99.1484
5.807-7.11	0.218	243	0.194	4042	X-RAY DIFFRACTION	97.9205
7.11-10.046	0.183	169	0.162	3198	X-RAY DIFFRACTION	99.5565
10.046-64.53	0.223	101	0.237	1740	X-RAY DIFFRACTION	99.5673

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	1.4012	-0.1888	-0.4059	1.1614	0.211	1.7097	0.0449	0.1441	-0.0104	-0.009	0.0565	0.06	0.0457	-0.1132	-0.1014	0.1284	-0.032	0.1266	0.4028	-0.0233	0.1494	-13.7207	3.0686	42.2418
2	1.0566	0.051	-0.1614	1.0995	0.0395	1.2135	0.1043	-0.0764	0.0733	0.1203	-0.0643	0.0242	0.0923	-0.1385	-0.04	0.0543	-0.0365	0.0361	0.0314	-0.0153	0.0435	11.9005	-11.3029	-39.8044
3	1.193	0.036	-0.1213	1.0558	0.0023	1.2983	0.1097	-0.0003	-0.0225	0.0004	-0.0797	0.003	0.0631	0.0354	-0.03	0.1038	0.0633	0.0753	0.3097	-0.0253	0.0949	-30.9567	-9.7671	2.7738
4	1.3266	-0.0905	-0.1347	1.3609	-0.1412	1.3807	0.148	0.0438	0.112	-0.1345	-0.017	-0.0401	0.0327	0.113	-0.1311	0.0701	0.0346	0.0634	0.0272	0.0247	0.0845	-44.157	8.901	94.1776

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	91 - 713
2	X-RAY DIFFRACTION	1	ALL	E	1
3	X-RAY DIFFRACTION	1	ALL	E	2
4	X-RAY DIFFRACTION	1	ALL	A	801
5	X-RAY DIFFRACTION	1	ALL	A	802
6	X-RAY DIFFRACTION	1	ALL	A	803
7	X-RAY DIFFRACTION	1	ALL	A	804
8	X-RAY DIFFRACTION	1	ALL	A	805
9	X-RAY DIFFRACTION	2	ALL	B	88 - 713
10	X-RAY DIFFRACTION	2	ALL	F	1
11	X-RAY DIFFRACTION	2	ALL	F	2
12	X-RAY DIFFRACTION	2	ALL	G	1
13	X-RAY DIFFRACTION	2	ALL	B	801
14	X-RAY DIFFRACTION	2	ALL	B	802
15	X-RAY DIFFRACTION	2	ALL	B	803
16	X-RAY DIFFRACTION	2	ALL	G	2
17	X-RAY DIFFRACTION	2	ALL	H	1
18	X-RAY DIFFRACTION	2	ALL	H	2
19	X-RAY DIFFRACTION	2	ALL	B	804
20	X-RAY DIFFRACTION	3	ALL	C	89 - 713
21	X-RAY DIFFRACTION	3	ALL	I	1
22	X-RAY DIFFRACTION	3	ALL	I	2
23	X-RAY DIFFRACTION	3	ALL	J	1
24	X-RAY DIFFRACTION	3	ALL	C	801
25	X-RAY DIFFRACTION	3	ALL	C	802
26	X-RAY DIFFRACTION	3	ALL	C	803
27	X-RAY DIFFRACTION	3	ALL	J	2
28	X-RAY DIFFRACTION	3	ALL	C	804
29	X-RAY DIFFRACTION	3	ALL	C	805
30	X-RAY DIFFRACTION	4	ALL	D	88 - 713
31	X-RAY DIFFRACTION	4	ALL	K	1
32	X-RAY DIFFRACTION	4	ALL	K	2
33	X-RAY DIFFRACTION	4	ALL	L	1
34	X-RAY DIFFRACTION	4	ALL	D	801
35	X-RAY DIFFRACTION	4	ALL	D	802
36	X-RAY DIFFRACTION	4	ALL	D	803
37	X-RAY DIFFRACTION	4	ALL	D	804
38	X-RAY DIFFRACTION	4	ALL	D	805
39	X-RAY DIFFRACTION	4	ALL	L	2

-
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

-
Protein , 1 types, 4 molecules ABCD

-
Sugars , 3 types, 22 molecules

-
Non-polymers , 3 types, 499 molecules

-
Details

-
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

-Protein , 1 types, 4 molecules ABCD

-Sugars , 3 types, 22 molecules

-Non-polymers , 3 types, 499 molecules

-Details

-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

-
Protein , 1 types, 4 molecules ABCD

-
Sugars , 3 types, 22 molecules

-
Non-polymers , 3 types, 499 molecules

-
Details

-
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