[English] 日本語
Yorodumi
- EMDB-21587: Structure of the S. cerevisiae ER membrane complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21587
TitleStructure of the S. cerevisiae ER membrane complex
Map dataER membrane complex
Sample
  • Complex: ER Membrane Complex
    • Protein or peptide: Endoplasmic reticulum membrane protein complex subunit 10
    • Protein or peptide: ER membrane protein complex subunit 1
    • Protein or peptide: ER membrane protein complex subunit 2
    • Protein or peptide: ER membrane protein complex subunit 3
    • Protein or peptide: ER membrane protein complex subunit 4
    • Protein or peptide: ER membrane protein complex subunit 5
    • Protein or peptide: ER membrane protein complex subunit 6
    • Protein or peptide: Protein SOP4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Keywordsinsertase / complex / ER / MEMBRANE PROTEIN
Function / homology
Function and homology information


EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / protein folding in endoplasmic reticulum / phospholipid transport / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / phospholipid metabolic process / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane ...EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / protein folding in endoplasmic reticulum / phospholipid transport / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / phospholipid metabolic process / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / nucleus / membrane
Similarity search - Function
Protein Sop4 / : / Suppressor of PMA 1-7 protein / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 ...Protein Sop4 / : / Suppressor of PMA 1-7 protein / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6-like / EMC6 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 2-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein DUF106 / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
ER membrane protein complex subunit 1 / ER membrane protein complex subunit 3 / Protein SOP4 / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / Endoplasmic reticulum membrane protein complex subunit 10 / ER membrane protein complex subunit 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae W303 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBai L / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA231466 United States
CitationJournal: Nature / Year: 2020
Title: Structure of the ER membrane complex, a transmembrane-domain insertase.
Authors: Lin Bai / Qinglong You / Xiang Feng / Amanda Kovach / Huilin Li /
Abstract: The endoplasmic reticulum (ER) membrane complex (EMC) cooperates with the Sec61 translocon to co-translationally insert a transmembrane helix (TMH) of many multi-pass integral membrane proteins into ...The endoplasmic reticulum (ER) membrane complex (EMC) cooperates with the Sec61 translocon to co-translationally insert a transmembrane helix (TMH) of many multi-pass integral membrane proteins into the ER membrane, and it is also responsible for inserting the TMH of some tail-anchored proteins. How EMC accomplishes this feat has been unclear. Here we report the first, to our knowledge, cryo-electron microscopy structure of the eukaryotic EMC. We found that the Saccharomyces cerevisiae EMC contains eight subunits (Emc1-6, Emc7 and Emc10), has a large lumenal region and a smaller cytosolic region, and has a transmembrane region formed by Emc4, Emc5 and Emc6 plus the transmembrane domains of Emc1 and Emc3. We identified a five-TMH fold centred around Emc3 that resembles the prokaryotic YidC insertase and that delineates a largely hydrophilic client protein pocket. The transmembrane domain of Emc4 tilts away from the main transmembrane region of EMC and is partially mobile. Mutational studies demonstrated that the flexibility of Emc4 and the hydrophilicity of the client pocket are required for EMC function. The EMC structure reveals notable evolutionary conservation with the prokaryotic insertases, suggests that eukaryotic TMH insertion involves a similar mechanism, and provides a framework for detailed understanding of membrane insertion for numerous eukaryotic integral membrane proteins and tail-anchored proteins.
History
DepositionMar 26, 2020-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wb9
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21587.png

Downloads & links

-
Map

FileDownload / File: emd_21587.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationER membrane complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 240 pix.
= 246.96 Å		1.03 Å/pix.
x 240 pix.
= 246.96 Å		1.03 Å/pix.
x 240 pix.
= 246.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.029 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.21250558 - 0.2880854
Average (Standard dev.)0.00030880127 (±0.006475034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 246.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0291.0291.029
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z246.960246.960246.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.2130.2880.000

-
Supplemental data

-
Sample components

+
Entire : ER Membrane Complex

EntireName: ER Membrane Complex
Components
  • Complex: ER Membrane Complex
    • Protein or peptide: Endoplasmic reticulum membrane protein complex subunit 10
    • Protein or peptide: ER membrane protein complex subunit 1
    • Protein or peptide: ER membrane protein complex subunit 2
    • Protein or peptide: ER membrane protein complex subunit 3
    • Protein or peptide: ER membrane protein complex subunit 4
    • Protein or peptide: ER membrane protein complex subunit 5
    • Protein or peptide: ER membrane protein complex subunit 6
    • Protein or peptide: Protein SOP4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

+
Supramolecule #1: ER Membrane Complex

SupramoleculeName: ER Membrane Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)

+
Macromolecule #1: Endoplasmic reticulum membrane protein complex subunit 10

MacromoleculeName: Endoplasmic reticulum membrane protein complex subunit 10
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 22.792824 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MLVRLLRVIL LASMVFCADI LQLSYSDDAK DAIPLGTFEI DSTSDGNVTV TTVNIQDVEV SGEYCLNAQI EGKLDMPCFS YMKLRTPLK YDLIVDVDED NEVKQVSLSY DETNDAITAT VRYPEAGPTA PVTKLKKKTK TYADKKASKN KDGSTAQFEE D EEVKEVSW ...String:
MLVRLLRVIL LASMVFCADI LQLSYSDDAK DAIPLGTFEI DSTSDGNVTV TTVNIQDVEV SGEYCLNAQI EGKLDMPCFS YMKLRTPLK YDLIVDVDED NEVKQVSLSY DETNDAITAT VRYPEAGPTA PVTKLKKKTK TYADKKASKN KDGSTAQFEE D EEVKEVSW FQKNWKMLLL GLLIYNFVAG SAKKQQQGGA GADQKTE

UniProtKB: Endoplasmic reticulum membrane protein complex subunit 10

+
Macromolecule #2: ER membrane protein complex subunit 1

MacromoleculeName: ER membrane protein complex subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 87.272938 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MKITCTDLVY VFILLFLNTS CVQAVFSDDA FITDWQLANL GPWEKVIPDS RDRNRVLILS NPTETSCLVS SFNVSSGQIL FRNVLPFTI DEIQLDSNDH NAMVCVNSSS NHWQKYDLHD WFLLEEGVDN APSTTILPQS SYLNDQVSIK NNELHILDEQ S KLAEWKLE ...String:
MKITCTDLVY VFILLFLNTS CVQAVFSDDA FITDWQLANL GPWEKVIPDS RDRNRVLILS NPTETSCLVS SFNVSSGQIL FRNVLPFTI DEIQLDSNDH NAMVCVNSSS NHWQKYDLHD WFLLEEGVDN APSTTILPQS SYLNDQVSIK NNELHILDEQ S KLAEWKLE LPQGFNKVEY FHREDPLALV LNVNDTQYMG FSANGTELIP VWQRDEWLTN VVDYAVLDVF DSRDVELNKD MK AELDSNS LWNAYWLRLT TNWNRLINLL KENQFSPGRV FTKLLALDAK DTTVSDLKFG FAKILIVLTH DGFIGGLDMV NKG QLIWKL DLEIDQGVKM FWTDKNHDEL VVFSHDGHYL TIEVTKDQPI IKSRSPLSER KTVDSVIRLN EHDHQYLIKF EDKD HLLFK LNPGKNTDVP IVANNHSSSH IFVTEHDTNG IYGYIIENDT VKQTWKKAVN SKEKMVAYSK RETTNLNTLG ITLGD KSVL YKYLYPNLAA YLIANEEHHT ITFNLIDTIT GEILITQEHK DSPDFRFPMD IVFGEYWVVY SYFSSEPVPE QKLVVV ELY ESLTPDERLS NSSDNFSYDP LTGHINKPQF QTKQFIFPEI IKTMSISKTT DDITTKAIVM ELENGQITYI PKLLLNA RG KPAEEMAKDK KKEFMATPYT PVIPINDNFI ITHFRNLLPG SDSQLISIPT NLESTSIICD LGLDVFCTRI TPSGQFDL M SPTFEKGKLL ITIFVLLVIT YFIRPSVSNK KLKSQWLIK

UniProtKB: ER membrane protein complex subunit 1

+
Macromolecule #3: ER membrane protein complex subunit 2

MacromoleculeName: ER membrane protein complex subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 33.893211 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MLKDLVREKL LTIMNTKAYT QFNPEQLLQL ENEMKIYMKS GDSALTEGNY FFLMEMLFYV LVYRNQDVDA QVVYNTLRDR LGENSYKMV IMKATLLQIN GNDKGAIEYL ENLLNDDLEY ETDFVTYVSI AKKLIAIKTT SKNLSQESVL KEVVALTDKF P LDAELWWY ...String:
MLKDLVREKL LTIMNTKAYT QFNPEQLLQL ENEMKIYMKS GDSALTEGNY FFLMEMLFYV LVYRNQDVDA QVVYNTLRDR LGENSYKMV IMKATLLQIN GNDKGAIEYL ENLLNDDLEY ETDFVTYVSI AKKLIAIKTT SKNLSQESVL KEVVALTDKF P LDAELWWY ASEIYFEMGQ FEKACYCLEQ VLCITPFNYA CFGRLSETLY YEALRSKKQT KTELLEKALK NALRSVELSE LY LKGWALV NIISRELGRN KQNDLIKLSA SKLKEISAKS NNKDKITAEL ILNKI

UniProtKB: ER membrane protein complex subunit 2

+
Macromolecule #4: ER membrane protein complex subunit 3

MacromoleculeName: ER membrane protein complex subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 28.372842 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MLLDDQLKYW VLLPISIVMV LTGVLKQYIM TLITGSSANE AQPRVKLTEW QYLQWAQLLI GNGGNLSSDA FAAKKEFLVK DLTEERHLA KAKQQDGSQA GEVPNPFNDP SMSNAMMNMA KGNMASFIPQ TIIMWWVNHF FAGFILMQLP FPLTAKFKEM L QTGIICQD ...String:
MLLDDQLKYW VLLPISIVMV LTGVLKQYIM TLITGSSANE AQPRVKLTEW QYLQWAQLLI GNGGNLSSDA FAAKKEFLVK DLTEERHLA KAKQQDGSQA GEVPNPFNDP SMSNAMMNMA KGNMASFIPQ TIIMWWVNHF FAGFILMQLP FPLTAKFKEM L QTGIICQD LDVRWVSSIS WYFISVLGLN PVYNLIGLND QDMGIQAGIG GPQGPQGPPQ SQVDKAMHAM ANDLTIIQHE TC LDNVEQR VLKQYM

UniProtKB: ER membrane protein complex subunit 3

+
Macromolecule #5: ER membrane protein complex subunit 4

MacromoleculeName: ER membrane protein complex subunit 4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 21.478721 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString:
MSEQEPYEWA KHLLDTKYIE KYNIQNSNTL PSPPGFEGNS SKGNVTRKQQ DATSQTTSLA QKNQITVLQV QKAWQIALQP AKSIPMNIF MSYMSGTSLQ IIPIMTALML LSGPIKAIFS TRSAFKPVLG NKATQSQVQT AMFMYIVFQG VLMYIGYRKL N SMGLIPNA KGDWLPWERI AHYNNGLQWF SD

UniProtKB: ER membrane protein complex subunit 4

+
Macromolecule #6: ER membrane protein complex subunit 5

MacromoleculeName: ER membrane protein complex subunit 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 15.926407 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString:
MSFVSKLLYT VSALVLFHSG FSSYEFHHLL KLNSLNNAQG AISKLPKDIM YETYAGLILF VLAVFTSFEK LQYLPIESND GKIISQGNY LKEIALNKAT NVDNLIGSNP NGEIIFTPSF VDVHMKRKIC REWASNTVKK EK

UniProtKB: ER membrane protein complex subunit 5

+
Macromolecule #7: ER membrane protein complex subunit 6

MacromoleculeName: ER membrane protein complex subunit 6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 12.401341 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString:
MSSNEEVFTQ INATANVVDN KKRLLFVQDS SALVLGLVAG FLQIESVHGF IWFLILYNLI NVIYIVWICQ LQPGKFYQSP LQDIFFESF FREITGFVMA WTFGYALIG

UniProtKB: ER membrane protein complex subunit 6

+
Macromolecule #8: Protein SOP4

MacromoleculeName: Protein SOP4 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 26.627627 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MFSQIVLLLS AFIYVASATA RRGTIKGRLD LAASNITGFV STRTSFKLYQ IGNFSTEYPY TSTTMFQDDE GNFEFANLPL NDGVNETTY YVMYPASMDF NLKPNRILIE FKNLENGTLQ LNAFKNFFGR EYFPSKDITY PEKLQSMKVH PYITVELLHK A PIRSYLQA ...String:
MFSQIVLLLS AFIYVASATA RRGTIKGRLD LAASNITGFV STRTSFKLYQ IGNFSTEYPY TSTTMFQDDE GNFEFANLPL NDGVNETTY YVMYPASMDF NLKPNRILIE FKNLENGTLQ LNAFKNFFGR EYFPSKDITY PEKLQSMKVH PYITVELLHK A PIRSYLQA RNVSIFSTGI VGNILNSRWK LAGVITLIAL VVFPIIVEKL DPETARAIRE EAKRKQREKY AAVASK

UniProtKB: Protein SOP4

+
Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

+
Macromolecule #10: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 10 / Number of copies: 2 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 590118
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Coot, UCSF Chimera) / Number images used: 355991
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION

-
Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6wb9:
Structure of the S. cerevisiae ER membrane complex

+
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