[English] 日本語
Yorodumi
- PDB-7qqf: Crystal structure of unliganded MYORG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qqf
TitleCrystal structure of unliganded MYORG
ComponentsMyogenesis-regulating glycosidase
KeywordsHYDROLASE / 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 / skeletal muscle fiber development / hydrolase activity, hydrolyzing O-glycosyl compounds / nuclear membrane / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum membrane
Similarity search - Function
: / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / MALONATE ION / Myogenesis-regulating glycosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsMeek, R.W. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society180016 United Kingdom
CitationJournal: 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
DepositionJan 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: 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 1.2Jan 31, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myogenesis-regulating glycosidase
B: Myogenesis-regulating glycosidase
C: Myogenesis-regulating glycosidase
D: Myogenesis-regulating glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,95333
Polymers289,8534
Non-polymers8,10029
Water5,747319
1
A: Myogenesis-regulating glycosidase
D: Myogenesis-regulating glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,37715
Polymers144,9262
Non-polymers3,45013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myogenesis-regulating glycosidase
C: Myogenesis-regulating glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,57718
Polymers144,9262
Non-polymers4,65016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.109, 78.986, 180.113
Angle α, β, γ (deg.)88.062, 78.801, 62.714
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUALAALAAA92 - 71314 - 635
221LEULEUALAALABB92 - 71314 - 635
332LEULEUALAALAAA92 - 71314 - 635
442LEULEUALAALACC92 - 71314 - 635
553PHEPHETRPTRPAA100 - 71222 - 634
663PHEPHETRPTRPDD100 - 71222 - 634
774LEULEUALAALABB92 - 71314 - 635
884LEULEUALAALACC92 - 71314 - 635
995PHEPHETRPTRPBB100 - 71222 - 634
10105PHEPHETRPTRPDD100 - 71222 - 634
11116PHEPHETRPTRPCC100 - 71222 - 634
12126PHEPHETRPTRPDD100 - 71222 - 634

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

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Myogenesis-regulating glycosidase / Uncharacterized family 31 glucosidase KIAA1161


Mass: 72463.234 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) / Strain (production host): Hi Five
References: UniProt: Q6NSJ0, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

-
Sugars , 5 types, 21 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 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.: 11 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 327 molecules

#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES pH 7.0, 10% PEG MME5000 and 5% tasimate pH 7.0.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.43→66.57 Å / Num. obs: 131515 / % possible obs: 98.2 % / Redundancy: 2.2 % / CC1/2: 0.983 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.066 / Rrim(I) all: 0.093 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.1 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
13.31-66.570.01529.87960.9640.0150.021
2.43-2.471.071165090.5151.0711.514

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F2H

2f2h


Resolution: 2.43→66.57 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.933 / SU B: 22.491 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.233
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.233 6445 4.902 %
Rwork0.2108 125031 -
all0.212 --
obs-131476 98.149 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 58.353 Å2
Baniso -1Baniso -2Baniso -3
1--0.158 Å20.096 Å2-1.604 Å2
2--1.904 Å20.501 Å2
3----3.268 Å2
Refinement stepCycle: LAST / Resolution: 2.43→66.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19386 0 531 319 20236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01320594
X-RAY DIFFRACTIONr_bond_other_d0.0010.01518617
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.68128134
X-RAY DIFFRACTIONr_angle_other_deg1.1391.60542754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03552421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.62720.1391152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.065152950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.56115189
X-RAY DIFFRACTIONr_chiral_restr0.0550.22610
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0223123
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025151
X-RAY DIFFRACTIONr_nbd_refined0.1840.23509
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.217412
X-RAY DIFFRACTIONr_nbtor_refined0.1640.29710
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.29302
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2606
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0460.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.29
X-RAY DIFFRACTIONr_nbd_other0.2450.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.22
X-RAY DIFFRACTIONr_mcbond_it0.9083.69715
X-RAY DIFFRACTIONr_mcbond_other0.9083.69713
X-RAY DIFFRACTIONr_mcangle_it1.535.39712123
X-RAY DIFFRACTIONr_mcangle_other1.535.39712124
X-RAY DIFFRACTIONr_scbond_it0.9083.70410879
X-RAY DIFFRACTIONr_scbond_other0.9083.70410876
X-RAY DIFFRACTIONr_scangle_it1.545.52716011
X-RAY DIFFRACTIONr_scangle_other1.545.52716012
X-RAY DIFFRACTIONr_lrange_it3.97268.60786627
X-RAY DIFFRACTIONr_lrange_other3.96668.5986530
X-RAY DIFFRACTIONr_ncsr_local_group_10.0760.0520544
X-RAY DIFFRACTIONr_ncsr_local_group_20.0770.0520413
X-RAY DIFFRACTIONr_ncsr_local_group_30.0920.0518984
X-RAY DIFFRACTIONr_ncsr_local_group_40.0780.0520594
X-RAY DIFFRACTIONr_ncsr_local_group_50.0920.0519043
X-RAY DIFFRACTIONr_ncsr_local_group_60.0850.0519106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.076340.0501
12BX-RAY DIFFRACTIONLocal ncs0.076340.0501
23AX-RAY DIFFRACTIONLocal ncs0.077450.0501
24CX-RAY DIFFRACTIONLocal ncs0.077450.0501
35AX-RAY DIFFRACTIONLocal ncs0.092250.0501
36DX-RAY DIFFRACTIONLocal ncs0.092250.0501
47BX-RAY DIFFRACTIONLocal ncs0.077920.0501
48CX-RAY DIFFRACTIONLocal ncs0.077920.0501
59BX-RAY DIFFRACTIONLocal ncs0.091580.0501
510DX-RAY DIFFRACTIONLocal ncs0.091580.0501
611CX-RAY DIFFRACTIONLocal ncs0.085050.0501
612DX-RAY DIFFRACTIONLocal ncs0.085050.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.4930.3264650.3219122X-RAY DIFFRACTION96.5555
2.493-2.5610.3094720.3059017X-RAY DIFFRACTION97.7341
2.561-2.6360.3244070.2968751X-RAY DIFFRACTION97.7896
2.636-2.7170.34090.2918514X-RAY DIFFRACTION98.0011
2.717-2.8060.2794340.2788172X-RAY DIFFRACTION97.5848
2.806-2.9040.2884620.2657925X-RAY DIFFRACTION98.0592
2.904-3.0140.2643450.2477699X-RAY DIFFRACTION97.6569
3.014-3.1370.283460.237456X-RAY DIFFRACTION98.1384
3.137-3.2760.2553940.227078X-RAY DIFFRACTION98.1866
3.276-3.4360.2393190.2186881X-RAY DIFFRACTION98.5087
3.436-3.6220.2443640.2116450X-RAY DIFFRACTION98.454
3.622-3.8410.2013350.1946075X-RAY DIFFRACTION98.3732
3.841-4.1070.2023190.1785777X-RAY DIFFRACTION98.7686
4.107-4.4350.1953240.1625353X-RAY DIFFRACTION99.1789
4.435-4.8580.1772520.1444960X-RAY DIFFRACTION99.1629
4.858-5.4310.1842370.1644452X-RAY DIFFRACTION98.7574
5.431-6.2710.2371940.1813988X-RAY DIFFRACTION99.524
6.271-7.6770.1971650.1893357X-RAY DIFFRACTION99.3232
7.677-10.8470.2141310.1812589X-RAY DIFFRACTION98.9811
10.847-66.570.286710.3111416X-RAY DIFFRACTION98.6729
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.243-0.0110.30990.724-0.14571.73860.0448-0.12010.03060.20.0015-0.04920.00770.1202-0.04640.08690.0029-0.05730.29360.01620.1956-39.2244-1.1995-34.9319
21.37170.00990.01230.9496-0.0081.34540.08870.12030.04460.1604-0.05360.0407-0.0683-0.0929-0.03520.1206-0.1071-0.03040.16580.04340.1791-28.8475-0.028259.4008
31.14370.089-0.03580.768-0.15781.56810.0566-0.001-0.0108-0.1512-0.0334-0.0141-0.0932-0.1247-0.02310.09690.0549-0.04790.0421-0.01550.190613.5793-0.823101.6312
41.62850.08780.6040.77870.44562.93070.04320.15250.0294-0.14750.0024-0.01810.02460.132-0.04560.1530.0614-0.06710.2220.0490.2427-11.1537-8.283718.5919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA92 - 714
2X-RAY DIFFRACTION1ALLA801
3X-RAY DIFFRACTION1ALLE1
4X-RAY DIFFRACTION1ALLE2
5X-RAY DIFFRACTION1ALLF1
6X-RAY DIFFRACTION1ALLF2
7X-RAY DIFFRACTION1ALLA802
8X-RAY DIFFRACTION1ALLA803
9X-RAY DIFFRACTION1ALLA804
10X-RAY DIFFRACTION1ALLA805
11X-RAY DIFFRACTION1ALLE3
12X-RAY DIFFRACTION2ALLB92 - 713
13X-RAY DIFFRACTION2ALLG1
14X-RAY DIFFRACTION2ALLG2
15X-RAY DIFFRACTION2ALLH1
16X-RAY DIFFRACTION2ALLB801
17X-RAY DIFFRACTION2ALLB802
18X-RAY DIFFRACTION2ALLB803
19X-RAY DIFFRACTION2ALLI1
20X-RAY DIFFRACTION2ALLI2
21X-RAY DIFFRACTION2ALLB804
22X-RAY DIFFRACTION2ALLB805
23X-RAY DIFFRACTION2ALLH2
24X-RAY DIFFRACTION3ALLC92 - 713
25X-RAY DIFFRACTION3ALLJ1
26X-RAY DIFFRACTION3ALLK1
27X-RAY DIFFRACTION3ALLK2
28X-RAY DIFFRACTION3ALLL1
29X-RAY DIFFRACTION3ALLL2
30X-RAY DIFFRACTION3ALLC801
31X-RAY DIFFRACTION3ALLC802
32X-RAY DIFFRACTION3ALLC803
33X-RAY DIFFRACTION3ALLJ3
34X-RAY DIFFRACTION3ALLJ2
35X-RAY DIFFRACTION3ALLC804
36X-RAY DIFFRACTION3ALLC805
37X-RAY DIFFRACTION4ALLD100 - 713
38X-RAY DIFFRACTION4ALLM1
39X-RAY DIFFRACTION4ALLM2
40X-RAY DIFFRACTION4ALLN1
41X-RAY DIFFRACTION4ALLD801
42X-RAY DIFFRACTION4ALLD802
43X-RAY DIFFRACTION4ALLN2
44X-RAY DIFFRACTION4ALLD803

+
About Yorodumi

-
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://pdbjlvh1.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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more