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- EMDB-22447: Plant Mitochondrial complex IV from Vigna radiata -

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Basic information

Entry
Database: EMDB / ID: EMD-22447
TitlePlant Mitochondrial complex IV from Vigna radiata
Map dataPlant Mitochondrial complex IV from Vigna radiata
Sample
  • Complex: Mitochondrial Respiratory Complex IV
    • Protein or peptide: x 10 types
  • Ligand: x 9 types
Function / homology
Function and homology information


respiratory chain complex IV / mitochondrial respiratory chain complex IV / mitochondrial respirasome / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / respirasome / mitochondrial inner membrane / membrane => GO:0016020 / copper ion binding / mitochondrion
Similarity search - Function
Cytochrome c oxidase subunit 5c / Protein of unknown function DUF1138 / Protein of unknown function (DUF1138) / Predicted cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb ...Cytochrome c oxidase subunit 5c / Protein of unknown function DUF1138 / Protein of unknown function (DUF1138) / Predicted cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxin
Similarity search - Domain/homology
uncharacterized protein LOC106757297 / uncharacterized protein LOC106759053 / Cytochrome c oxidase subunit 2 / cytochrome c oxidase subunit 5b-2, mitochondrial / cytochrome c oxidase subunit 6a, mitochondrial / Cytochrome c oxidase subunit 5C / uncharacterized protein LOC106772338 / cytochrome c oxidase subunit 6b-1
Similarity search - Component
Biological speciesVigna radiata (mung bean) / Mung bean (mung bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMaldonado M / Letts JA
CitationJournal: Elife / Year: 2021
Title: Atomic structures of respiratory complex III, complex IV, and supercomplex III-IV from vascular plants.
Authors: Maria Maldonado / Fei Guo / James A Letts /
Abstract: Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes ...Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII, CIV, and SC III+IV from determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII revealed long-range, coordinated movements across the complex, as well as the motion of CIII's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.
History
DepositionAug 12, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jro
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22447.png

Downloads & links

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Map

FileDownload / File: emd_22447.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlant Mitochondrial complex IV from Vigna radiata
Voxel sizeX=Y=Z: 0.8332 Å
Density
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.056330264 - 0.07118392
Average (Standard dev.)-2.6365628e-06 (±0.0016525936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.5984 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.833199218750.833199218750.83319921875
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z426.598426.598426.598
α/β/γ90.00090.00090.000
start NX/NY/NZ937643
NX/NY/NZ114126230
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0560.071-0.000

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Supplemental data

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Mask #1

Fileemd_22447_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Plant Mitochondrial complex IV from Vigna radiata. Half map 1.

Fileemd_22447_half_map_1.map
AnnotationPlant Mitochondrial complex IV from Vigna radiata. Half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Plant Mitochondrial complex IV from Vigna radiata. Half map 2.

Fileemd_22447_half_map_2.map
AnnotationPlant Mitochondrial complex IV from Vigna radiata. Half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial Respiratory Complex IV

EntireName: Mitochondrial Respiratory Complex IV
Components
  • Complex: Mitochondrial Respiratory Complex IV
    • Protein or peptide: COX1
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: COX3
    • Protein or peptide: COX4
    • Protein or peptide: cytochrome c oxidase subunit 5b-2, mitochondrial
    • Protein or peptide: cytochrome c oxidase subunit 6a, mitochondrial
    • Protein or peptide: cytochrome c oxidase subunit 6b-1
    • Protein or peptide: Cytochrome c oxidase subunit 5C
    • Protein or peptide: COX7a
    • Protein or peptide: COX7c
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
  • Ligand: CARDIOLIPIN
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: ZINC ION
  • Ligand: LYSINE

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Supramolecule #1: Mitochondrial Respiratory Complex IV

SupramoleculeName: Mitochondrial Respiratory Complex IV / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Vigna radiata (mung bean) / Tissue: hypocotyl / Organelle: mitochondria
Molecular weightTheoretical: 485 KDa

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Macromolecule #1: COX1

MacromoleculeName: COX1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mung bean (mung bean)
Molecular weightTheoretical: 57.960559 KDa
SequenceString: MTNPVRWLFS TNHKDIGTLY FIFGAIAGVM GTCFSVLIRM ELARPGDQIL GGNHQLYNVL ITAHAFLMIF FMVMPAMIGG FGNWFVPIL IGAPDMAFPR LNNISFWLLP PSLLLLLSSA LVEVGSGTGW TVYPPLSGIT SHSGGAVDLA IFSLHLSGVS S ILGSINFI ...String:
MTNPVRWLFS TNHKDIGTLY FIFGAIAGVM GTCFSVLIRM ELARPGDQIL GGNHQLYNVL ITAHAFLMIF FMVMPAMIGG FGNWFVPIL IGAPDMAFPR LNNISFWLLP PSLLLLLSSA LVEVGSGTGW TVYPPLSGIT SHSGGAVDLA IFSLHLSGVS S ILGSINFI TTIFNMRGPG MTMHRSPLFV WSVLVTAFLL LLSLPVLAGA ITMLLTDRNF NTTFFDPAGG GDPILYQHLF WF FGHPEVY ILILPGFGII SHIVSTFSGK PVFGYLGMVY AMISIGVLGF LVWAHHMFTV GLDVDTRAYF TAATMIIAVP TGI KIFSWI ATMWGGSIQY KTPMLFAVGF IFLFTIGGLT GIVLANSGLD IALHDTYYVV AHFHYVLSMG AVFALFAGFY YWVG KIFGR TYPETLGQIH FWITFFGVNL TFFPMHFLGL SGMPRRIPDY PDAYAGWNAL SSFGSYISVV GICCFFVVVT ITSTS GNNI TRANIPWAVE QNSTTLEWLV QSPPAFHTFG ELPAIKETKS YVK

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Macromolecule #2: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mung bean (mung bean)
Molecular weightTheoretical: 28.391602 KDa
SequenceString: MCGGFPAISF CDAPEPWQLG FQDAATPIMQ GIMDLHHDIF FFLVQIAVFV LWVLSRALWC FRSKISPIPQ RIVHGTTIEI LWTIFPSII LMFIAIPSFT LLYSMDDVVV DPAITIKAIG HQWYWSYEYS DYNNSDEQSL AFDSYMVPED DLELGQLRLL E VDNRVVVP ...String:
MCGGFPAISF CDAPEPWQLG FQDAATPIMQ GIMDLHHDIF FFLVQIAVFV LWVLSRALWC FRSKISPIPQ RIVHGTTIEI LWTIFPSII LMFIAIPSFT LLYSMDDVVV DPAITIKAIG HQWYWSYEYS DYNNSDEQSL AFDSYMVPED DLELGQLRLL E VDNRVVVP AKTHLRVLIT SADVLHSWAV PSLGVKCDAV PGRLNQISTF IQREGVYYGQ CSEICGTNHA FMPIVVEAVS TK DYGSWVS NQIQ

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Macromolecule #3: COX3

MacromoleculeName: COX3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mung bean (mung bean)
Molecular weightTheoretical: 29.967893 KDa
SequenceString: MIESQRHSYH LVDPSPWPIS GSLGALATTV GGVMYMHSFQ GGATLLSLGL IFILYTMFVW WRDVLRESTL EGHHTKVVQL GLRYGFILF IVSEVMFLFA FFWAFFHSSL APTVEIGGIW PPLGIWVLDP WEIPFLNTLI LLSSGAAVTW AHHAILAGKE K RAVYALVA ...String:
MIESQRHSYH LVDPSPWPIS GSLGALATTV GGVMYMHSFQ GGATLLSLGL IFILYTMFVW WRDVLRESTL EGHHTKVVQL GLRYGFILF IVSEVMFLFA FFWAFFHSSL APTVEIGGIW PPLGIWVLDP WEIPFLNTLI LLSSGAAVTW AHHAILAGKE K RAVYALVA TVLLALVFTG FQGMEYYQAP FTISDSIYGS TFFLATGFHG FHVIIGTLFL IICGIRQYLG HLTKEHHVGF EA AAWYWHF VDVVWLFLFV SIYWWGGI

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Macromolecule #4: COX4

MacromoleculeName: COX4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mung bean (mung bean)
Molecular weightTheoretical: 8.81102 KDa
SequenceString:
MSTKYIVSAI LGSFGIAWVC DYYVSEKKIF GGSTPGTITN KEWGEETDKK FQAWPRTAGP PVVVNPITRQ NFVVKSRSE

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Macromolecule #5: cytochrome c oxidase subunit 5b-2, mitochondrial

MacromoleculeName: cytochrome c oxidase subunit 5b-2, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mung bean (mung bean)
Molecular weightTheoretical: 16.694705 KDa
SequenceString:
MLRRFLSHSN LRSLHTALSP SRPRFAAPLL TRHVTAQSGA SSVRKRVEDV VPIATGHERE EIQASLEGRD ILEINHPEGP FGTKEAPAI VKSYFDRRIV GCPGGEGEDE HDVVWFWLEN GKPHECPVCS QYFELKVVGP GGDPYGHGDH H

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Macromolecule #6: cytochrome c oxidase subunit 6a, mitochondrial

MacromoleculeName: cytochrome c oxidase subunit 6a, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mung bean (mung bean)
Molecular weightTheoretical: 11.225671 KDa
SequenceString:
MATSLVRSGF LRTALRGGAR GSQVPKRNFS SAGHHDDAYE TAKWEKITYL GIVSCTGLAI YNLSKGHPHT EEPPAYPYLH IRNKEFPWG PDGLFETKKH H

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Macromolecule #7: cytochrome c oxidase subunit 6b-1

MacromoleculeName: cytochrome c oxidase subunit 6b-1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mung bean (mung bean)
Molecular weightTheoretical: 20.018635 KDa
SequenceString:
MAETAANKSQ SLAEEYHVSD KQEKTAVVEK PVEVKEVENP QEAGSVEAVV EKIVEETTPV APAVAQESSE VSPPPAEESA EESTEEQSS GNVEDNSGNE DAAEKTPEIK LETAPADFRF PTTNQTRHCF TRYIEYHRCV AAKGEGASEC DKFAKYYRSL C PGEWIDRW NEQRENGTFP GPL

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Macromolecule #8: Cytochrome c oxidase subunit 5C

MacromoleculeName: Cytochrome c oxidase subunit 5C / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mung bean (mung bean)
Molecular weightTheoretical: 7.120326 KDa
SequenceString:
MAGPRIAHAT LKGPSVVKEI IIGITLGLAA GSVWKMHHWN EQRKIRTFYD LLEKGEIGVV VDEQ

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Macromolecule #9: COX7a

MacromoleculeName: COX7a / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mung bean (mung bean)
Molecular weightTheoretical: 7.622931 KDa
SequenceString:
MSEPPFRPRE KLIEKQKHFQ SVHKHTYLKG PYDKITSVAI PLALAASSLY LIGRGIYNMS HGIGKKE

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Macromolecule #10: COX7c

MacromoleculeName: COX7c / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mung bean (mung bean)
Molecular weightTheoretical: 10.505158 KDa
SequenceString:
MAFNNALRSA AKLIASSESS ISTSVSRGFH STPMKRMGGG HGHDEPYYIH AKHMYNLDRM KHRGLKMSLA VFSAFSIGVA VPVYAVIFQ QKKTASA

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Macromolecule #11: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 11 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A / Heme A

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Macromolecule #12: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

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Macromolecule #13: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #14: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 14 / Number of copies: 2 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

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Macromolecule #15: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / type: ligand / ID: 15 / Number of copies: 17 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da

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Macromolecule #16: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 16 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Macromolecule #17: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Macromolecule #18: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #19: LYSINE

MacromoleculeName: LYSINE / type: ligand / ID: 19 / Number of copies: 1 / Formula: LYS
Molecular weightTheoretical: 147.195 Da
Chemical component information

ChemComp-LYS:
LYSINE / Lysine

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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

Concentration6 mg/mL
BufferpH: 7.8
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMsodium chlorideNaClSodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acid
0.2 %digitonin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK III
DetailsThis sample was monodisperse on size exclusion chromatography but was a mixture of different mitochondrial respiratory complexes

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 60010 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 9816 / Average exposure time: 3.0 sec. / Average electron dose: 86.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 150000000
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: NONE / Details: Ab initio model generation
Initial angle assignmentType: OTHER / Software - Name: RELION / Details: Stochastic gradient descent
Final angle assignmentType: OTHER / Software - Name: RELION / Details: Stochastic gradient descent
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 29348
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

6q9e

,

5b1a

)
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 67 / Target criteria: correlation coefficient
Output model

PDB-7jro:
Plant Mitochondrial complex IV from Vigna radiata

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