[English] 日本語
Yorodumi
- EMDB-22228: R. capsulatus CIII2CIV tripartite super-complex, conformation A (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22228
TitleR. capsulatus CIII2CIV tripartite super-complex, conformation A (SC-1A)
Map dataCIII2CIV tripartite super-complex, conformation A (SC-1A)
Sample
  • Complex: CIII2CIV tripartite super-complex, conformation A (SC-1A)
    • Complex: CIII2
      • Protein or peptide: Ubiquinol-cytochrome c reductase iron-sulfur subunit
      • Protein or peptide: Cytochrome b
      • Protein or peptide: Cytochrome c1
    • Complex: CIV
      • Protein or peptide: Cytochrome c oxidase, Cbb3-type, subunit I
      • Protein or peptide: Cytochrome c oxidase, Cbb3-type, subunit II
      • Protein or peptide: Cbb3-type cytochrome c oxidase subunit CcoP,Cytochrome c-type cyt cy
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: HEME C
  • Ligand: COPPER (II) ION
Keywordscytochrome bc1 / cbb3-COX / Complex III / Complex IV / OXIDOREDUCTASE / TRANSLOCASE-Oxidoreductase complex
Function / homology
Function and homology information


cytochrome-c oxidase / : / respiratory chain complex III / oxidative phosphorylation / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / : / photosynthesis ...cytochrome-c oxidase / : / respiratory chain complex III / oxidative phosphorylation / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / : / photosynthesis / respiratory electron transport chain / proton transmembrane transport / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / Cytochrome C oxidase, mono-heme subunit/FixO / N-terminal domain of cytochrome oxidase-cbb3, FixP / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / : ...Cytochrome c oxidase, monohaem subunit/FixO / Cytochrome c oxidase cbb3-type, subunit I / Cytochrome c oxidase cbb3-type, subunit III / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal / Cbb3-type cytochrome c oxidase subunit CcoP, N-terminal domain superfamily / Cytochrome C oxidase, mono-heme subunit/FixO / N-terminal domain of cytochrome oxidase-cbb3, FixP / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / : / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c, class IA/ IB / Cytochrome b / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / : / 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 c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / 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 / Cytochrome c / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1 / cytochrome-c oxidase / Cytochrome c oxidase, Cbb3-type, subunit II / Cbb3-type cytochrome c oxidase subunit CcoP / Cytochrome c-type cyt cy
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria) / Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsSteimle S / Van Eeuwen T
Funding support United States, Israel, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM38237 United States
Department of Energy (DOE, United States)DE-FG02-91ER20052 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123233 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008275 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD023592 United States
Israel Science Foundation1466/18 Israel
United States - Israel Binational Science Foundation (BSF)2016070 Israel
Israel Ministry of Science and Technology80802 Israel
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structures of engineered active bc-cbb type CIIICIV super-complexes and electronic communication between the complexes.
Authors: Stefan Steimle / Trevor van Eeuwen / Yavuz Ozturk / Hee Jong Kim / Merav Braitbard / Nur Selamoglu / Benjamin A Garcia / Dina Schneidman-Duhovny / Kenji Murakami / Fevzi Daldal /
Abstract: Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc (Complex ...Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc (Complex III, CIII), and may have specific cbb-type cyt c oxidases (Complex IV, CIV) instead of the canonical aa-type CIV. Electron transfer between these complexes is mediated by soluble (c) and membrane-anchored (c) cyts. Here, we report the structure of an engineered bc-cbb type SC (CIIICIV, 5.2 Å resolution) and three conformers of native CIII (3.3 Å resolution). The SC is active in vivo and in vitro, contains all catalytic subunits and cofactors, and two extra transmembrane helices attributed to cyt c and the assembly factor CcoH. The cyt c is integral to SC, its cyt domain is mobile and it conveys electrons to CIV differently than cyt c. The successful production of a native-like functional SC and determination of its structure illustrate the characteristics of membrane-confined and membrane-external respiratory electron transport pathways in Gram-negative bacteria.
History
DepositionJun 27, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6xkx
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22228.png

Downloads & links

-
Map

FileDownload / File: emd_22228.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCIII2CIV tripartite super-complex, conformation A (SC-1A)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.020245712 - 0.07263976
Average (Standard dev.)0.00025467935 (±0.0020266462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0200.0730.000

-
Supplemental data

-
Sample components

+
Entire : CIII2CIV tripartite super-complex, conformation A (SC-1A)

EntireName: CIII2CIV tripartite super-complex, conformation A (SC-1A)
Components
  • Complex: CIII2CIV tripartite super-complex, conformation A (SC-1A)
    • Complex: CIII2
      • Protein or peptide: Ubiquinol-cytochrome c reductase iron-sulfur subunit
      • Protein or peptide: Cytochrome b
      • Protein or peptide: Cytochrome c1
    • Complex: CIV
      • Protein or peptide: Cytochrome c oxidase, Cbb3-type, subunit I
      • Protein or peptide: Cytochrome c oxidase, Cbb3-type, subunit II
      • Protein or peptide: Cbb3-type cytochrome c oxidase subunit CcoP,Cytochrome c-type cyt cy
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: HEME C
  • Ligand: COPPER (II) ION

+
Supramolecule #1: CIII2CIV tripartite super-complex, conformation A (SC-1A)

SupramoleculeName: CIII2CIV tripartite super-complex, conformation A (SC-1A)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: super-complex assembly with genetic fusion between cyt c1 and CcoP and between CcoP and cyt cy
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)

+
Supramolecule #2: CIII2

SupramoleculeName: CIII2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Details: ubiquinol:cytochrome c reductase (cytochrome bc1, CIII2) portion of the super-complex
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)

+
Supramolecule #3: CIV

SupramoleculeName: CIV / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#6
Details: cbb3-type cytochrome c oxidase (CIV) portion of the super-complex
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)

+
Macromolecule #1: Ubiquinol-cytochrome c reductase iron-sulfur subunit

MacromoleculeName: Ubiquinol-cytochrome c reductase iron-sulfur subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003
Molecular weightTheoretical: 20.465109 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus SB 1003 (bacteria)
SequenceString:
MSHAEDNAGT RRDFLYHATA ATGVVVTGAA VWPLINQMNA SADVKAMASI FVDVSAVEVG TQLTVKWRGK PVFIRRRDEK DIELARSVP LGALRDTSAE NANKPGAEAT DENRTLPAFD GTNTGEWLVM LGVCTHLGCV PMGDKSGDFG GWFCPCHGSH Y DSAGRIRK GPAPRNLDIP VAAFVDETTI KLG

UniProtKB: Ubiquinol-cytochrome c reductase iron-sulfur subunit

+
Macromolecule #2: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003
Molecular weightTheoretical: 49.386469 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus SB 1003 (bacteria)
SequenceString: MSGIPHDHYE PKTGIEKWLH DRLPIVGLVY DTIMIPTPKN LNWWWIWGIV LAFTLVLQIV TGIVLAMHYT PHVDLAFASV EHIMRDVNG GWAMRYIHAN GASLFFLAVY IHIFRGLYYG SYKAPREITW IVGMVIYLLM MGTAFMGYVL PWGQMSFWGA T VITGLFGA ...String:
MSGIPHDHYE PKTGIEKWLH DRLPIVGLVY DTIMIPTPKN LNWWWIWGIV LAFTLVLQIV TGIVLAMHYT PHVDLAFASV EHIMRDVNG GWAMRYIHAN GASLFFLAVY IHIFRGLYYG SYKAPREITW IVGMVIYLLM MGTAFMGYVL PWGQMSFWGA T VITGLFGA IPGIGPSIQA WLLGGPAVDN ATLNRFFSLH YLLPFVIAAL VAIHIWAFHT TGNNNPTGVE VRRTSKADAE KD TLPFWPY FVIKDLFALA LVLLGFFAVV AYMPNYLGHP DNYVQANPLS TPAHIVPEWY FLPFYAILRA FAADVWVVIL VDG LTFGIV DAKFFGVIAM FGAIAVMALA PWLDTSKVRS GAYRPKFRMW FWFLVLDFVV LTWVGAMPTE YPYDWISLIA STYW FAYFL VILPLLGATE KPEPIPASIE EDFNSHYGNP AE

UniProtKB: Cytochrome b

+
Macromolecule #3: Cytochrome c1

MacromoleculeName: Cytochrome c1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003
Molecular weightTheoretical: 30.352615 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus SB 1003 (bacteria)
SequenceString: MKKLLISAVS ALVLGSGAAF ANSNVPDHAF SFEGIFGKYD QAQLRRGFQV YNEVCSACHG MKFVPIRTLA DDGGPQLDPT FVREYAAGL DTIIDKDSGE ERDRKETDMF PTRVGDGMGP DLSVMAKARA GFSGPAGSGM NQLFKGMGGP EYIYNYVIGF E ENPECAPE ...String:
MKKLLISAVS ALVLGSGAAF ANSNVPDHAF SFEGIFGKYD QAQLRRGFQV YNEVCSACHG MKFVPIRTLA DDGGPQLDPT FVREYAAGL DTIIDKDSGE ERDRKETDMF PTRVGDGMGP DLSVMAKARA GFSGPAGSGM NQLFKGMGGP EYIYNYVIGF E ENPECAPE GIDGYYYNKT FQIGGVPDTC KDAAGVKITH GSWARMPPPL VDDQVTYEDG TPATVDQMAQ DVSAFLMWAA EP KLVARKQ MGLVAMVMLG LLSVMLYLTN KRLWAPYKGH KA

UniProtKB: Cytochrome c1

+
Macromolecule #4: Cytochrome c oxidase, Cbb3-type, subunit I

MacromoleculeName: Cytochrome c oxidase, Cbb3-type, subunit I / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003
Molecular weightTheoretical: 58.975086 KDa
SequenceString: MWDYVKLVAL GVVVAIAAYA ASQARDLPYM VNMVEVALAA VIAFIWVLRT MGDAKPSKDE YFDGVIRAGV IATTFWGIVG FLVAVIIAF QLAFPALNLE FGNGMLNFGR LRPLHTSAVI FAFGGNALIA SAFYVVQRTS AARLFGGTAL GWFVFWGWQL I IVTAATSY ...String:
MWDYVKLVAL GVVVAIAAYA ASQARDLPYM VNMVEVALAA VIAFIWVLRT MGDAKPSKDE YFDGVIRAGV IATTFWGIVG FLVAVIIAF QLAFPALNLE FGNGMLNFGR LRPLHTSAVI FAFGGNALIA SAFYVVQRTS AARLFGGTAL GWFVFWGWQL I IVTAATSY LLGGSQGKEY AELNWHLDIL VAIVWVAYLI AFLGTIFKRK EPHIYVANWF YLSFIVTIAM LHIVNNLAVP VS IFGTKSV QLMAGVQDAM TQWWYGHNAV GFFLTAGFLG MMYYFVPKQA ERPVYSYKLS IVHFWALIFL YIWAGPHHLH YTA LPDWAS TLGMVMSVIL WMPSWGGMIN GLMTLSGAWD KLRTDPVIRM MVVSIGFYGM STFEGPMMSI KAVNSLSHYT DWTI GHVHS GALGWNGMIT FGMLYFLTPR LWGRSGLYSL KLVSWHFWLA TIGIVLYASS MWVSGIMEGL MWREVDAQGF LVNGF ADTV GAKFPMNVVR GVGGVLYLTG GLIMAYNLWA TVAKQPKTAN LAVAVPAE

UniProtKB: cytochrome-c oxidase

+
Macromolecule #5: Cytochrome c oxidase, Cbb3-type, subunit II

MacromoleculeName: Cytochrome c oxidase, Cbb3-type, subunit II / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003
Molecular weightTheoretical: 26.99865 KDa
SequenceString: MSIMDKHHVL EKNATLLLIF AFLVVTIGGI VEIAPLFYLE NTIEKVEGMR PYTPLELTGR DIYIREGCYV CHSQMIRPMR DEVERYGHY SLAAESMYDH PFQWGSKRTG PDLARVGGRY SDAWHVEHLS NPQSVVPESV MPSYSYLANV PLDSTWIEDR V STDALVGV ...String:
MSIMDKHHVL EKNATLLLIF AFLVVTIGGI VEIAPLFYLE NTIEKVEGMR PYTPLELTGR DIYIREGCYV CHSQMIRPMR DEVERYGHY SLAAESMYDH PFQWGSKRTG PDLARVGGRY SDAWHVEHLS NPQSVVPESV MPSYSYLANV PLDSTWIEDR V STDALVGV PYSAEMIAAA KADFVAQADP NADSATLVAN YGEKVNIRNF DGKPGLTEMD ALVAYLQVLG TMVDFSTFQP VA SR

UniProtKB: Cytochrome c oxidase, Cbb3-type, subunit II

+
Macromolecule #6: Cbb3-type cytochrome c oxidase subunit CcoP,Cytochrome c-type cyt cy

MacromoleculeName: Cbb3-type cytochrome c oxidase subunit CcoP,Cytochrome c-type cyt cy
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Strain: ATCC BAA-309 / NBRC 16581 / SB1003
Molecular weightTheoretical: 50.036148 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus SB 1003 (bacteria)
SequenceString: MSKKPTTKKE VQTTGHSWDG IEELNTPLPR WWLWTFYATI VWGVAYSIAM PAWPIFASGA TPGILGSSTR ADVEKDIAKF AEMNKAVED KLVATDLTAI AADPELVTYT RNAGAAVFRT WCAQCHGAGA GGNTGFPSLL DGDWLHGGSI ETIYTNIKHG I RDPLDPDT ...String:
MSKKPTTKKE VQTTGHSWDG IEELNTPLPR WWLWTFYATI VWGVAYSIAM PAWPIFASGA TPGILGSSTR ADVEKDIAKF AEMNKAVED KLVATDLTAI AADPELVTYT RNAGAAVFRT WCAQCHGAGA GGNTGFPSLL DGDWLHGGSI ETIYTNIKHG I RDPLDPDT LPVANMPAHL TDELLEPAQI DDVVQYVLKI SGQPADEARA TAGQQVFADN CVSCHGEDAK GMVEMGAPNL TD GIWLYGG DANTITTTIQ LGRGGVMPSW SWAADGAKPR LSEAQIRAVA SYVHSLGGGQ LFATRPATAV AVGADGKALL PSV DEAAMP AKAPAAAAPA AETAEAAAPA EPAAPPPPAY VEVDPATITG DAKAGEEKFN KTCKACHKID GKNAVGPHLN GVIG RATAT VEGFKYSTAM KNHVGNWTPE RLDIYLVSPK AEVPGTKMSF VGLPEAADRA NVIAYLNTLP RDYKDDDDK

UniProtKB: Cbb3-type cytochrome c oxidase subunit CcoP, Cytochrome c-type cyt cy

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

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 7 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

+
Macromolecule #8: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 8 / Number of copies: 11 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

+
Macromolecule #9: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 560860
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 61934
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6xi0


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 184 / Target criteria: Correlation coefficient
Output model

PDB-6xkx:
R. capsulatus CIII2CIV tripartite super-complex, conformation A (SC-1A)

+
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