[English] 日本語
Yorodumi
- EMDB-35618: Cryo-EM structure of porcine bc1 complex in isolated state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35618
TitleCryo-EM structure of porcine bc1 complex in isolated state
Map data
Sample
  • Complex: porcine Cytochrome bc1 complex
    • Protein or peptide: x 10 types
  • Protein or peptide: x 1 types
  • Ligand: x 5 types
KeywordsComplex / mitochondria / ELECTRON TRANSPORT
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / pyramidal neuron development / cerebellar Purkinje cell layer development / thalamus development / Respiratory electron transport / Mitochondrial protein degradation / : / quinol-cytochrome-c reductase ...Complex III assembly / subthalamus development / pons development / pyramidal neuron development / cerebellar Purkinje cell layer development / thalamus development / Respiratory electron transport / Mitochondrial protein degradation / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / : / hippocampus development / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome b-c1 complex, subunit 6 / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome b-c1 complex, subunit 6 / Globular protein, non-globular alpha/beta subunit / 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 / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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 Rieske, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 6 / Cytochrome b / Complex III subunit 9
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsWang YX / Dong JQ / Yang GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of porcine bc1 complex in isolated state
Authors: Wang YX / Dong JQ / Yang GF
History
DepositionMar 11, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_35618.png

Downloads & links

-
Map

FileDownload / File: emd_35618.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.3680341 - 3.6266444
Average (Standard dev.)0.0038988374 (±0.11321616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 240.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_35618_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35618_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : porcine Cytochrome bc1 complex

EntireName: porcine Cytochrome bc1 complex
Components
  • Complex: porcine Cytochrome bc1 complex
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c1, heme protein, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 1, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 6
    • Protein or peptide: Cytochrome b-c1 complex subunit 7
    • Protein or peptide: Cytochrome b-c1 complex subunit 8
    • Protein or peptide: Complex III subunit 9
    • Protein or peptide: Cytochrome b-c1 complex subunit 10
  • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: CARDIOLIPIN

+
Supramolecule #1: porcine Cytochrome bc1 complex

SupramoleculeName: porcine Cytochrome bc1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Sus scrofa (pig)

+
Macromolecule #1: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 42.840715 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: MTNIRKSHPL MKIINNAFID LPAPSNISSW WNFGSLLGIC LILQILTGLF LAMHYTSDTT TAFSSVTHIC RDVNYGWVIR YLHANGASM FFICLFIHVG RGLYYGSYMF LETWNIGVVL LFTVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTD L VEWIWGGF ...String:
MTNIRKSHPL MKIINNAFID LPAPSNISSW WNFGSLLGIC LILQILTGLF LAMHYTSDTT TAFSSVTHIC RDVNYGWVIR YLHANGASM FFICLFIHVG RGLYYGSYMF LETWNIGVVL LFTVMATAFM GYVLPWGQMS FWGATVITNL LSAIPYIGTD L VEWIWGGF SVDKATLTRF FAFHFILPFI ITALAAVHLL FLHETGSNNP TGISSDMDKI PFHPYYTIKD ILGALFMMLI LL ILVLFSP DLLGDPDNYT PANPLNTPPH IKPEWYFLFA YAILRSIPNK LGGVLALVAS ILILILMPML HTSKQRSMMF RPL SQCLFW MLVADLITLT WIGGQPVEHP FIIIGQLASI LYFLIILVLM PITSIIENNL LKW

UniProtKB: Cytochrome b

+
Macromolecule #2: Cytochrome c1, heme protein, mitochondrial

MacromoleculeName: Cytochrome c1, heme protein, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 35.48893 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: MSAAAAASLR GAVLGPRGAG LPGARARGLL CGPRPGQLPL RTPQALSLSS KSGLSRGRKV ILSALGMLAA GGAGLAVALH SAVSATDLE LHAPSYPWSH RGLLSSLDHT SIRRGFQVYK QVCSSCHSMD YVAYRHLVGV CYTEEEAKAL AEEVEVQDGP N EDGEMFMR ...String:
MSAAAAASLR GAVLGPRGAG LPGARARGLL CGPRPGQLPL RTPQALSLSS KSGLSRGRKV ILSALGMLAA GGAGLAVALH SAVSATDLE LHAPSYPWSH RGLLSSLDHT SIRRGFQVYK QVCSSCHSMD YVAYRHLVGV CYTEEEAKAL AEEVEVQDGP N EDGEMFMR PGKLSDYFPK PYPNPEAARA ANNGALPPDL SYIVRARHGG EDYVFSLLTG YCEPPTGVSL REGLYFNPYF PG QAIAMAP PIYNEVLEFD DGTPATMSQV AKDVCTFLRW ASEPEHDHRK RMGLKMLMMM GLLLPLVYAM KRHKWSVLKS RKL AYRPPK

UniProtKB: Cytochrome c1, heme protein, mitochondrial

+
Macromolecule #3: Cytochrome b-c1 complex subunit Rieske, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.610492 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: SHTDIRVPDF SDYRRAEVLD STKSSKESSD ARKGFSYLIT ATTTVGVAYA AKNAVSQFVS SMSASADVLA MSKIEIKLSD IPEGKNMAF KWRGKPLFVR HRTKKEIDQE AAVEVSQLRD PQHDLERVKK PEWVILIGVC THLGCVPIAN AGDFGGYYCP C HGSHYDAS ...String:
SHTDIRVPDF SDYRRAEVLD STKSSKESSD ARKGFSYLIT ATTTVGVAYA AKNAVSQFVS SMSASADVLA MSKIEIKLSD IPEGKNMAF KWRGKPLFVR HRTKKEIDQE AAVEVSQLRD PQHDLERVKK PEWVILIGVC THLGCVPIAN AGDFGGYYCP C HGSHYDAS GRIRKGPAPL NLEVPTYEFT SDDLVIVG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

+
Macromolecule #4: Cytochrome b-c1 complex subunit 1, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 1, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 52.75632 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: MAASAVCRVA GTGSRVLLRT CRSPALLRSP ALRGTATYAQ ALQSVPETQV SQLDNGLRVA SEQSSQPTCT VGVWIDAGSR YENEKNNGA GYFVEHLAFK GTKNRPGSAL EKEVESMGAH LNAYSTREHT AYYIKALSKD LPKAVELLAD IVQNCSLEDS Q IEKERDVI ...String:
MAASAVCRVA GTGSRVLLRT CRSPALLRSP ALRGTATYAQ ALQSVPETQV SQLDNGLRVA SEQSSQPTCT VGVWIDAGSR YENEKNNGA GYFVEHLAFK GTKNRPGSAL EKEVESMGAH LNAYSTREHT AYYIKALSKD LPKAVELLAD IVQNCSLEDS Q IEKERDVI LQELQENDSS MRDVVFDYLH ATAFQGTPLA QSVEGPSENV RKLSRADLTE YVSQHYKAPR MVLAAAGGVE HR QLLDLAQ KHFSSLSGTY VEDAVPAFTP CRFTGSEIRH RDDALPLAHV AIAVEGPGWA NPDNVPLQVA NAIIGHYDST YGG GTHMSS TLASVAATRK LCQSFQTFNI CYAETGLLGA HFVCDNMSID DMMFFLQGQW MRLCTSATES EVVRGKNILR NALV SHLDG TTPVCEDIGR SLLTYGRRIP LAEWESRIAE VDASVVREVC SKYFYDQCPA VAGLGPIEQL PDYNRIRSGM FWLRF

UniProtKB: Cytochrome b-c1 complex subunit 1, mitochondrial

+
Macromolecule #5: Cytochrome b-c1 complex subunit 2, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 48.264477 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString: MKLITRAGSF SRFYSLKVAP KALASAAPAG VPLQPQDLEF TRLPNGLVIA SLENYAPASR IGLFIKAGSR YEDSNNLGTS HLLRLASSL TTKGASSFKI TRGIEAVGGK LSVTSTRESM AYTVECLRDD IEILMEFLLN VTAAPEFRRW EVAALQSQLR I DKAVAFQN ...String:
MKLITRAGSF SRFYSLKVAP KALASAAPAG VPLQPQDLEF TRLPNGLVIA SLENYAPASR IGLFIKAGSR YEDSNNLGTS HLLRLASSL TTKGASSFKI TRGIEAVGGK LSVTSTRESM AYTVECLRDD IEILMEFLLN VTAAPEFRRW EVAALQSQLR I DKAVAFQN PQAQVLENLH AAAYRNALAN SLYCPDYRIG KVTPDQLHYY VQNHFTSARM ALIGLGVSHP VLKQVAERFL NM RGGLGLS GAKAKYRGGE IRDQNGDSLV HAALVAESAA TGSAEANAFS VLQHVLGAGP HVKRGSNATS SLYQAVAKGV HQP FDVSAF NASYSDSGLF GIYTISQAAS AGDVIKSAYD QVKAIAQGNL SNTDVQAAKN KLKAGYLMSV ESSEGFLDEV GSQA LVAGS YMQPSTVLQQ IDSVADADVI NAAKKFVSGR KSMAASGNLG HTPFVDEL

UniProtKB: Cytochrome b-c1 complex subunit 2, mitochondrial

+
Macromolecule #6: Cytochrome b-c1 complex subunit 6

MacromoleculeName: Cytochrome b-c1 complex subunit 6 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 10.685803 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
MGLEDEQRML TGSGDPKEEE EEEEELVDPL TTVREQCEQI EKCIKARERL ELCDQRVSSR SQTEEDCTEE LFDFLHARDH CVAHKLFNS LK

UniProtKB: Cytochrome b-c1 complex subunit 6

+
Macromolecule #7: Cytochrome b-c1 complex subunit 7

MacromoleculeName: Cytochrome b-c1 complex subunit 7 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.587549 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
MASRPAVAAS SKWLEGIRKW YYNAAGFNKL GLMRDDTIYE DDDVKEAIRR LPENLYNDRV FRIKRALDLT MRQQILPKEQ WTKYEEDKF YLEPYLKEVI RERKEREEWA KK

UniProtKB: Cytochrome b-c1 complex subunit 7

+
Macromolecule #8: Cytochrome b-c1 complex subunit 8

MacromoleculeName: Cytochrome b-c1 complex subunit 8 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 9.784339 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
MGREFGHLTR MRHVITYSLS PFEQRAFPHY FTKGIPNVLR RTRACILRVA PPFVVFYLVY TWGTQEFEKS KRKNPAAYEN DK

UniProtKB: Cytochrome b-c1 complex subunit 8

+
Macromolecule #9: Complex III subunit 9

MacromoleculeName: Complex III subunit 9 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.41253 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
MAAPTLTARL YSLLFRRTST FALTIAVGAL FFERAFDQGA DAIYEHINQG KLWKHIKHKY ENKE

UniProtKB: Complex III subunit 9

+
Macromolecule #10: Cytochrome b-c1 complex subunit 10

MacromoleculeName: Cytochrome b-c1 complex subunit 10 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 6.560654 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
MLSRFLGPRY RELARNWIPT ASMWGAVGAV GLVWATDWRL ILDWVPYING KFKKED

UniProtKB: Cytochrome b-c1 complex subunit 10

+
Macromolecule #11: Cytochrome b-c1 complex subunit Rieske, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 11
Details: Author stated: Chain C/c and Chain K/k are truly from one polypeptide, and the polypeptide will be cleaved into two chains upon maturation.
Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.900107 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
MLSVASRSGP FAPVLSATSR GVAGALRPLV QAALPATSES PVLDAKRSFL CRESLSGQAA GRPLVASVGL NVPASVRY

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

+
Macromolecule #12: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 12 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #13: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 13 / Number of copies: 3 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

+
Macromolecule #14: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 14 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

+
Macromolecule #15: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 15 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

+
Macromolecule #16: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 16 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4 / Details: PBS, 0.1% DDM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 701 / Average electron dose: 49.21 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 96000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 191014
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98300
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial modelPDB ID:

5gup


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8iog:
Cryo-EM structure of porcine bc1 complex in isolated state

+
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