[English] 日本語
Yorodumi
- PDB-3tax: A Neutral Diphosphate Mimic Crosslinks the Active Site of Human O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tax
TitleA Neutral Diphosphate Mimic Crosslinks the Active Site of Human O-GlcNAc Transferase
Components
  • Casein kinase II subunit alpha
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / thiocarbamate crosslink / covalent inhibitor / gylcosyltransferase inhibitor / O-GlcNAc Transferase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / regulation of insulin receptor signaling pathway / acetylglucosaminyltransferase activity / NSL complex / regulation of Rac protein signal transduction / regulation of necroptotic process ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / regulation of insulin receptor signaling pathway / acetylglucosaminyltransferase activity / NSL complex / regulation of Rac protein signal transduction / regulation of necroptotic process / protein O-linked glycosylation / negative regulation of stem cell population maintenance / regulation of gluconeogenesis / Phosphorylation and nuclear translocation of BMAL1 (ARNTL) and CLOCK / protein kinase CK2 complex / positive regulation of aggrephagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / regulation of glycolytic process / symbiont-mediated disruption of host cell PML body / RIPK1-mediated regulated necrosis / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / regulation of synapse assembly / Receptor Mediated Mitophagy / Formation of WDR5-containing histone-modifying complexes / hemopoiesis / positive regulation of stem cell population maintenance / Sin3-type complex / Synthesis of PC / positive regulation of proteolysis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of apoptotic signaling pathway / negative regulation of signal transduction by p53 class mediator / Maturation of hRSV A proteins / phosphatidylinositol-3,4,5-trisphosphate binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / histone acetyltransferase complex / negative regulation of double-strand break repair via homologous recombination / mitophagy / positive regulation of Wnt signaling pathway / Wnt signaling pathway / negative regulation of protein ubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / response to nutrient / rhythmic process / positive regulation of TORC1 signaling / negative regulation of cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / response to insulin / Signal transduction by L1 / protein processing / cellular response to glucose stimulus / circadian regulation of gene expression / positive regulation of translation / chromatin DNA binding / Hsp90 protein binding / peptidyl-serine phosphorylation / PML body / kinase activity / Regulation of necroptotic cell death / SPOP-mediated proteasomal degradation of PD-L1(CD274) / mitochondrial membrane / Regulation of PTEN stability and activity / double-strand break repair / positive regulation of protein catabolic process / KEAP1-NFE2L2 pathway / UCH proteinases / positive regulation of cell growth / positive regulation of cold-induced thermogenesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / HATs acetylate histones / protein folding / heterochromatin formation / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / non-specific serine/threonine protein kinase / protein stabilization / negative regulation of translation / apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / DNA damage response / positive regulation of DNA-templated transcription / chromatin / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMYL GROUP / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsLazarus, M.B. / Jiang, J. / Pasquina, L. / Sliz, P. / Walker, S.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: A neutral diphosphate mimic crosslinks the active site of human O-GlcNAc transferase.
Authors: Jiang, J. / Lazarus, M.B. / Pasquina, L. / Sliz, P. / Walker, S.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,99912
Polymers164,7464
Non-polymers1,2538
Water18,3391018
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
hetero molecules

A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,99912
Polymers164,7464
Non-polymers1,2538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10510 Å2
ΔGint-122 kcal/mol
Surface area52880 Å2
MethodPISA
2
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9996
Polymers82,3732
Non-polymers6264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-51 kcal/mol
Surface area28870 Å2
MethodPISA
3
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules

C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,99912
Polymers164,7464
Non-polymers1,2538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10530 Å2
ΔGint-123 kcal/mol
Surface area52690 Å2
MethodPISA
4
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9996
Polymers82,3732
Non-polymers6264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-52 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.600, 136.640, 153.319
Angle α, β, γ (deg.)90.00, 103.02, 90.00
Int Tables number5
Space group name H-MI121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / O-GlcNAc transferase subunit p110 / O-linked N-acetylglucosamine transferase 110 kDa subunit


Mass: 80974.508 Da / Num. of mol.: 2 / Fragment: UNP residues 323-1041
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli (E. coli)
References: UniProt: O15294, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein/peptide Casein kinase II subunit alpha / CK II alpha


Mass: 1398.562 Da / Num. of mol.: 2 / Fragment: UNP residues 340-352 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human)
References: UniProt: P68400, non-specific serine/threonine protein kinase

-
Non-polymers , 4 types, 1026 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1018 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Nonpolymer detailsTHE INHIBITOR, 4-METHOXYPHENYL 6-ACETYL-2-BENZOXAZOLINONE- CARBOXYLATE, CROSSLINKS THE ACTIVE SITE ...THE INHIBITOR, 4-METHOXYPHENYL 6-ACETYL-2-BENZOXAZOLINONE- CARBOXYLATE, CROSSLINKS THE ACTIVE SITE OF OGT. EXPERIMENTAL EVIDENCE SUGGESTS THAT LYSINE 842 REACTS WITH ONE OF THE TWO CARBAMATES OF THE INHIBITOR, RELEASING 6-ACETYL-2-BENZOXAZOLINONE. THEN, THE NEARBY CYSTEINE 917 REACTS AGAIN WITH THE LYSINE ADDUCT TO RELEASE 4-METHOXYPHENOL AND GENERATES A COVALENT THIOCARBAMATE LINKAGE BETWEEN LYSINE 842 AND CYSTEINE 917.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6M Lithium Sulfate, 0.1M Bis Tris Propane pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.875→45 Å / Num. obs: 160121 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 23.74 Å2
Reflection shellResolution: 1.875→1.98 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.4 / Num. unique all: 22892 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.11.1refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE4

3pe4


Resolution: 1.88→37.6 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.9068 / SU R Cruickshank DPI: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 7950 5 %RANDOM
Rwork0.2191 ---
all0.22 166942 --
obs0.22 158992 99.2 %-
Displacement parametersBiso mean: 27.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.8602 Å20 Å2-2.4031 Å2
2--3.1149 Å20 Å2
3----2.2547 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 1.88→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11180 0 74 1018 12272
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00911574HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9815716HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4044SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes302HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1658HARMONIC5
X-RAY DIFFRACTIONt_it11574HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion16.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1514SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies10HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14130SEMIHARMONIC4
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2332 565 4.95 %
Rwork0.2172 10852 -
all0.218 11417 -
obs--99.2 %
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)
11.7568-1.01060.96732.03531.13170.4491-0.0095-0.02470.0014-0.09710.03210.1039-0.0458-0.0514-0.0225-0.06380.0977-0.09670.0950.108-0.056935.491236.5634-36.2652
20.5215-0.1487-0.3180.80840.86221.70050.0168-0.0023-0.0212-0.18350.04960.06450.0069-0.0144-0.06640.05810.0191-0.0830.03590.0717-0.058943.099832.6335-37.2162
31.9834-0.4522-1.12250.88980.26330.80150.1310.20270.1022-0.04870.01120.1593-0.1337-0.1137-0.1422-0.0630.03990.0786-0.03370.0357-0.043244.188341.265-14.9219
41.1950.63871.20152.42540.54932.27060.09720.18150.1339-0.4607-0.02890.2966-0.0594-0.2167-0.06840.0070.07450.0776-0.05670.0559-0.023724.053644.4691-2.8613
50.4662-0.13570.04780.9764-0.0970.87730.07830.1544-0.0044-0.3157-0.05510.14240.0793-0.0769-0.02320.00840.03930.0186-0.0676-0.0037-0.079723.770616.8801-2.3
6-0.03090.02730.0640.03930.04720.04670.0010.00460.0046-0.0046-0.0003-0.004-0.00750.0082-0.00070.0729-0.0013-0.08260.03030.0030.026433.202730.140143.8203
72.3353-0.7509-0.11621.2191-1.64290.4728-0.0172-0.2828-0.00790.37870.02840.2193-0.1181-0.0532-0.01120.03040.01770.1065-0.0546-0.0119-0.104531.905817.843838.5946
82.5802-0.056-2.48191.1083-2.79751.5774-0.0833-0.24210.21830.51460.17060.0938-0.1441-0.0448-0.08730.07820.0130.03270.0379-0.1029-0.018237.55322.475140.0407
90.4715-0.04870.01380.8168-0.01590.40380.052-0.04210.06030.0694-0.01890.0963-0.0396-0.0178-0.0331-0.02910.01550.1059-0.0631-0.0129-0.033826.645931.222321.9692
102.0671-0.68760.85980.0050.16151.322-0.04030.1231-0.1442-0.12760.00270.21590.1379-0.10590.03770.036-0.0054-0.10320.0082-0.01650.04297.484113.3763-4.7375
110.53820.4521-1.3711.6334-1.01122.4624-0.0701-0.1811-0.11940.1513-0.0726-0.21020.00640.35130.1427-0.04780.02970.0568-0.02750.0329-0.109367.5149-28.65482.8323
122.24350.3521.03471.34240.60160.4118-0.0456-0.1068-0.01970.17720.0116-0.2610.12930.14480.0340.02040.06080.0661-0.03510.0529-0.045555.0936-33.0224.4436
130.8342-0.0319-0.04480.9087-0.06520.4597-0.0013-0.05820.07850.0813-0.0384-0.2766-0.00590.15720.0397-0.05980.00430.0393-0.06660.0318-0.008954.5488-5.281224.9274
140.02520.0727-0.01240.0669-0.052-0.0071-0.00180.0098-0.0034-0.00790.00240.0010.00240.0038-0.00060.0606-0.0019-0.08920.00680.02460.04187.5581-18.563321.0801
151.378-2.47810.3860.09-0.4872.80630.0017-0.13-0.04650.14790.07920.37320.0092-0.3129-0.081-0.0963-0.00910.1155-0.04760.03050.032912.8919-6.271321.7457
160.2116-0.3404-0.171100.1882-0.0225-0.0037-0.00610.00250.02740.00030.0113-0.0083-0.00320.0034-0.00730.00650.09050.1538-0.01130.127315.3806-4.841833.3865
17-0.6208-2.00841.21680.1869-0.1041.08550.0549-0.1045-0.210.00270.06620.52040.1916-0.2781-0.121-0.0772-0.11290.0268-0.02950.02940.04569.8213-12.166412.7742
180.4439-0.09810.03430.70650.01110.5365-0.0369-0.0325-0.02710.1056-0.01040.03530.0555-0.01750.0473-0.0175-0.00820.0954-0.0660.0221-0.054232.7627-17.961926.4582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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