[English] 日本語
Yorodumi
- PDB-5n2j: UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium ther... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n2j
TitleUDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum (closed form)
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsTRANSFERASE / glycoprotein / misfolding / endoplasmic reticulum
Function / homology
Function and homology information


UDP-glucose:glycoprotein glucosyltransferase activity / protein N-linked glycosylation via asparagine / ERAD pathway / unfolded protein binding / endoplasmic reticulum lumen / nucleotide binding / metal ion binding
Similarity search - Function
UDP-glucose:glycoprotein glucosyltransferase, thioredoxin-like domain 4 / UGGT, thioredoxin-like domain 3 / UGGT, thioredoxin-like domain 1 / UGGT, thioredoxin-like domain 2 / UDP-glucose:Glycoprotein Glucosyltransferase / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Glucosyltransferase 24, catalytic domain ...UDP-glucose:glycoprotein glucosyltransferase, thioredoxin-like domain 4 / UGGT, thioredoxin-like domain 3 / UGGT, thioredoxin-like domain 1 / UGGT, thioredoxin-like domain 2 / UDP-glucose:Glycoprotein Glucosyltransferase / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Glucosyltransferase 24, catalytic domain / Glucosyltransferase 24 / UDP-glucose:Glycoprotein Glucosyltransferase / Nucleotide-diphospho-sugar transferases / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å
AuthorsRoversi, P. / Caputo, A.T. / Hill, J. / Alonzi, D.S. / Zitzmann, N.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust097300/Z/11/Z United Kingdom
Wellcome Trust106272/Z/14/Z United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Interdomain conformational flexibility underpins the activity of UGGT, the eukaryotic glycoprotein secretion checkpoint.
Authors: Roversi, P. / Marti, L. / Caputo, A.T. / Alonzi, D.S. / Hill, J.C. / Dent, K.C. / Kumar, A. / Levasseur, M.D. / Lia, A. / Waksman, T. / Basu, S. / Soto Albrecht, Y. / Qian, K. / McIvor, J.P. ...Authors: Roversi, P. / Marti, L. / Caputo, A.T. / Alonzi, D.S. / Hill, J.C. / Dent, K.C. / Kumar, A. / Levasseur, M.D. / Lia, A. / Waksman, T. / Basu, S. / Soto Albrecht, Y. / Qian, K. / McIvor, J.P. / Lipp, C.B. / Siliqi, D. / Vasiljevic, S. / Mohammed, S. / Lukacik, P. / Walsh, M.A. / Santino, A. / Zitzmann, N.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-glucose-glycoprotein glucosyltransferase-like protein
B: UDP-glucose-glycoprotein glucosyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,14715
Polymers339,2772
Non-polymers4,87113
Water362
1
A: UDP-glucose-glycoprotein glucosyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,1058
Polymers169,6381
Non-polymers2,4667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-glucose-glycoprotein glucosyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0437
Polymers169,6381
Non-polymers2,4046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.600, 148.600, 179.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein UDP-glucose-glycoprotein glucosyltransferase-like protein


Mass: 169638.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0048990 / Plasmid: pHLSec / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0SB58

-
Sugars , 4 types, 10 molecules

#2: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 4
Source method: isolated from a genetically manipulated source
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, 5 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 58 % / Description: Needles
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Morpheus Amino acids mix, 0.1 M Morpheus Buffer System 2 pH 7.5, 50 % v/v Morpheus Precipitant Mix 4, i.e. 12.5% v/v MPD; 12.5% w/v PEG 1000, 12.5% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92821 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92821 Å / Relative weight: 1
ReflectionResolution: 4.3→179.97 Å / Num. all: 372151 / Num. obs: 26703 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 115.37 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.783 / Rpim(I) all: 0.217 / Rrim(I) all: 0.812 / Rsym value: 0.815 / Net I/σ(I): 4.9
Reflection shellResolution: 4.3→4.5 Å / Redundancy: 14.4 % / Rmerge(I) obs: 3.548 / Mean I/σ(I) obs: 1.3 / Num. measured obs: 55855 / Num. unique all: 3889 / CC1/2: 0.444 / Rpim(I) all: 0.967 / Rrim(I) all: 3.679 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N2J

Resolution: 4.4→114.59 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.032
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1282 5.16 %RANDOM
Rwork0.201 ---
obs0.203 24865 100 %-
Displacement parametersBiso mean: 243.36 Å2
Baniso -1Baniso -2Baniso -3
1--11.1219 Å20 Å20 Å2
2---11.1219 Å20 Å2
3---22.2438 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: LAST / Resolution: 4.4→114.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22130 0 315 2 22447
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0145150HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2381687HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10042SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes582HARMONIC2
X-RAY DIFFRACTIONt_gen_planes6471HARMONIC5
X-RAY DIFFRACTIONt_it45148HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.65
X-RAY DIFFRACTIONt_other_torsion18.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2996SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact49864SEMIHARMONIC4
LS refinement shellResolution: 4.4→4.59 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2749 165 5.47 %
Rwork0.2293 2849 -
all0.2318 3014 -
obs--99.93 %
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)
11.58-2.73180.34547.99592.91048.31550.1134-0.28190.32130.2568-0.31040.24810.05330.01380.19710.3040.03080.1520.1896-0.152-0.024442.6867111.665122.909
22.15630.2476-0.47598.31552.91048.3155-0.1255-0.0033-0.0361-0.1742-0.03030.05270.01020.42090.15580.30370.152-0.02590.1531-0.1001-0.30473.790175.545380.259
36.12041.48632.91043.8285-0.78617.10370.01260.11520.27670.29910.1231-0.15520.09110.3146-0.13570.1167-0.01530.1424-0.0211-0.0873-0.156373.5748106.581105.278
43.83260.8416-1.80253.0468-1.573.55980.01660.44140.4547-0.14840.10.4888-0.20370.0484-0.11660.24720.0562-0.0272-0.11770.08860.303340.8369118.90582.3382
58.3155-2.91042.91046.60480.8353.91570.02570.3180.3962-0.1609-0.01720.4190.0928-0.3177-0.00850.1290.1460.0750.103-0.13740.245317.4008111.7894.6935
61.9-0.33540.82477.73382.61028.31550.04170.04130.01840.033-0.08670.32120.15540.260.0450.21510.1520.08520.28210.1086-0.27342.500786.2102103.287
78.24912.4120.80113.58631.63866.0751-0.0194-0.37370.4955-0.2770.13330.53050.0817-0.519-0.1139-0.18940.11740.02770.3040.09030.017613.180382.189791.0413
83.13942.91042.91046.64862.91048.31550.108-0.4340.28940.3535-0.1122-0.22790.2049-0.19860.00430.27510.0967-0.1520.304-0.152-0.2885133.2645.6457122.547
92.47392.49712.40826.62172.91048.3155-0.13770.0742-0.0143-0.15090.0630.1240.21150.28890.07470.3040.12720.00980.3039-0.0535-0.304149.5351.2178.5943
105.8064-0.87482.91043.0355-1.0017.67930.0690.15260.1171-0.22860.2773-0.2416-0.03480.4565-0.3463-0.0258-0.00230.01050.3039-0.1367-0.1283160.11229.5594104.715
114.0336-2.91041.82325.44482.91047.62890.03870.38220.5005-0.2409-0.1143-0.1706-0.4251-0.01040.07560.1901-0.1373-0.08840.16850.1235-0.1116133.26653.70681.8835
127.4645-2.91042.8038.08-0.51745.2052-0.0166-0.1010.3201-0.2621-0.17430.3219-0.1136-0.27760.19090.26980.1434-0.1520.3034-0.152-0.3009109.8855.062794.2167
131.7188-0.6781.96298.31250.73327.32660.0314-0.1999-0.16060.0323-0.0642-0.1220.2637-0.35270.03270.20960.00620.02530.3040.1127-0.2257124.0122.0085102.839
148.3155-1.61360.32017.9892.91043.74230.0071-0.54420.2044-0.3224-0.50330.4878-0.0132-0.35180.4963-0.02140.152-0.12020.304-0.152-0.294795.256928.712290.5119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|39 - A|225 A|2056 - A|2060}
2X-RAY DIFFRACTION2{ A|414 - A|666 A|1638 - A|1644}
3X-RAY DIFFRACTION3{ A|667 - A|880 }
4X-RAY DIFFRACTION4{ A|279 - A|413 A|881 - A|950 A|2329 - A|2334 A|1894 - A|1898 }
5X-RAY DIFFRACTION5{ A|27 - A|38 A|226 - A|245 A|951 - A|1037 }
6X-RAY DIFFRACTION6{ A|1038 - A|1152 }
7X-RAY DIFFRACTION7{ A|1187 - A|1476 A|2227 - A|2233 A|9000 }
8X-RAY DIFFRACTION8{ B|39 - B|225 B|2056 - B|2060}
9X-RAY DIFFRACTION9{ B|414 - B|666 B|1638 - B|1644}
10X-RAY DIFFRACTION10{ B|667 - B|880 }
11X-RAY DIFFRACTION11{ B|279 - B|413 B|881 - B|950 B|2329 - B|2334 B|1894 - B|1898 }
12X-RAY DIFFRACTION12{ B|27 - B|38 B|226 - B|245 B|951 - B|1037 }
13X-RAY DIFFRACTION13{ B|1038 - B|1152 }
14X-RAY DIFFRACTION14{ B|1187 - B|1476 B|2227 - B|2233 B|9000 }

+
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://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