[English] 日本語
Yorodumi
- PDB-6btm: Structure of Alternative Complex III from Flavobacterium johnsoni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6btm
TitleStructure of Alternative Complex III from Flavobacterium johnsoniae (Wild Type)
Components(Alternative Complex III subunit ...) x 6
KeywordsMEMBRANE PROTEIN / Electron transport chain / triacylated cysteine / heme c domain / iron-sulfur cluster
Function / homology
Function and homology information


electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / NrfD family / Alternative complex III, ActD subunit / MoCo/4Fe-4S cofactor protein extended Tat translocation domain / Polysulphide reductase, NrfD / Alternative complex III, ActD subunit / Cytochrome c7 and related cytochrome c / Class III cytochrome C / Class III cytochrome C family / Cytochrome C oxidase, cbb3-type, subunit III ...: / NrfD family / Alternative complex III, ActD subunit / MoCo/4Fe-4S cofactor protein extended Tat translocation domain / Polysulphide reductase, NrfD / Alternative complex III, ActD subunit / Cytochrome c7 and related cytochrome c / Class III cytochrome C / Class III cytochrome C family / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome superfamily / Cytochrome c / 4Fe-4S dicluster domain / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
DECANOIC ACID / FE3-S4 CLUSTER / (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate / HEME C / IRON/SULFUR CLUSTER / Quinol:cytochrome C oxidoreductase / Cytochrome c, class I / 4Fe-4S ferredoxin, iron-sulfur binding domain protein / Polysulphide reductase, NrfD / Quinol:cytochrome c oxidoreductase membrane protein / Hypothetical lipoprotein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSun, C. / Benlekbir, S. / Venkatakrishnan, P. / Yuhang, W. / Tajkhorshid, E. / Rubinstein, J.L. / Gennis, R.B.
Funding support United States, Canada, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-HL16101 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM104601 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM087519 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123455 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/Office of the DirectorOD019994 United States
Simons Foundation349247 United States
Canadian Institutes of Health Research (CIHR)MOP-81294 Canada
CitationJournal: Nature / Year: 2018
Title: Structure of the alternative complex III in a supercomplex with cytochrome oxidase.
Authors: Chang Sun / Samir Benlekbir / Padmaja Venkatakrishnan / Yuhang Wang / Sangjin Hong / Jonathan Hosler / Emad Tajkhorshid / John L Rubinstein / Robert B Gennis /
Abstract: Alternative complex III (ACIII) is a key component of the respiratory and/or photosynthetic electron transport chains of many bacteria. Like complex III (also known as the bc complex), ACIII ...Alternative complex III (ACIII) is a key component of the respiratory and/or photosynthetic electron transport chains of many bacteria. Like complex III (also known as the bc complex), ACIII catalyses the oxidation of membrane-bound quinol and the reduction of cytochrome c or an equivalent electron carrier. However, the two complexes have no structural similarity. Although ACIII has eluded structural characterization, several of its subunits are known to be homologous to members of the complex iron-sulfur molybdoenzyme (CISM) superfamily , including the proton pump polysulfide reductase. We isolated the ACIII from Flavobacterium johnsoniae with native lipids using styrene maleic acid copolymer, both as an independent enzyme and as a functional 1:1 supercomplex with an aa-type cytochrome c oxidase (cyt aa). We determined the structure of ACIII to 3.4 Å resolution by cryo-electron microscopy and constructed an atomic model for its six subunits. The structure, which contains a [3Fe-4S] cluster, a [4Fe-4S] cluster and six haem c units, shows that ACIII uses known elements from other electron transport complexes arranged in a previously unknown manner. Modelling of the cyt aa component of the supercomplex revealed that it is structurally modified to facilitate association with ACIII, illustrating the importance of the supercomplex in this electron transport chain. The structure also resolves two of the subunits of ACIII that are anchored to the lipid bilayer with N-terminal triacylated cysteine residues, an important post-translational modification found in numerous prokaryotic membrane proteins that has not previously been observed structurally in a lipid bilayer.
History
DepositionDec 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Feb 20, 2019Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_audit_support / pdbx_entity_nonpoly / pdbx_struct_conn_angle
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 2.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / cell / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _pdbx_audit_support.funding_organization
Revision 3.0Apr 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_entity_assembly / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_entity_assembly.entity_id_list / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_conn_type.id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_seq_id
Revision 3.1Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7286
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alternative Complex III subunit A
B: Alternative Complex III subunit B
C: Alternative Complex III subunit C
D: Alternative Complex III subunit D
E: Alternative Complex III subunit E
F: Alternative Complex III subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,97318
Polymers295,2456
Non-polymers5,72912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, subunits have been verified using mass spectrometry.
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Alternative Complex III subunit ... , 6 types, 6 molecules ABCDEF

#1: Protein Alternative Complex III subunit A


Mass: 48236.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / References: UniProt: A5FJF1
#2: Protein Alternative Complex III subunit B


Mass: 102911.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / References: UniProt: A5FJF2
#3: Protein Alternative Complex III subunit C / Polysulphide reductase / NrfD


Mass: 53269.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / References: UniProt: A5FJF3
#4: Protein Alternative Complex III subunit D


Mass: 19720.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / References: UniProt: A5FJF4
#5: Protein Alternative Complex III subunit E


Mass: 18179.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / References: UniProt: A5FJF5
#6: Protein Alternative Complex III subunit F


Mass: 52926.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Flavobacterium johnsoniae UW101 (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / References: UniProt: A5FJE2

-
Non-polymers , 5 types, 12 molecules

#7: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2
#11: Chemical ChemComp-FAW / (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate


Mass: 512.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H60O5

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: ACIII-cyt aa3 supercomplex / Type: COMPLEX
Details: Alternative complex III-- cytochrome aa3 oxidase supercomplex purified with styrene maleic acid copolymer
Entity ID: #1, #3-#4, #6 / Source: NATURAL
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationCryogen name: ETHANE-PROPANE

-
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 FIELD
Image recordingAverage exposure time: 10 sec. / Electron dose: 61 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2017
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 1-40

-
Processing

SoftwareName: PHENIX / Version: dev_2722: / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
2Leginonimage acquisition
4CTFFIND4CTF correction
12cryoSPARC3D reconstruction
13PHENIX2722model refinement
14MDFFmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3044
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164239 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
RefinementHighest resolution: 3.4 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00919517
ELECTRON MICROSCOPYf_angle_d1.18626557
ELECTRON MICROSCOPYf_dihedral_angle_d8.911197
ELECTRON MICROSCOPYf_chiral_restr0.0552864
ELECTRON MICROSCOPYf_plane_restr0.0073321

+
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