[English] 日本語
Yorodumi
- EMDB-32228: Structure of the Acidobacteria homodimeric reaction center bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32228
TitleStructure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the larger form)
Map data
Sample
  • Complex: CabRC complex, the larger form
    • Protein or peptide: x 9 types
  • Ligand: x 12 types
Function / homology
Function and homology information


thylakoid / iron-sulfur cluster binding / photosynthesis / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding
Similarity search - Function
Cytochrome c, class IC / Cytochrome C oxidase, cbb3-type, subunit III / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster domain / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site ...Cytochrome c, class IC / Cytochrome C oxidase, cbb3-type, subunit III / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster domain / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem P840 reaction center iron-sulfur protein / Cytochrome c domain-containing protein / Cytochrome c, mono-and diheme variants / Photosynthetic reaction center subunit M / Cytochrome b6-f complex subunit PetG / UPF0291 protein / Stage III sporulation protein AF / MetS family NSS transporter small subunit
Similarity search - Component
Biological speciesChloracidobacterium thermophilum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsHuang GQ / Dong SS / Qin XC / Sui SF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c.
Authors: Shishang Dong / Guoqiang Huang / Changhui Wang / Jiajia Wang / Sen-Fang Sui / Xiaochun Qin /
Abstract: Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer ...Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer (ET) reactions. Here, we present cryo-electron microscopy (cryo-EM) structures of two forms of the RC from the microaerophilic Chloracidobacterium thermophilum (CabRC): one containing 10 subunits, including two different cytochromes; and the other possessing two additional subunits, PscB and PscZ. The larger form contained 2 Zn-bacteriochlorophylls, 16 bacteriochlorophylls, 10 chlorophylls, 2 lycopenes, 2 hemes, 3 FeS clusters, 12 lipids, 2 Ca ions and 6 water molecules, revealing a type I RC with an ET chain involving two hemes and a hybrid antenna containing bacteriochlorophylls and chlorophylls. Our results provide a structural basis for understanding the excitation energy and ET within the CabRC and offer evolutionary insights into the origin and adaptation of photosynthetic RCs.
History
DepositionNov 16, 2021-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateFeb 22, 2023-
Current statusFeb 22, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32228.png

Downloads & links

-
Map

FileDownload / File: emd_32228.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0825 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.0103453 - 2.3813515
Average (Standard dev.)0.008471262 (±0.09360899)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 238.15 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : CabRC complex, the larger form

EntireName: CabRC complex, the larger form
Components
  • Complex: CabRC complex, the larger form
    • Protein or peptide: PscA
    • Protein or peptide: Cytochrome c, mono-and diheme variants
    • Protein or peptide: PscE
    • Protein or peptide: PscF
    • Protein or peptide: PscG
    • Protein or peptide: undefined polypeptide
    • Protein or peptide: Cytochrome c domain-containing protein
    • Protein or peptide: Photosystem P840 reaction center iron-sulfur protein
    • Protein or peptide: PscD'
  • Ligand: [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: CHLOROPHYLL A
  • Ligand: LYCOPENE
  • Ligand: CALCIUM IONCalcium
  • Ligand: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
  • Ligand: UNKNOWN LIGAND
  • Ligand: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium
  • Ligand: HEME C
  • Ligand: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: water

+
Supramolecule #1: CabRC complex, the larger form

SupramoleculeName: CabRC complex, the larger form / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)

+
Macromolecule #1: PscA

MacromoleculeName: PscA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 98.537555 KDa
SequenceString: ANGVKRWYQK LELPMPPERI FGAHMMLIGG LACLIGTYFF ASMTMWNDGY VNLTLRPRLI SLGIYDPYDT EQIQRVWLPL IGEFSTSKL PFFGQYPLTM TDFRLFGWGC FHIGLGLWLV YAGAAHYYGA RGGATIGEIF WLLPYVPGLK GLCQIKWFTP E GPWYKVGL ...String:
ANGVKRWYQK LELPMPPERI FGAHMMLIGG LACLIGTYFF ASMTMWNDGY VNLTLRPRLI SLGIYDPYDT EQIQRVWLPL IGEFSTSKL PFFGQYPLTM TDFRLFGWGC FHIGLGLWLV YAGAAHYYGA RGGATIGEIF WLLPYVPGLK GLCQIKWFTP E GPWYKVGL PWGSFANTPW PILRRTYADA LSPHTIYIGL LFFIWGFVLW FVLDKPPVPL QPAQVMTPNG LMPLEQAPFP YG WFDPYLN QVMHPMNTIN GETTMCFVWG VLFVALGAYW WYRPPRSINI THLEDTKAVF HVHLTAIGYV SFALAIVGFL ALR NHPSYL MLNDMNVIIY GKKIVNPGRM IHNMITFNHV QVGLLYVAAG VFHGGQYLHG LNISGAYKQA RSKFITWFQN PDLQ TKIVG TTMFVSFVTV VFGYGMICWN TGAELDLNFG IYQFRSFRAI QMDGEAGNIG YRVFRPKNPW DPTAGGDWVK NPDGT AKLV KARNLQVGDR ILNEELGIGS SPTYSFTTIE EINYKPEWGQ PKLYAVQWGS WTHFLRKVNP LFWVDKGIWY LQNQKT FEA TRKADEAYLA AHLKAVSLLN QIDDAQTEEA KQKAQAELDK FRPELEKAHA NMLEWNERLA STPAVLYSNL RDQHRDG EI NDAIFFWLMI GGWLFGFIPL LRIAFHNYQS PWYRDFEWRK QSPDFPCIGP VKGGTCGVSI QDQLWFCILF SIKPLSAI A WYLDGGWIAT MMARGNEAYY LTHNISHTGG VFLYMWNETT WIWTDNHLTA MLLLGHLIWF VSFALWFKDR GSRAEGGDI QSRWVRLMGK RLGIKTLQEV RFPVSNLATA KLWGTVFFYT GTFVLVFLYF ADGFFQNR

+
Macromolecule #2: Cytochrome c, mono-and diheme variants

MacromoleculeName: Cytochrome c, mono-and diheme variants / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 22.36982 KDa
SequenceString: LLVGGCFVGS RDPNETRYPK APMPLQNQTS TLKTAEEIRR ESVAQNTPGA REAAALRDRV TPLNLQQVNE QDVAGNDPLG SPARVVLDE GEMYRDPVEI YREGRALFQN NCVGCHGHNG CGNVPRSTNF TDPGWQENNS DGGIYSSIYN GKGIGNGGGA M PAYYNQLS ...String:
LLVGGCFVGS RDPNETRYPK APMPLQNQTS TLKTAEEIRR ESVAQNTPGA REAAALRDRV TPLNLQQVNE QDVAGNDPLG SPARVVLDE GEMYRDPVEI YREGRALFQN NCVGCHGHNG CGNVPRSTNF TDPGWQENNS DGGIYSSIYN GKGIGNGGGA M PAYYNQLS PQQIRYLVAY LRAFKGRQCN GLPTLSDVER MVAERQ

+
Macromolecule #3: PscE

MacromoleculeName: PscE / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 3.684458 KDa
SequenceString:
MTAILLACLF VLGGYAALWG IIKFVVANTK DIAAN

+
Macromolecule #4: PscF

MacromoleculeName: PscF / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 3.885684 KDa
SequenceString:
MWNVVGQIIS VLCFFILTVG TLFGIVYVSH LLSRG

+
Macromolecule #5: PscG

MacromoleculeName: PscG / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 4.293273 KDa
SequenceString:
DISKVAWAWF GVLLAICLIG AFGNYVPKLF VKMLMFLN

+
Macromolecule #6: undefined polypeptide

MacromoleculeName: undefined polypeptide / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 1.635006 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

+
Macromolecule #7: Cytochrome c domain-containing protein

MacromoleculeName: Cytochrome c domain-containing protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 15.664669 KDa
SequenceString:
VMATGCFVGA RNASEPRLGS SSIAASRTAP AYLREAQVLY EGSTDGLPKD TPADEIAHYK AMLAELQTRN YAACAGCHQV NGGGNKAIN ATNFQDAGWQ ANNSSPGMVT SIVNGKGKVM PAYKDKLTLQ QINYLVEYIR RFEKKR

+
Macromolecule #8: Photosystem P840 reaction center iron-sulfur protein

MacromoleculeName: Photosystem P840 reaction center iron-sulfur protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 8.19933 KDa
SequenceString:
QIYTIIEELC IGCGFCTDEC PPKVNAILPR DVEAVLDGGE TYWIDQTRCI SCSLCFVAGT CPTDAVVFTE GGVSRT

+
Macromolecule #9: PscD'

MacromoleculeName: PscD' / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chloracidobacterium thermophilum (bacteria)
Molecular weightTheoretical: 8.622735 KDa
SequenceString:
MARTPEEIVK RYKEANIWLR HWKQQIGLAK DEEQREMFTQ YYEERVQEIA ALEEPYRAAL KILNQQESQR

+
Macromolecule #10: [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-o...

MacromoleculeName: [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc
type: ligand / ID: 10 / Number of copies: 2 / Formula: 2GO
Molecular weightTheoretical: 948.576 Da
Chemical component information

ChemComp-2GO:
[methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc

+
Macromolecule #11: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 11 / Number of copies: 16 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

+
Macromolecule #12: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 12 / Number of copies: 10 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #13: LYCOPENE

MacromoleculeName: LYCOPENE / type: ligand / ID: 13 / Number of copies: 2 / Formula: LYC
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-LYC:
LYCOPENE / Lycopene

+
Macromolecule #14: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #15: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-m...

MacromoleculeName: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
type: ligand / ID: 15 / Number of copies: 6 / Formula: 85I
Molecular weightTheoretical: 663.906 Da
Chemical component information

ChemComp-85I:
[(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate

+
Macromolecule #16: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 16 / Number of copies: 32 / Formula: UNL
Molecular weightTheoretical: 663.906 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

+
Macromolecule #17: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]met...

MacromoleculeName: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium
type: ligand / ID: 17 / Number of copies: 4 / Formula: 85N
Molecular weightTheoretical: 671.023 Da
Chemical component information

ChemComp-85N:
[(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium

+
Macromolecule #18: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 18 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

+
Macromolecule #19: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetra...

MacromoleculeName: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate
type: ligand / ID: 19 / Number of copies: 2 / Formula: 84Q
Molecular weightTheoretical: 649.879 Da
Chemical component information

ChemComp-84Q:
[(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate

+
Macromolecule #20: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 20 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

+
Macromolecule #21: water

MacromoleculeName: water / type: ligand / ID: 21 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52612

+
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