[English] 日本語
Yorodumi
- PDB-4ay6: Human O-GlcNAc transferase (OGT) in complex with UDP-5SGlcNAc and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ay6
TitleHuman O-GlcNAc transferase (OGT) in complex with UDP-5SGlcNAc and substrate peptide
Components
  • TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1
  • UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANS FERASE 110 KDA SUBUNIT
KeywordsTRANSFERASE / GLYCOSYL TRANSFERASE
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / protein O-acetylglucosaminyltransferase activity / RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity / RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / cardiac septum development / acetylglucosaminyltransferase activity ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / protein O-acetylglucosaminyltransferase activity / RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity / RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / cardiac septum development / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance / positive regulation of cGAS/STING signaling pathway / protein O-linked glycosylation / coronary vasculature development / NSL complex / non-canonical NF-kappaB signal transduction / aorta development / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / protein serine/threonine phosphatase activity / regulation of synapse assembly / mitogen-activated protein kinase p38 binding / Formation of WDR5-containing histone-modifying complexes / Sin3-type complex / positive regulation of stem cell population maintenance / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / positive regulation of proteolysis / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / heart morphogenesis / mitophagy / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / IRAK2 mediated activation of TAK1 complex / response to nutrient / Alpha-protein kinase 1 signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / transforming growth factor beta receptor signaling pathway / TRAF6-mediated induction of TAK1 complex within TLR4 complex / protein serine/threonine kinase activator activity / negative regulation of cell migration / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of translation / TNFR1-induced NF-kappa-B signaling pathway / cell projection / activated TAK1 mediates p38 MAPK activation / response to insulin / lung development / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / mitochondrial membrane / cellular response to glucose stimulus / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / protein processing / chromatin DNA binding / Regulation of necroptotic cell death / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / UCH proteinases / chromatin organization / HATs acetylate histones / positive regulation of cold-induced thermogenesis / molecular adaptor activity / in utero embryonic development / positive regulation of MAPK cascade / endosome membrane / Ub-specific processing proteases / apoptotic process / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / protein-containing complex binding / positive regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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 / Protein phosphatase 2C / TPR repeat / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain ...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 / Protein phosphatase 2C / TPR repeat / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Tetratricopeptide repeat / Tetratricopeptide repeat / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-12V / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.3 Å
AuthorsSchimpl, M. / Zheng, X. / Blair, D.E. / Schuettelkopf, A.W. / Navratilova, I. / Aristotelous, T. / Ferenbach, A.T. / Macnaughtan, M.A. / Borodkin, V.S. / van Aalten, D.M.F.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: O-Glcnac Transferase Invokes Nucleotide Sugar Pyrophosphate Participation in Catalysis
Authors: Schimpl, M. / Zheng, X. / Borodkin, V.S. / Blair, D.E. / Ferenbach, A.T. / Schuettelkopf, A.W. / Navratilova, I. / Aristotelous, T. / Albarbarawi, O. / Robinson, D.A. / Macnaughtan, M.A. / Van Aalten, D.M.F.
History
DepositionJun 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANS FERASE 110 KDA SUBUNIT
B: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANS FERASE 110 KDA SUBUNIT
C: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANS FERASE 110 KDA SUBUNIT
D: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANS FERASE 110 KDA SUBUNIT
E: TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1
F: TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1
G: TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1
H: TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,01416
Polymers329,1368
Non-polymers2,8788
Water00
1
A: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANS FERASE 110 KDA SUBUNIT
E: TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0034
Polymers82,2842
Non-polymers7192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-23 kcal/mol
Surface area28550 Å2
MethodPISA
2
B: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANS FERASE 110 KDA SUBUNIT
F: TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0034
Polymers82,2842
Non-polymers7192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-24.2 kcal/mol
Surface area28520 Å2
MethodPISA
3
C: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANS FERASE 110 KDA SUBUNIT
G: TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0034
Polymers82,2842
Non-polymers7192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-24.3 kcal/mol
Surface area28550 Å2
MethodPISA
4
D: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANS FERASE 110 KDA SUBUNIT
H: TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0034
Polymers82,2842
Non-polymers7192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-24.2 kcal/mol
Surface area28540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)275.439, 275.439, 142.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A312 - 1028
2111B312 - 1028
3111C312 - 1028
4111D312 - 1028
1211A1100
2211B1100
3211C1100
4211D1100
1311A1200
2311B1200
3311C1200
4311D1200
1411A1389 - 1399
2411B1389 - 1399
3411C1389 - 1399
4411D1389 - 1399

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.031547, 0.354297, 0.934601), (-0.917564, -0.381049, 0.11348), (0.396334, -0.853976, 0.337111)107.15491, 75.68388, 5.39533
3given(-0.28886, -0.774846, -0.562294), (0.186212, -0.621586, 0.760891), (-0.939087, 0.115085, 0.323837)242.75354, -61.10855, 111.31463
4given(-0.792419, 0.48415, 0.37104), (0.486111, 0.133793, 0.863594), (0.368467, 0.864695, -0.341371)287.65637, -129.98322, 8.82611

-
Components

#1: Protein
UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANS FERASE 110 KDA SUBUNIT / 2.4.1.255 / O-GLCNAC TRANSFERASE SUBUNIT P110 / O-LINKED N-ACETYLGLUCOSAMINE TRANSFERASE 110 KDA SUBUNIT / OGT


Mass: 80974.508 Da / Num. of mol.: 4
Fragment: TPR (TRUNCATED) AND CATALYTIC DOMAIN, RESIDUES 197-915
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ARCTICEXPRESS RIL / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide
TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1 / MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 1 / TGF-BETA-ACTIVATED KINASE ...MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 1 / TGF-BETA-ACTIVATED KINASE 1-BINDING PROTEIN 1 / TAK1-BINDING PROTEIN 1


Mass: 1309.403 Da / Num. of mol.: 4 / Fragment: RESIDUES 389-401 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15750
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-12V / (2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE


Mass: 623.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O16P2S
Has protein modificationN
Nonpolymer detailsSULFATE ION (SO4): FROM CRYOPROTECTANT, LI2SO4
Sequence detailsSYNTHETIC PEPTIDE COVERING RESIDUES 398-401 WITH SER395 REPLACED BY 3-AMINO-ALANINE, DNP ACCORDING ...SYNTHETIC PEPTIDE COVERING RESIDUES 398-401 WITH SER395 REPLACED BY 3-AMINO-ALANINE, DNP ACCORDING TO THE PDB LIGAND DICTIONARY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.75 Å3/Da / Density % sol: 74.08 % / Description: NONE
Crystal growpH: 9.3 / Details: 1.45 M K2HPO4, 10 MM EDTA, 1 % XYLITOL, pH 9.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 91074 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.7

-
Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.3→40 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.822 / SU B: 23.864 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R: 3.781 / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 715-718 AND 747-761 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.27216 435 0.5 %RANDOM
Rwork0.22665 ---
obs0.22686 91074 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.914 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å21.07 Å20 Å2
2--2.15 Å20 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22368 0 176 0 22544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223064
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.96631308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71252820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07124.5631052
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.515153940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.77915120
X-RAY DIFFRACTIONr_chiral_restr0.080.23480
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117420
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5636 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A7.43
2B7.5
3C6.92
4D9.75
LS refinement shellResolution: 3.304→3.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 33 -
Rwork0.319 6328 -
obs--96.85 %

+
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