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- EMDB-24484: Complex III2 from Candida albicans, inhibitor free, Rieske head d... -

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Basic information

Entry
Database: EMDB / ID: EMD-24484
TitleComplex III2 from Candida albicans, inhibitor free, Rieske head domain in intermediate position
Map dataCandida albicans complex III2, inhibitor free, Rieske head domain intermediate state
Sample
  • Complex: Respiratory complex III2 from Candida albicans
    • Protein or peptide: x 9 types
  • Ligand: x 4 types
Function / homology
Function and homology information


regulation of filamentous growth / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / heterochromatin ...regulation of filamentous growth / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / heterochromatin / aerobic respiration / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / mitochondrion / membrane / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily ...Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit 8, mitochondrial / Cytochrome b-c1 complex catalytic subunit, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 9, mitochondrial / Cytochrome b-c1 complex reductase subunit, mitochondrial / Cytochrome b / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast) / Yeast (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDi Trani JM / Rubinstein JL
Funding support Canada, Sweden, 5 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Canadian Institutes of Health Research (CIHR)FDN154288 Canada
Knut and Alice Wallenberg Foundation2019.0043 Sweden
Swedish Research Council2018-04619 Sweden
Canada Research Chairs Canada
CitationJournal: Structure / Year: 2022
Title: Rieske head domain dynamics and indazole-derivative inhibition of Candida albicans complex III.
Authors: Justin M Di Trani / Zhongle Liu / Luke Whitesell / Peter Brzezinski / Leah E Cowen / John L Rubinstein /
Abstract: Electron transfer between respiratory complexes drives transmembrane proton translocation, which powers ATP synthesis and membrane transport. The homodimeric respiratory complex III (CIII) oxidizes ...Electron transfer between respiratory complexes drives transmembrane proton translocation, which powers ATP synthesis and membrane transport. The homodimeric respiratory complex III (CIII) oxidizes ubiquinol to ubiquinone, transferring electrons to cytochrome c and translocating protons through a mechanism known as the Q cycle. The Q cycle involves ubiquinol oxidation and ubiquinone reduction at two different sites within each CIII monomer, as well as movement of the head domain of the Rieske subunit. We determined structures of Candida albicans CIII by cryoelectron microscopy (cryo-EM), revealing endogenous ubiquinone and visualizing the continuum of Rieske head domain conformations. Analysis of these conformations does not indicate cooperativity in the Rieske head domain position or ligand binding in the two CIIIs of the CIII dimer. Cryo-EM with the indazole derivative Inz-5, which inhibits fungal CIII and is fungicidal when administered with fungistatic azole drugs, showed that Inz-5 inhibition alters the equilibrium of Rieske head domain positions.
History
DepositionJul 20, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.63
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.63
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rjc
  • Surface level: 0.63
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24484.png

Downloads & links

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Map

FileDownload / File: emd_24484.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCandida albicans complex III2, inhibitor free, Rieske head domain intermediate state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 288 pix.
= 296.64 Å		1.03 Å/pix.
x 288 pix.
= 296.64 Å		1.03 Å/pix.
x 288 pix.
= 296.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.63 / Movie #1: 0.63
Minimum - Maximum-5.440914 - 7.2719474
Average (Standard dev.)0.004449707 (±0.16364466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 296.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z296.640296.640296.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ330330330
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-5.4417.2720.004

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Supplemental data

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Sample components

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Entire : Respiratory complex III2 from Candida albicans

EntireName: Respiratory complex III2 from Candida albicans
Components
  • Complex: Respiratory complex III2 from Candida albicans
    • Protein or peptide: Ubiquinol--cytochrome-c reductase subunit
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Ubiquinol--cytochrome-c reductase catalytic subunit
    • Protein or peptide: Cytochrome b-c1 complex subunit 7
    • Protein or peptide: Ubiquinol--cytochrome-c reductase subunit 8
    • Protein or peptide: Ubiquinol--cytochrome-c reductase subunit 6
    • Protein or peptide: Ubiquinol--cytochrome-c reductase subunit 9
    • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: UBIQUINONE-10
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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Supramolecule #1: Respiratory complex III2 from Candida albicans

SupramoleculeName: Respiratory complex III2 from Candida albicans / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Candida albicans SC5314 (yeast)

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Macromolecule #1: Ubiquinol--cytochrome-c reductase subunit

MacromoleculeName: Ubiquinol--cytochrome-c reductase subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (yeast) / Strain: SC5314 / ATCC MYA-2876
Molecular weightTheoretical: 48.004805 KDa
SequenceString: MIRGSSALKS LTSRRLYSTG VKYTTLSNGV TVATETNPAA KTSSVGLFFG AGSRSEHSHS NGISALTTNV LASQSAKGSL LTAKNDREF NGIIAQTTND NITEAGKLIA SIASNAVDIV EKTDLTKHKQ YLSAQASAVE ADPKSKVLSH LYSSAFQGYS L ALPTLGTT ...String:
MIRGSSALKS LTSRRLYSTG VKYTTLSNGV TVATETNPAA KTSSVGLFFG AGSRSEHSHS NGISALTTNV LASQSAKGSL LTAKNDREF NGIIAQTTND NITEAGKLIA SIASNAVDIV EKTDLTKHKQ YLSAQASAVE ADPKSKVLSH LYSSAFQGYS L ALPTLGTT ESVENLENQD SLRHLAKHLV NNNTVIAASG NFDHDKLADA IEANLKIAEG VKPEIKPASF LGSEVRMRDD TL PKAYISI AVHGEGLNSP NYYLAKVAAA IYGDFYLHST IAKFTSPKLA SIVQEYNIVE SYNHYSKSFS DTGIWGYYAE IAD KFTVDD FTHFSLKEWN RLSISISEAE VARAKAQVKT ALAKELANSF AVTSDIAEKV LLVGHRQSLR EAFEKIDAIK VNDV KEWGK SKVWDRDIVI SGTGLIEDLL DYNRNRNEMA MMRW

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Macromolecule #2: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (yeast) / Strain: SC5314 / ATCC MYA-2876
Molecular weightTheoretical: 43.738457 KDa
SequenceString: MPTRKSNTYL SLVNSYLIDS PQPSSINYWW NLGSLLGLCL VIQIASGVFL AMHYSSNIEL AFDSVEHIMR DVNAGWLIRY IHANGASFF FICMYLHIGK ALYYGSYKQP RVMLWVIGVV IFILTMAIAF MGYCLVYGQM SHWGATVITN LLSAIPFIGN D IVPFIWGG ...String:
MPTRKSNTYL SLVNSYLIDS PQPSSINYWW NLGSLLGLCL VIQIASGVFL AMHYSSNIEL AFDSVEHIMR DVNAGWLIRY IHANGASFF FICMYLHIGK ALYYGSYKQP RVMLWVIGVV IFILTMAIAF MGYCLVYGQM SHWGATVITN LLSAIPFIGN D IVPFIWGG FSVSNPTIQR FFALHFLLPF ILAALVCMHL MALHVHGSSN PVGITGNIDR LPMHPYFIFK DLITVFVFLL IF SLFVFYS PNTLGHPDNY IPGNPMVTPP SIVPEWYLLP FYAILRSIPD KLGGVIAMFG AILILLSLPY TDRSIIRGNS FKV LSKLAF YLFVFNFILL GNLGQLHVEV PYIQLGQFAT AYYFAHYIIV VPVISTLENI LYYIGTQTRV K

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Macromolecule #3: Ubiquinol--cytochrome-c reductase catalytic subunit

MacromoleculeName: Ubiquinol--cytochrome-c reductase catalytic subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (yeast) / Strain: SC5314 / ATCC MYA-2876
Molecular weightTheoretical: 32.261389 KDa
SequenceString: MFRTAYKTMN QSMVQKFIAG GVGVTGLTAS YLLYQDSMTA DAMTAAEHGL HPPAYNWPHN GMFETFDHAS IRRGFQVYRE VCAACHSLD RIAWRNLVGV SHTTSEAKAM AEELEYDDEP DDEGKPRKRP GKLADYIPGP YENEQAARAA NQGAYPPDLS L IVKARHGG ...String:
MFRTAYKTMN QSMVQKFIAG GVGVTGLTAS YLLYQDSMTA DAMTAAEHGL HPPAYNWPHN GMFETFDHAS IRRGFQVYRE VCAACHSLD RIAWRNLVGV SHTTSEAKAM AEELEYDDEP DDEGKPRKRP GKLADYIPGP YENEQAARAA NQGAYPPDLS L IVKARHGG SDYIFSLLTG YPDEPPAGVV LPEGSNYNPY FPGGAIAMGR VLFDDLVEYE DGTPATTSQM AKDVSTFLNW AS EPEHDDR KKWGLKALVV LSSLYLLSIW VKRFKWTPIK NRKFRFDPPK K

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Macromolecule #4: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (yeast) / Strain: SC5314 / ATCC MYA-2876
Molecular weightTheoretical: 14.44071 KDa
SequenceString:
MVQSMTSVVK AANFILARPT LSKIITPLAQ KFTAYAGYRE MGLKFNDLLL EETPIMQTAI KRLPSELNYS RNFRILTAHQ LALSHQLLP AEKAVKPEED DNYLIPYILE AEKEAFEKAE LDNIEVKA

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Macromolecule #5: Ubiquinol--cytochrome-c reductase subunit 8

MacromoleculeName: Ubiquinol--cytochrome-c reductase subunit 8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (yeast) / Strain: SC5314 / ATCC MYA-2876
Molecular weightTheoretical: 11.125672 KDa
SequenceString:
MAGAPHPHTY MGWWGSLGSP KQKYITQYTI SPYAAKPLKG AAYNAVFNTF RRTKNQFLYV AIPFVVVWSI WTRARDYNEY LYTKEGREE LERVNV

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Macromolecule #6: Ubiquinol--cytochrome-c reductase subunit 6

MacromoleculeName: Ubiquinol--cytochrome-c reductase subunit 6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (yeast) / Strain: SC5314 / ATCC MYA-2876
Molecular weightTheoretical: 16.042014 KDa
SequenceString:
MSFFRDLLES VVPTAYAEEP VEDVEVEQPE DAPEEEVSEE TVEEEEEDDE DDDEDDEEEE ETADPLDTLR EECTKTAACK PFDHHFHEC IERVTKEQEE PDYEHKHYKE DCIEEFFHLQ HCVNDCVAPR LFNRLK

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Macromolecule #7: Ubiquinol--cytochrome-c reductase subunit 9

MacromoleculeName: Ubiquinol--cytochrome-c reductase subunit 9 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (yeast) / Strain: SC5314 / ATCC MYA-2876
Molecular weightTheoretical: 4.538231 KDa
SequenceString:
ATIFGGAFAF QGFFDVAVNK WWEEHNKAKL WKNVKGKFL

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Macromolecule #8: Cytochrome b-c1 complex subunit 2, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (yeast) / Strain: SC5314 / ATCC MYA-2876
Molecular weightTheoretical: 39.593352 KDa
SequenceString: MLSRASIRAY SSIPNSVKIA AKESATDLTK LSVIINNAGS KTGKSGVSHL LSKFTFLNNG AKSALRFTRE SELLGGTFES KVTRDALIL NTTFLKQDLP YYVEALGNVV SNTQFAPHEF NEIVLPTANA ETKLANANPA FKGVEKLHEI TFRRGLGNPL F YNESTPIK ...String:
MLSRASIRAY SSIPNSVKIA AKESATDLTK LSVIINNAGS KTGKSGVSHL LSKFTFLNNG AKSALRFTRE SELLGGTFES KVTRDALIL NTTFLKQDLP YYVEALGNVV SNTQFAPHEF NEIVLPTANA ETKLANANPA FKGVEKLHEI TFRRGLGNPL F YNESTPIK LEEVAQFSKE QFSGENISIV AEGANEEDLT KFVSESAFCY LPSSSSNGAK ALPTNTFTGQ EARVPSSGAS SA LIGIPVK PADFGKYEVL SAAIGTSTLP STSTPLAQIP GATSHLYKYQ DAGLFVISVS GEASQVAQGI KQAKSVAESV SSS ALSEAV KAAELSVALQ STVDSPLNVK VVAEEAPISK FNYVAVGDLD VLPYADEL

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Macromolecule #9: Cytochrome b-c1 complex subunit Rieske, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Yeast (yeast) / Strain: SC5314 / ATCC MYA-2876
Molecular weightTheoretical: 23.233385 KDa
SequenceString: MSSLAFRTLR NGLGLKSSVR ALSTTTTTLS NYQQPDYSSY LNNKSGQGSR NFTYFMVGSM GLLSAAGAKS TVEAFLSSFA ASADVLAMA KVEVKLGAIP EGKNVIIKWQ GKPVFIRHRT ADEIEEANQV DIKTLRDPQN DADRVKKPEW LIMLGICTHL G CVPIGEAG ...String:
MSSLAFRTLR NGLGLKSSVR ALSTTTTTLS NYQQPDYSSY LNNKSGQGSR NFTYFMVGSM GLLSAAGAKS TVEAFLSSFA ASADVLAMA KVEVKLGAIP EGKNVIIKWQ GKPVFIRHRT ADEIEEANQV DIKTLRDPQN DADRVKKPEW LIMLGICTHL G CVPIGEAG DFGGWFCPCH GSHYDISGRI RKGPAPLNLE IPEYDFTDDE TLLVG

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Macromolecule #10: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 10 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #11: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 11 / Number of copies: 2 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #12: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 12 / Number of copies: 1 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #13: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 13 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.0 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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58556
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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