[English] 日本語
Yorodumi
- PDB-7voy: Rba sphaeroides PufX-KO RC-LH1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7voy
TitleRba sphaeroides PufX-KO RC-LH1
Components
  • (Light-harvesting protein B-875 ...) x 2
  • (Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / Photosystem / Complex / Mutant
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding / plasma membrane
Similarity search - Function
Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex ...Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein H chain / Light-harvesting protein B-875 beta chain / Light-harvesting protein B-875 alpha chain / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesCereibacter sphaeroides 2.4.1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsBracun, L. / Yamagata, A. / Liu, L.N. / Shirouzu, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex.
Authors: Peng Cao / Laura Bracun / Atsushi Yamagata / Bern M Christianson / Tatsuki Negami / Baohua Zou / Tohru Terada / Daniel P Canniffe / Mikako Shirouzu / Mei Li / Lu-Ning Liu /
Abstract: The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species ...The reaction center (RC) and light-harvesting complex 1 (LH1) form a RC-LH1 core supercomplex that is vital for the primary reactions of photosynthesis in purple phototrophic bacteria. Some species possess the dimeric RC-LH1 complex with a transmembrane polypeptide PufX, representing the largest photosynthetic complex in anoxygenic phototrophs. However, the details of the architecture and assembly mechanism of the RC-LH1 dimer are unclear. Here we report seven cryo-electron microscopy (cryo-EM) structures of RC-LH1 supercomplexes from Rhodobacter sphaeroides. Our structures reveal that two PufX polypeptides are positioned in the center of the S-shaped RC-LH1 dimer, interlocking association between the components and mediating RC-LH1 dimerization. Moreover, we identify another transmembrane peptide, designated PufY, which is located between the RC and LH1 subunits near the LH1 opening. PufY binds a quinone molecule and prevents LH1 subunits from completely encircling the RC, creating a channel for quinone/quinol exchange. Genetic mutagenesis, cryo-EM structures, and computational simulations provide a mechanistic understanding of the assembly and electron transport pathways of the RC-LH1 dimer and elucidate the roles of individual components in ensuring the structural and functional integrity of the photosynthetic supercomplex.
History
DepositionOct 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Light-harvesting protein B-875 alpha chain
B: Light-harvesting protein B-875 beta chain
D: Light-harvesting protein B-875 alpha chain
E: Light-harvesting protein B-875 beta chain
F: Light-harvesting protein B-875 alpha chain
G: Light-harvesting protein B-875 beta chain
I: Light-harvesting protein B-875 alpha chain
J: Light-harvesting protein B-875 beta chain
K: Light-harvesting protein B-875 alpha chain
N: Light-harvesting protein B-875 beta chain
O: Light-harvesting protein B-875 alpha chain
P: Light-harvesting protein B-875 beta chain
Q: Light-harvesting protein B-875 alpha chain
R: Light-harvesting protein B-875 beta chain
S: Light-harvesting protein B-875 alpha chain
T: Light-harvesting protein B-875 beta chain
U: Light-harvesting protein B-875 alpha chain
V: Light-harvesting protein B-875 beta chain
W: Light-harvesting protein B-875 alpha chain
X: Light-harvesting protein B-875 beta chain
Y: Light-harvesting protein B-875 alpha chain
Z: Light-harvesting protein B-875 beta chain
1: Light-harvesting protein B-875 alpha chain
2: Light-harvesting protein B-875 beta chain
7: Light-harvesting protein B-875 alpha chain
8: Light-harvesting protein B-875 beta chain
9: Light-harvesting protein B-875 alpha chain
0: Light-harvesting protein B-875 beta chain
4: Light-harvesting protein B-875 alpha chain
t: Light-harvesting protein B-875 beta chain
6: Light-harvesting protein B-875 alpha chain
5: Light-harvesting protein B-875 beta chain
C: Light-harvesting protein B-875 alpha chain
3: Light-harvesting protein B-875 beta chain
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Reaction center protein H chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,81281
Polymers305,01937
Non-polymers38,79344
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.604793502587, -0.6966699927, 0.385844192), (0.204743528029, -0.604230268927, -0.770055757619), (0.769613478935, -0.386725617698, 0.508073212891)137.098164175, 143.931672404, 2.47245985533
2given(-0.713449599817, -0.421541642167, 0.559725211546), (-0.10968285189, -0.721769618565, -0.683387364324), (0.692068884232, -0.548954699074, 0.468710356022)114.663828303, 169.052762743, 21.5137101138
3given(-0.718549485475, -0.111321563206, 0.686508664541), (-0.405299068049, -0.735136142543, -0.543422043503), (0.565171922836, -0.668716951701, 0.483113171157)85.9987932765, 181.409820539, 37.5569917747
4given(-0.393262112764, 0.471358690896, 0.789408573035), (-0.886544309325, -0.421965428826, -0.189695451917), (0.243688527155, -0.77444571236, 0.583823381118)16.9358611524, 172.462685564, 60.715793935
5given(0.211958822127, 0.746603198505, 0.630600603952), (-0.975913098844, 0.195800656012, 0.0962066869276), (-0.0516437917578, -0.635803245578, 0.77012151748)-35.4432361304, 118.868939797, 61.0641512804
6given(0.524949447982, 0.691761521467, 0.495877075979), (-0.839461961582, 0.516956355575, 0.167510422026), (-0.140469541609, -0.504204446478, 0.852083437248)-44.8626397672, 82.2928408676, 53.8766686294
7given(0.779664520257, 0.536694621167, 0.322617605631), (-0.605504575815, 0.77749438135, 0.16990201775), (-0.159647876651, -0.327813011608, 0.93115583277)-41.6019443479, 47.3431395287, 38.1879521423
8given(0.939847183866, 0.306414678156, 0.1509878008), (-0.323810629811, 0.939922543117, 0.108130888104), (-0.10878394643, -0.150517965544, 0.982603885117)-26.4454334905, 20.4544049213, 19.3171794564
9given(-0.110560107985, 0.664015749835, 0.739499524336), (-0.990180375071, -0.13764150435, -0.0244466992584), (0.0855528336568, -0.734940746082, 0.672713023809)-13.2954712201, 150.346553412, 63.5702744013
10given(0.937006479639, -0.326297733665, -0.124694210453), (0.304269526998, 0.937748934272, -0.167472359546), (0.171577714334, 0.118982037621, 0.97795928477)34.9514292616, -7.02267239323, -20.173708245
11given(0.770173755269, -0.613782751147, -0.173502510327), (0.53380164617, 0.769143340392, -0.351389135399), (0.349124890608, 0.178014764344, 0.920012257763)69.5081166883, 0.33728699195, -33.7480281331
12given(0.509869015084, -0.845173541952, -0.16035981866), (0.68259742385, 0.510929538294, -0.522505276387), (0.523540203241, 0.156948051542, 0.83742042291)103.38649002, 18.3950797826, -39.323174194
13given(0.224448661458, -0.971149536941, -0.0805690714129), (0.720961575748, 0.221111985944, -0.656752537846), (0.6556197104, 0.0893200233465, 0.749789789718)126.184223551, 43.7595201925, -38.3254379675
14given(-0.10633682865, -0.993092382504, 0.049598373822), (0.650024609086, -0.107175600789, -0.752317352038), (0.752436367047, -0.0477588777991, 0.65693120122)143.604989001, 77.4551785949, -29.5897612343
15given(-0.379820089018, -0.903567414426, 0.198248903064), (0.485946863165, -0.377246417106, -0.788378580988), (0.787141884388, -0.203103590241, 0.582371518426)146.774262823, 108.769706635, -16.2254237334
16given(-0.607777607266, 0.204004078034, 0.767456002812), (-0.68114656703, -0.630738436688, -0.371763874937), (0.408222652887, -0.748699780039, 0.522305375274)51.5940574647, 183.172162871, 51.3886763316

-
Components

-
Light-harvesting protein B-875 ... , 2 types, 34 molecules ADFIKOQSUWY17946CBEGJNPRTVXZ28...

#1: Protein
Light-harvesting protein B-875 alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 6816.169 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A4
#2: Protein/peptide
Light-harvesting protein B-875 beta chain / Antenna pigment protein beta chain / LH-3A


Mass: 5592.361 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A3

-
Reaction center protein ... , 3 types, 3 molecules LMH

#3: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31477.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A5
#4: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34529.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J1A6
#5: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 28066.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / Strain: 2.4.1. / References: UniProt: Q3J170

-
Non-polymers , 5 types, 44 molecules

#6: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Rhodobacter sphaeroides PufX-KO RC-LH1 / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain: PufX-KO
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid 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 FIELD
Image recordingElectron dose: 46.549 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66058 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 76.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007723118
ELECTRON MICROSCOPYf_angle_d0.923232179
ELECTRON MICROSCOPYf_chiral_restr0.04313298
ELECTRON MICROSCOPYf_plane_restr0.00543870
ELECTRON MICROSCOPYf_dihedral_angle_d21.15467359

+
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