[English] 日本語
Yorodumi
- EMDB-45808: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45808
TitleG115 gamma delta TCR/CD3 complex bound by OKT3 Fab
Map data
Sample
  • Complex: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab
    • Protein or peptide: OKT3 Fab heavy chain
    • Protein or peptide: OKT3 Fab light chain
    • Protein or peptide: G115 TCR delta chain
    • Protein or peptide: G115 TCR gamma chain
    • Protein or peptide: T-cell surface glycoprotein CD3 delta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 epsilon chain
    • Protein or peptide: T-cell surface glycoprotein CD3 gamma chain
    • Protein or peptide: T-cell surface glycoprotein CD3 zeta chain
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsTCR / CD3 / gamma delta / Fab / OKT3 / immune receptor / T cell / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / gamma-delta T cell activation / CD4-positive, alpha-beta T cell proliferation / Fc-gamma receptor signaling pathway / negative thymic T cell selection ...regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / gamma-delta T cell activation / CD4-positive, alpha-beta T cell proliferation / Fc-gamma receptor signaling pathway / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / positive thymic T cell selection / positive regulation of protein localization to cell surface / signal complex assembly / Nef and signal transduction / positive regulation of cell-matrix adhesion / T cell receptor complex / smoothened signaling pathway / establishment or maintenance of cell polarity / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of interleukin-4 production / dendrite development / protein complex oligomerization / alpha-beta T cell activation / Generation of second messenger molecules / FCGR activation / immunological synapse / Co-inhibition by PD-1 / Role of phospholipids in phagocytosis / T cell receptor binding / positive regulation of T cell proliferation / T cell costimulation / negative regulation of smoothened signaling pathway / positive regulation of interleukin-2 production / cerebellum development / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / protein tyrosine kinase binding / T cell activation / FCGR3A-mediated phagocytosis / apoptotic signaling pathway / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Downstream TCR signaling / protein transport / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / signaling receptor complex adaptor activity / T cell receptor signaling pathway / Clathrin-mediated endocytosis / cell body / protein-containing complex assembly / regulation of apoptotic process / dendritic spine / adaptive immune response / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / protein heterodimerization activity / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / protein kinase binding / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 zeta subunit / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. ...CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 zeta subunit / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 epsilon chain / T-cell surface glycoprotein CD3 gamma chain / T-cell surface glycoprotein CD3 zeta chain
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsHoque M / Saotome K / Franklin MC
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural characterization of two γδ TCR/CD3 complexes.
Authors: Mohammed Hoque / John Benji Grigg / Trudy Ramlall / Jennifer Jones / Luke L McGoldrick / John C Lin / William C Olson / Eric Smith / Matthew C Franklin / Tong Zhang / Kei Saotome /
Abstract: The T-cell receptor (TCR)/CD3 complex plays an essential role in the immune response and is a key player in cancer immunotherapies. There are two classes of TCR/CD3 complexes, defined by their TCR ...The T-cell receptor (TCR)/CD3 complex plays an essential role in the immune response and is a key player in cancer immunotherapies. There are two classes of TCR/CD3 complexes, defined by their TCR chain usage (αβ or γδ). Recently reported structures have revealed the organization of the αβ TCR/CD3 complex, but similar studies regarding the γδ TCR/CD3 complex have lagged behind. Here, we report cryoelectron microscopy (cryoEM) structural analysis of two γδ TCRs, G115 (Vγ9 Vδ2) and 9C2 (Vγ5 Vδ1), in complex with CD3 subunits. Our results show that the overall subunit organization of the γδ TCR/CD3 complexes is similar to αβ TCRs. However, both γδ TCRs display highly mobile extracellular domains (ECDs), unlike αβ TCRs, which have TCR ECDs that are rigidly coupled to its transmembrane (TM) domains. We corroborate this finding in cells by demonstrating that a γδ T-cell specific antibody can bind a site that would be inaccessible in the more rigid αβ TCR/CD3 complex. Furthermore, we observed that the Vγ5 Vδ1 complex forms a TCR γ5 chain-mediated dimeric species whereby two TCR/CD3 complexes are assembled. Collectively, these data shed light on γδ TCR/CD3 complex formation and may aid the design of γδ TCR-based therapies.
History
DepositionJul 19, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45808.png

Downloads & links

-
Map

FileDownload / File: emd_45808.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 400 pix.
= 335.6 Å		0.84 Å/pix.
x 400 pix.
= 335.6 Å		0.84 Å/pix.
x 400 pix.
= 335.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.44
Minimum - Maximum-65.90504 - 90.543364999999994
Average (Standard dev.)-0.000000000003242 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 335.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_45808_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_45808_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : G115 gamma delta TCR/CD3 complex bound by OKT3 Fab

EntireName: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab
Components
  • Complex: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab
    • Protein or peptide: OKT3 Fab heavy chain
    • Protein or peptide: OKT3 Fab light chain
    • Protein or peptide: G115 TCR delta chain
    • Protein or peptide: G115 TCR gamma chain
    • Protein or peptide: T-cell surface glycoprotein CD3 delta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 epsilon chain
    • Protein or peptide: T-cell surface glycoprotein CD3 gamma chain
    • Protein or peptide: T-cell surface glycoprotein CD3 zeta chain
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

+
Supramolecule #1: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab

SupramoleculeName: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: OKT3 Fab heavy chain

MacromoleculeName: OKT3 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.735826 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLQQSGAE LARPGASVKM SCKASGYTFT RYTMHWVKQR PGQGLEWIGY INPSRGYTNY NQKFKDKATL TTDKSSSTAY MQLSSLTSE DSAVYYCARY YDDHYCLDYW GQGTTLTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
QVQLQQSGAE LARPGASVKM SCKASGYTFT RYTMHWVKQR PGQGLEWIGY INPSRGYTNY NQKFKDKATL TTDKSSSTAY MQLSSLTSE DSAVYYCARY YDDHYCLDYW GQGTTLTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSCDKTHTC PPCPAPELLG

+
Macromolecule #2: OKT3 Fab light chain

MacromoleculeName: OKT3 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.194719 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QIVLTQSPAI MSASPGEKVT MTCSASSSVS YMNWYQQKSG TSPKRWIYDT SKLASGVPAH FRGSGSGTSY SLTISGMEAE DAATYYCQQ WSSNPFTFGS GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
QIVLTQSPAI MSASPGEKVT MTCSASSSVS YMNWYQQKSG TSPKRWIYDT SKLASGVPAH FRGSGSGTSY SLTISGMEAE DAATYYCQQ WSSNPFTFGS GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

+
Macromolecule #3: G115 TCR delta chain

MacromoleculeName: G115 TCR delta chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.519264 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AIELVPEHQT VPVSIGVPAT LRCSMKGEAI GNYYINWYRK TQGNTMTFIY REKDIYGPGF KDNFQGDIDI AKNLAVLKIL APSERDEGS YYCACDTLGM GGEYTDKLIF GKGTRVTVEP RSQPHTKPSV FVMKNGTNVA CLVKEFYPKD IRINLVSSKK I TEFDPAIV ...String:
AIELVPEHQT VPVSIGVPAT LRCSMKGEAI GNYYINWYRK TQGNTMTFIY REKDIYGPGF KDNFQGDIDI AKNLAVLKIL APSERDEGS YYCACDTLGM GGEYTDKLIF GKGTRVTVEP RSQPHTKPSV FVMKNGTNVA CLVKEFYPKD IRINLVSSKK I TEFDPAIV ISPSGKYNAV KLGKYEDSNS VTCSVQHDNK TVHSTDFEVK TDSTDHVKPK ETENTKQPSK SCHKPKAIVH TE KVNMMSL TVLGLRMLFA KTVAVNFLLT AKLFFLSRGR AKRGSG

+
Macromolecule #4: G115 TCR gamma chain

MacromoleculeName: G115 TCR gamma chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.349344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AGHLEQPQIS STKTLSKTAR LECVVSGITI SATSVYWYRE RPGEVIQFLV SISYDGTVRK ESGIPSGKFE VDRIPETSTS TLTIHNVEK QDIATYYCAL WEAQQELGKK IKVFGPGTKL IITDKQLDAD VSPKPTIFLP SIAETKLQKA GTYLCLLEKF F PDVIKIHW ...String:
AGHLEQPQIS STKTLSKTAR LECVVSGITI SATSVYWYRE RPGEVIQFLV SISYDGTVRK ESGIPSGKFE VDRIPETSTS TLTIHNVEK QDIATYYCAL WEAQQELGKK IKVFGPGTKL IITDKQLDAD VSPKPTIFLP SIAETKLQKA GTYLCLLEKF F PDVIKIHW QEKKSNTILG SQEGNTMKTN DTYMKFSWLT VPEKSLDKEH RCIVRHENNK NGVDQEIIFP PIKTDVITMD PK DNCSKDA NDTLLLQLTN TSAYYMYLLL LLKSVVYFAI ITCCLLRRTA FCCNGEKS

+
Macromolecule #5: T-cell surface glycoprotein CD3 delta chain

MacromoleculeName: T-cell surface glycoprotein CD3 delta chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.150719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEHSTFLSGL VLATLLSQVS PFKIPIEELE DRVFVNCNTS ITWVEGTVGT LLSDITRLDL GKRILDPRGI YRCNGTDIYK DKESTVQVH YRMCQSCVEL DPATVAGIIV TDVIATLLLA LGVFCFAGHE TGRLSGAADT QALLRNDQVY QPLRDRDDAQ Y SHLGGNWA RNKGSG

UniProtKB: T-cell surface glycoprotein CD3 delta chain

+
Macromolecule #6: T-cell surface glycoprotein CD3 epsilon chain

MacromoleculeName: T-cell surface glycoprotein CD3 epsilon chain / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.375408 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQSGTHWRVL GLCLLSVGVW GQDGNEEMGG ITQTPYKVSI SGTTVILTCP QYPGSEILWQ HNDKNIGGDE DDKNIGSDED HLSLKEFSE LEQSGYYVCY PRGSKPEDAN FYLYLRARVC ENCMEMDVMS VATIVIVDIC ITGGLLLLVY YWSKNRKAKA K PVTRGAGA ...String:
MQSGTHWRVL GLCLLSVGVW GQDGNEEMGG ITQTPYKVSI SGTTVILTCP QYPGSEILWQ HNDKNIGGDE DDKNIGSDED HLSLKEFSE LEQSGYYVCY PRGSKPEDAN FYLYLRARVC ENCMEMDVMS VATIVIVDIC ITGGLLLLVY YWSKNRKAKA K PVTRGAGA GGRQRGQNKE RPPPVPNPDY EPIRKGQRDL YSGLNQRRIG SG

UniProtKB: T-cell surface glycoprotein CD3 epsilon chain

+
Macromolecule #7: T-cell surface glycoprotein CD3 gamma chain

MacromoleculeName: T-cell surface glycoprotein CD3 gamma chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.694639 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEQGKGLAVL ILAIILLQGT LAQSIKGNHL VKVYDYQEDG SVLLTCDAEA KNITWFKDGK MIGFLTEDKK KWNLGSNAKD PRGMYQCKG SQNKSKPLQV YYRMCQNCIE LNAATISGFL FAEIVSIFVL AVGVYFIAGQ DGVRQSRASD KQTLLPNDQL Y QPLKDRED DQYSHLQGNQ LRRNGSG

UniProtKB: T-cell surface glycoprotein CD3 gamma chain

+
Macromolecule #8: T-cell surface glycoprotein CD3 zeta chain

MacromoleculeName: T-cell surface glycoprotein CD3 zeta chain / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.654486 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MKWKALFTAA ILQAQLPITE AQSFGLLDPK LCYLLDGILF IYGVILTALF LRVKFSRSAD APAYQQGQNQ LYNELNLGRR EEYDVLDKR RGRDPEMGGK PQRRKNPQEG LYNELQKDKM AEAYSEIGMK GERRRGKGHD GLYQGLSTAT KDTYDALHMQ A LPPRGSGL EVLFQ

UniProtKB: T-cell surface glycoprotein CD3 zeta chain

+
Macromolecule #11: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 11 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

+
Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 290758
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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