[English] 日本語
Yorodumi
- PDB-4uel: UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uel
TitleUCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain
Components
  • POLYUBIQUITIN-B
  • PROTEASOMAL UBIQUITIN RECEPTOR ADRM1
  • UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
KeywordsHYDROLASE / DEUBIQUITINATING ENZYME / DUB / UCH37 / UCHL5 / PROTEASOME / ADRM1 / RPN13 / DEUBAD / UCH / UBIQUITIN-PROPARGYL
Function / homology
Function and homology information


lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / positive regulation of smoothened signaling pathway / proteasome regulatory particle, lid subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination ...lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / positive regulation of smoothened signaling pathway / proteasome regulatory particle, lid subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / fat pad development / mitochondrion transport along microtubule / endopeptidase inhibitor activity / Somitogenesis / molecular function inhibitor activity / female gonad development / seminiferous tubule development / proteasome binding / regulation of chromosome organization / midbrain development / male meiosis I / regulation of DNA replication / regulation of embryonic development / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein deubiquitination / endopeptidase activator activity / proteasome assembly / regulation of DNA repair / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / telomere maintenance / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / proteasome complex / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / positive regulation of DNA repair / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / positive regulation of protein ubiquitination / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / UCH37-like (ULD) domain profile. / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / Ubiquitin C-terminal Hydrolase UCH-l3 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / UCH37-like (ULD) domain profile. / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / RPN13, DEUBAD domain / RPN13, DEUBAD domain superfamily / UCH-binding domain / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Proteasomal ubiquitin receptor ADRM1 / Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSahtoe, D.D. / Van Dijk, W.J. / El Oualid, F. / Ekkebus, R. / Ovaa, H. / Sixma, T.K.
CitationJournal: Mol.Cell / Year: 2015
Title: Mechanism of Uch-L5 Activation and Inhibition by Deubad Domains in Rpn13 and Ino80G.
Authors: Sahtoe, D.D. / Van Dijk, W.J. / El Oualid, F. / Ekkebus, R. / Ovaa, H. / Sixma, T.K.
History
DepositionDec 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2024Group: 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 / pdbx_modification_feature / struct_conn
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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
B: POLYUBIQUITIN-B
C: PROTEASOMAL UBIQUITIN RECEPTOR ADRM1


Theoretical massNumber of molelcules
Total (without water)59,3593
Polymers59,3593
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-50.2 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.340, 98.600, 100.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 / UCH-L5 / UBIQUITIN C-TERMINAL HYDROLASE UCH37 / UBIQUITIN THIOESTERASE L5


Mass: 37734.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACTIVE SITE CYS88 COVALENTLY LINKED TO UBIQUITIN-PROPARGYL
Source: (gene. exp.) HOMO SAPIENS (human) / Variant: ISOFORM 3 / Plasmid: PGEX-NKI-3C-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q9Y5K5, ubiquitinyl hydrolase 1
#2: Protein POLYUBIQUITIN-B / UBIQUITIN


Mass: 8558.857 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically
Details: GLY76 OF UBIQUITIN IS REPLACED BY GLY-AYE THAT IS COVALENTLY LINKED TO THE ACTIVE SITE CYS88 OF UCH-L5
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P0CG47
#3: Protein PROTEASOMAL UBIQUITIN RECEPTOR ADRM1 / RPN13 / 110 KDA CELL MEMBRANE GLYCOPROTEIN / GP110 / ADHESION-REGULATING MOLECULE 1 / ARM-1 / ...RPN13 / 110 KDA CELL MEMBRANE GLYCOPROTEIN / GP110 / ADHESION-REGULATING MOLECULE 1 / ARM-1 / PROTEASOME REGULATORY PARTICLE NON-ATPASE 13 / HRPN13 / RPN13 HOMOLOG


Mass: 13065.674 Da / Num. of mol.: 1 / Fragment: DEUBAD DOMAIN, RESIDUES 266-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDF-NKI-HIS-3C-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q16186
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGLY76 IN NATIVE UBIQUITIN IS REPLACED BY AYE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Description: MOLECULAR REPLACEMENT WAS PERFORMED WITH THE PARTIALLY BUILD UCH-L5-RPN13 STRUCTURE, SEE RELATED PDB
Crystal growTemperature: 277 K
Details: 100 MM BIS-TRIS-PROPANE PH 5.8, 300 MM NABR, 21% PEG3350. 4 DEGREES CELSIUS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0 Å / Relative weight: 1
ReflectionResolution: 2.3→45.34 Å / Num. obs: 26979 / % possible obs: 99.8 % / Observed criterion σ(I): 1.6 / Redundancy: 4.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.6 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→70.28 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.37 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23426 1354 5 %RANDOM
Rwork0.19141 ---
obs0.19365 25531 99.74 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.613 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å20 Å2
2---0.63 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→70.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 0 234 3996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193830
X-RAY DIFFRACTIONr_bond_other_d0.0010.023717
X-RAY DIFFRACTIONr_angle_refined_deg0.9931.975169
X-RAY DIFFRACTIONr_angle_other_deg0.68338570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0845472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0625.668187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32315706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.081519
X-RAY DIFFRACTIONr_chiral_restr0.0550.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
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_it2.9321.8771897
X-RAY DIFFRACTIONr_mcbond_other2.9331.8771896
X-RAY DIFFRACTIONr_mcangle_it4.2782.7992363
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0212.2731933
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
LS refinement shellResolution: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 97 -
Rwork0.286 1827 -
obs--98.36 %
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)
11.323-0.3286-0.54951.45340.34451.4525-0.0639-0.05640.0045-0.02980.0338-0.03960.11740.07020.03010.13060.0252-0.00070.0793-0.01820.0229-0.1797.48630.211
23.716-3.65271.99196.4542-2.56441.2248-0.00450.1630.09470.0251-0.1083-0.2318-0.07760.08110.11270.37320.0026-0.01760.2614-0.02410.06644.17589.9766.673
35.014-3.64473.21682.7039-2.37032.14720.26350.5891-0.3876-0.0772-0.27840.23480.06730.39890.01490.9239-0.07410.17730.7959-0.00191.144136.31178.63514.855
42.21420.1824-1.23452.5717-0.8973.6940.03180.01810.1706-0.26480.0368-0.2127-0.0290.3038-0.06850.1585-0.00720.03160.1096-0.0140.102319.81897.34611.973
510.31751.73290.85090.4522-0.73695.265-0.0507-0.04570.99370.0265-0.2630.0574-0.27331.38120.31370.6208-0.05740.06060.5308-0.00130.761923.50273.5727.055
61.6690.15240.74215.685-0.87172.44230.12040.0208-0.0228-0.1824-0.1262-0.361-0.05520.03190.00580.0714-0.01560.03190.0936-0.0070.087115.09871.73214.748
79.9702-0.5523-6.80670.26680.799316.5324-0.4380.12720.28990.2606-0.0954-0.47080.37040.4360.53350.4375-0.0037-0.44560.37640.22611.162329.90862.18720.665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 228
2X-RAY DIFFRACTION2A229 - 315
3X-RAY DIFFRACTION3A316 - 320
4X-RAY DIFFRACTION4B1 - 75
5X-RAY DIFFRACTION5C287 - 307
6X-RAY DIFFRACTION6C308 - 363
7X-RAY DIFFRACTION7C364 - 384

+
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