[English] 日本語
Yorodumi
- PDB-6wti: The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wti
TitleThe Cryo-EM structure of the ubiquinol oxidase from Escherichia coli
Components
  • (Cytochrome o ubiquinol oxidase, subunit ...) x 2
  • Cytochrome o ubiquinol oxidase
  • Ubiquinol oxidase subunit 2
KeywordsOXIDOREDUCTASE / ubiquinol oxidase cytochrome bo3 / membrane protein
Function / homology
Function and homology information


ubiquinol oxidase (H+-transporting) / cytochrome o ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / electron transport coupled proton transport / cytochrome-c oxidase activity / aerobic respiration / respirasome / copper ion binding / heme binding ...ubiquinol oxidase (H+-transporting) / cytochrome o ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / electron transport coupled proton transport / cytochrome-c oxidase activity / aerobic respiration / respirasome / copper ion binding / heme binding / integral component of membrane / plasma membrane
COX aromatic rich motif / Cytochrome o ubiquinol oxidase, subunit I / Cytochrome o ubiquinol oxidase, subunit III / Cupredoxin / Cytochrome o ubiquinol oxidase subunit II / Cytochrome C oxidase subunit IV, prokaryotes / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome c oxidase subunit I / Cytochrome c oxidase subunit III-like / Cytochrome o ubiquinol oxidase subunit IV ...COX aromatic rich motif / Cytochrome o ubiquinol oxidase, subunit I / Cytochrome o ubiquinol oxidase, subunit III / Cupredoxin / Cytochrome o ubiquinol oxidase subunit II / Cytochrome C oxidase subunit IV, prokaryotes / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome c oxidase subunit I / Cytochrome c oxidase subunit III-like / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase, subunit I, copper-binding site / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase subunit III / Ubiquinol oxidase subunit III domain / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C oxidase subunit II, transmembrane domain
Ubiquinol oxidase subunit 2 / Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome bo(3) ubiquinol oxidase subunit 4
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsSu, C.-C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Methods / Year: 2021
Title: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.
Authors: Chih-Chia Su / Meinan Lyu / Christopher E Morgan / Jani Reddy Bolla / Carol V Robinson / Edward W Yu /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein ...Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-21897
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome o ubiquinol oxidase, subunit I
B: Ubiquinol oxidase subunit 2
C: Cytochrome o ubiquinol oxidase
D: Cytochrome o ubiquinol oxidase, subunit IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,55518
Polymers144,0524
Non-polymers9,50314
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area28250 Å2
ΔGint-336 kcal/mol
Surface area42100 Å2

-
Components

-
Cytochrome o ubiquinol oxidase, subunit ... , 2 types, 2 molecules AD

#1: Protein Cytochrome o ubiquinol oxidase, subunit I


Mass: 74424.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoB, ECDEC2C_0430 / Production host: Escherichia coli (E. coli)
References: UniProt: H4KCU1, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
#4: Protein Cytochrome o ubiquinol oxidase, subunit IV


Mass: 12037.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoD, EC12741_3890 / Production host: Escherichia coli (E. coli)
References: UniProt: I2RK84, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor

-
Protein , 2 types, 2 molecules BC

#2: Protein Ubiquinol oxidase subunit 2 /


Mass: 34947.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024L5V9
#3: Protein Cytochrome o ubiquinol oxidase


Mass: 22642.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECDG_00226 / Production host: Escherichia coli (E. coli) / References: UniProt: D6I7E4

-
Non-polymers , 6 types, 14 molecules

#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-HEO / HEME O / Heme O


Mass: 838.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H58FeN4O5
#7: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H74O4
#9: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#10: Chemical ChemComp-U9V / pentadecyl(tetradecyl)peroxyanhydride


Mass: 524.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H64O4

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: ubiquinol oxidase / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 334222 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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