[English] 日本語
Yorodumi
- PDB-3mhs: Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to u... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mhs
TitleStructure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde
Components
  • (SAGA-associated factor ...) x 2
  • Protein SUS1
  • Ubiquitin carboxyl-terminal hydrolase 8
  • Ubiquitin
KeywordsHydrolase/transcription regulator/protein binding / Multi-protein complex / Hydrolase-transcription regulator-protein binding complex / Acetylation / Cytoplasm / Isopeptide bond / Nucleus / Phosphoprotein / Ubl conjugation
Function / homology
Function and homology information


RITS complex assembly / DUBm complex / : / : / : / regulation of nucleocytoplasmic transport / transcription export complex 2 / protein modification process => GO:0036211 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear mRNA surveillance ...RITS complex assembly / DUBm complex / : / : / : / regulation of nucleocytoplasmic transport / transcription export complex 2 / protein modification process => GO:0036211 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear mRNA surveillance / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / enzyme activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / nuclear pore / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / cytosolic ribosome / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / RNA splicing / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation
Similarity search - Function
Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / ENY2/SUS1 / SAGA complex, Sgf11 subunit / SAGA-associated factor 73, zinc finger domain / Sgf11 (transcriptional regulation protein) / Zinc finger domain / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 ...Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / ENY2/SUS1 / SAGA complex, Sgf11 subunit / SAGA-associated factor 73, zinc finger domain / Sgf11 (transcriptional regulation protein) / Zinc finger domain / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAGA-associated factor 73 / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Helix Hairpins - #210 / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Classic Zinc Finger / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Serum Albumin; Chain A, Domain 1 / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Cathepsin B; Chain A / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Double Stranded RNA Binding Domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Helix Hairpins / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin carboxyl-terminal hydrolase 8 / SAGA-associated factor 73 / Ubiquitin-60S ribosomal protein L40 / SAGA-associated factor 11 / Transcription and mRNA export factor SUS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å
AuthorsSamara, N.L. / Datta, A.B. / Berndsen, C.E. / Zhang, X. / Yao, T. / Cohen, R.E. / Wolberger, C.
CitationJournal: Science / Year: 2010
Title: Structural insights into the assembly and function of the SAGA deubiquitinating module.
Authors: Samara, N.L. / Datta, A.B. / Berndsen, C.E. / Zhang, X. / Yao, T. / Cohen, R.E. / Wolberger, C.
History
DepositionApr 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 8
B: Protein SUS1
C: SAGA-associated factor 11
D: Ubiquitin
E: SAGA-associated factor 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,48815
Polymers95,8115
Non-polymers67710
Water15,223845
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21400 Å2
ΔGint-96 kcal/mol
Surface area34050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.600, 102.084, 120.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 3 types, 3 molecules ABD

#1: Protein Ubiquitin carboxyl-terminal hydrolase 8 / Ubiquitin thioesterase 8 / Ubiquitin-specific-processing protease 8 / Deubiquitinating enzyme 8


Mass: 54033.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBP8, YMR223W, YM9959.05 / Plasmid details: T7 based / Plasmid: pET32a, pCDF, pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta2 pLysS / References: UniProt: P50102, EC: 3.1.2.15
#2: Protein Protein SUS1


Mass: 11094.497 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUS1, YBR111W-A / Plasmid details: T7 based / Plasmid: pET32a, pCDF, pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta2 pLysS / References: UniProt: Q6WNK7
#4: Protein Ubiquitin /


Mass: 8560.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA52, UBB, UBC / Plasmid details: T7 based / Plasmid: pET32a, pCDF, pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta2 pLysS / References: UniProt: P62988, UniProt: P0CG48*PLUS

-
SAGA-associated factor ... , 2 types, 2 molecules CE

#3: Protein SAGA-associated factor 11 / 11 kDa SAGA-associated factor


Mass: 11297.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SGF11, YPL047W / Plasmid details: T7 based / Plasmid: pET32a, pCDF, pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta2 pLysS / References: UniProt: Q03067
#5: Protein SAGA-associated factor 73 / 73 kDa SAGA-associated factor / SAGA histone acetyltransferase complex 73 kDa subunit


Mass: 10824.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SGF73, YGL066W / Plasmid details: T7 based / Plasmid: pET32a, pCDF, pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettta2 pLysS / References: UniProt: P53165

-
Non-polymers , 4 types, 855 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 845 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.41 %
Description: THE INITIAL STRUCTURE WAS DETERMINED WITH 3 WAVELENGTH SE-MAD USING THE FOLLOWING WAVELENGTHS (EV): PEAK: 12658.7 HIGH REMOTE: 13058.7 INFLECTION: 12656.9 THE STRUCTURE WAS THEN REFINED ...Description: THE INITIAL STRUCTURE WAS DETERMINED WITH 3 WAVELENGTH SE-MAD USING THE FOLLOWING WAVELENGTHS (EV): PEAK: 12658.7 HIGH REMOTE: 13058.7 INFLECTION: 12656.9 THE STRUCTURE WAS THEN REFINED AGAINST A NATIVE DATA SET COLLECTED AT A WAVELENGTH OF 13058.7 (EV). THE FINAL COORDINATES REPRESENT THE NATIVE DATA SET.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94944 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2010
Details: K-B pair of biomorph mirrors with two additional horizontally deflecting mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94944 Å / Relative weight: 1
ReflectionResolution: 1.89→35.1 Å / Num. all: 78011 / Num. obs: 73928 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 29.5
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 2.25 / Rsym value: 0.886 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXDphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.89→35.1 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.921 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20757 3934 5.1 %RANDOM
Rwork0.15904 ---
obs0.16148 73928 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.89→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6391 0 18 845 7254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226776
X-RAY DIFFRACTIONr_bond_other_d0.0010.024631
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.969167
X-RAY DIFFRACTIONr_angle_other_deg0.8593.00311385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26325.539334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.993151276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4561529
X-RAY DIFFRACTIONr_chiral_restr0.180.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021285
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_it1.3471.54098
X-RAY DIFFRACTIONr_mcbond_other0.4281.51655
X-RAY DIFFRACTIONr_mcangle_it2.29326673
X-RAY DIFFRACTIONr_scbond_it3.79232678
X-RAY DIFFRACTIONr_scangle_it5.2454.52465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 240 -
Rwork0.235 4990 -
obs--92.26 %
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)
10.58150.2181-0.00420.9011-0.12030.54120.0104-0.1215-0.00030.1473-0.0343-0.02910.0290.03940.0240.03860.01630.00730.04910.010.043750.944723.120785.7836
21.47630.8384-0.46211.5178-0.09433.5259-0.0643-0.074-0.10490.0333-0.0359-0.3790.30110.81530.10020.06310.0921-0.0490.2820.08880.266176.229825.492891.2926
31.2640.43510.27651.0433-0.01930.5630.0652-0.0124-0.1970.1783-0.0228-0.1220.14010.0572-0.04240.1520.07330.01910.13710.08910.092150.1478.894592.2796
41.3345-0.3020.66661.89650.35210.6849-0.02390.07350.0341-0.187-0.04650.23370.0041-0.07350.07030.0468-0.0307-0.01620.05350.00510.078936.799427.289260.2129
50.330.37220.13391.3448-0.35660.75760.0182-0.12590.0810.3002-0.0676-0.1452-0.10290.07370.04940.14670.0204-0.04430.1856-0.05960.153759.05934.63896.5105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999

+
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