[English] 日本語
Yorodumi
- EMDB-53030: CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II WITH THE IN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53030
TitleCRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II WITH THE INHIBITOR BIXAFEN
Map datayeast complex II with inhibitor bixafen
Sample
  • Complex: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 and SDH4 SOAKED WITH THE INHIBITOR BIXAFEN
    • Protein or peptide: x 4 types
  • Ligand: x 8 types
KeywordsCOMPLEX II / MEMBRANE PROTEIN / OXIDOREDUCTASE / OXIDOREDUCTASE INHIBITOR COMPLEX / BIXAFEN
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / TIM22 mitochondrial import inner membrane insertion complex / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / protein insertion into mitochondrial inner membrane / cellular respiration / 3 iron, 4 sulfur cluster binding ...Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of TCA cycle / TIM22 mitochondrial import inner membrane insertion complex / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / protein insertion into mitochondrial inner membrane / cellular respiration / 3 iron, 4 sulfur cluster binding / ubiquinone binding / quinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit ...Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae W303 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPinotsis N / Marechal A / Berry EA / Shu C
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/T032154/1 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Commun Biol / Year: 2026
Title: Cryo-EM structure of bixafen-bound S. cerevisiae complex II unravels SDHI specificity against pathogenic fungi
Authors: Pinotsis N / Burn-Leefe C / Jones S / Chen S / Lukoyanova N / Meunier B / Berry EA / Marechal A
History
DepositionMar 6, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53030.png

Downloads & links

-
Map

FileDownload / File: emd_53030.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationyeast complex II with inhibitor bixafen
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 340 pix.
= 281.52 Å		0.83 Å/pix.
x 340 pix.
= 281.52 Å		0.83 Å/pix.
x 340 pix.
= 281.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.316
Minimum - Maximum-1.8458108 - 3.685111
Average (Standard dev.)0.0014395183 (±0.061926942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 281.52 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map A yeast complex II with inhibitor bixafen

Fileemd_53030_half_map_1.map
Annotationhalf map A yeast complex II with inhibitor bixafen
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B yeast complex II with inhibitor bixafen

Fileemd_53030_half_map_2.map
Annotationhalf map B yeast complex II with inhibitor bixafen
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 ...

EntireName: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 and SDH4 SOAKED WITH THE INHIBITOR BIXAFEN
Components
  • Complex: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 and SDH4 SOAKED WITH THE INHIBITOR BIXAFEN
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
    • Protein or peptide: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: POTASSIUM ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: bixafen
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: water

+
Supramolecule #1: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 ...

SupramoleculeName: THE YEAST MITOCHONDRIAL COMPLEX II, COMPOSED OF SDH1, SDH2, SDH3 and SDH4 SOAKED WITH THE INHIBITOR BIXAFEN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 128 KDa

+
Macromolecule #1: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitoch...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 70.404453 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLSLKKSALS KLTLLRNTRT FTSSALVRQT QGSVNGSASR SADGKYHIID HEYDCVVIGA GGAGLRAAFG LAEAGYKTAC ISKLFPTRS HTVAAQGGIN AALGNMHKDN WKWHMYDTVK GSDWLGDQDS IHYMTREAPK SIIELEHYGV PFSRTENGKI Y QRAFGGQT ...String:
MLSLKKSALS KLTLLRNTRT FTSSALVRQT QGSVNGSASR SADGKYHIID HEYDCVVIGA GGAGLRAAFG LAEAGYKTAC ISKLFPTRS HTVAAQGGIN AALGNMHKDN WKWHMYDTVK GSDWLGDQDS IHYMTREAPK SIIELEHYGV PFSRTENGKI Y QRAFGGQT KEYGKGAQAY RTCAVADRTG HALLHTLYGQ ALRHDTHFFI EYFALDLLTH NGEVVGVIAY NQEDGTIHRF RA HKTIIAT GGYGRAYFSC TSAHT(CME)TGDG NAMVSRAGFP LQDLEFVQFH PSGIYGSGCL ITEGARGEGG FLVNSEGER FMERYAPTAK DLACRDVVSR AITMEIREGR GVGKKKDHMY LQLSHLPPEV LKERLPGISE TAAIFAGVDV TKEPIPIIPT VHYNMGGIP TKWNGEALTI DEETGEDKVI PGLMACGEAA CVSVHGANRL GANSLLDLVV FGRAVAHTVA DTLQPGLPHK P LPSDLGKE SIANLDKLRN ANGSRSTAEI RMNMKQTMQK DVSVFRTQSS LDEGVRNITA VEKTFDDVKT TDRSMIWNSD LV ETLELQN LLTCASQTAV SAANRKESRG AHAREDYPNR DDEHWMKHTL SWQKDVAAPV TLKYRRVIDH TLDEKECPSV PPT VRAY

UniProtKB: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

+
Macromolecule #2: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitocho...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 30.34741 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLNVLLRRKA FCLVTKKGMA TATTAAATHT PRLKTFKVYR WNPDEPSAKP HLQSYQVDLN DCGPMVLDAL LKIKDEQDST LTFRRSCRE GICGSCAMNI GGRNTLACI(CME) KIDQNESKQL KIYPLPHMFI VKDLVPDLTN FYQQYKSIQP YLQRSSF PK DGTEVLQSIE ...String:
MLNVLLRRKA FCLVTKKGMA TATTAAATHT PRLKTFKVYR WNPDEPSAKP HLQSYQVDLN DCGPMVLDAL LKIKDEQDST LTFRRSCRE GICGSCAMNI GGRNTLACI(CME) KIDQNESKQL KIYPLPHMFI VKDLVPDLTN FYQQYKSIQP YLQRSSF PK DGTEVLQSIE DRKKLDGLYE CILCACCSTS CPSYWWNQEQ YLGPAVLMQA YRWLIDSRDQ ATKTRKAMLN NSMSLYRC H TIMNCTRTCP KGLNPGLAIA EIKKSLAFA

UniProtKB: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

+
Macromolecule #3: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitoch...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508/S288c
Molecular weightTheoretical: 22.167031 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MSAMMVKLGL NKPALLLKPS AFSRAAALSS SRRLLFNTAR TNFLSTSPLK NVASEMNTKA AIAEEQILNK QRARRPISPH LTIYQPQLT WYLSSFHRIS LVLMGLGFYL FTILFGVSGL LGLGLTTEKV SNWYHQKFSK ITEWSIKGSF AYLFAIHYGG A IRHLIWDT ...String:
MSAMMVKLGL NKPALLLKPS AFSRAAALSS SRRLLFNTAR TNFLSTSPLK NVASEMNTKA AIAEEQILNK QRARRPISPH LTIYQPQLT WYLSSFHRIS LVLMGLGFYL FTILFGVSGL LGLGLTTEKV SNWYHQKFSK ITEWSIKGSF AYLFAIHYGG A IRHLIWDT AKELTLKGVY RTGYALIGFT AVLGTYLLTL

UniProtKB: Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial

+
Macromolecule #4: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, ...

MacromoleculeName: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
type: protein_or_peptide / ID: 4 / Details: Modified with an N-terminal His-Tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508/S288c
Molecular weightTheoretical: 22.081473 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MMLPRSMKFM TGRRIFHTAT VRAFQSTAKK SLTIPFLPVL PQKPGGVRGT PNDAYVPPPE NKLEGSYHWY MEKIFALSVV PLATTAMLT TGPLSTAADS FFSVMLLGYC YMEFNSCITD YISERVYGVW HKYAMYMLGL GSAVSLFGIY KLETENDGVV G LVKSLWDS ...String:
MMLPRSMKFM TGRRIFHTAT VRAFQSTAKK SLTIPFLPVL PQKPGGVRGT PNDAYVPPPE NKLEGSYHWY MEKIFALSVV PLATTAMLT TGPLSTAADS FFSVMLLGYC YMEFNSCITD YISERVYGVW HKYAMYMLGL GSAVSLFGIY KLETENDGVV G LVKSLWDS SEKDNSQKIE AKKGARGSHH HHHHHHHH

UniProtKB: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

+
Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

+
Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

+
Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

+
Macromolecule #8: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 8 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #9: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 9 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

+
Macromolecule #10: bixafen

MacromoleculeName: bixafen / type: ligand / ID: 10 / Number of copies: 1 / Formula: A1I6X
Molecular weightTheoretical: 414.209 Da

+
Macromolecule #11: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 11 / Number of copies: 1 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

+
Macromolecule #12: water

MacromoleculeName: water / type: ligand / ID: 12 / Number of copies: 27 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.021 mg/mL
BufferpH: 7.2 / Component - Concentration: 50.0 mM / Component - Name: HEPES / Details: 150 mM NaCl 0.05% GDN
GridModel: C-flat-1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 279 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 20000 / Average exposure time: 2.5 sec. / Average electron dose: 19.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 146416
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

0711

source_name: AlphaFold, initial_model_type: in silico model

1801

source_name: AlphaFold, initial_model_type: in silico model

3421

source_name: AlphaFold, initial_model_type: in silico model

7298

source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qdm:
CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II WITH THE INHIBITOR BIXAFEN

+
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