[English] 日本語
Yorodumi
- PDB-9m8m: Structure of photosynthetic LH1-RC complex the Halophilic Nonsulf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9m8m
TitleStructure of photosynthetic LH1-RC complex the Halophilic Nonsulfur Purple Bacterium, Rhodothalassium salexigens
Components
  • (Light-harvesting complex 1 ...) x 2
  • (Photosynthetic reaction center ...) x 2
  • (Reaction center protein ...) x 2
KeywordsPHOTOSYNTHESIS / LH1-RC COMPLEX / PURPLE BACTERIA
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 / : / endomembrane system / electron transfer activity / iron ion binding ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / endomembrane system / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-PGV / PALMITIC ACID / UBIQUINONE-10 ...: / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-PGV / PALMITIC ACID / UBIQUINONE-10 / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center subunit H / Light-harvesting complex 1 beta chain / Photosynthetic reaction center cytochrome c subunit / Light-harvesting complex 1 alpha chain
Similarity search - Component
Biological speciesRhodothalassium salexigens DSM 2132 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsTani, K. / Kanno, R. / Inami, M. / Ooya, T. / Matsushita, R. / Minamino, A. / Takenaka, S. / Takaichi, S. / Purba, E.R. / Hall, M. ...Tani, K. / Kanno, R. / Inami, M. / Ooya, T. / Matsushita, R. / Minamino, A. / Takenaka, S. / Takaichi, S. / Purba, E.R. / Hall, M. / Mochizuki, T. / Yu, L.-J. / Mizoguchi, A. / Humbel, B.M. / Madigan, M.T. / Kimura, Y. / Wang-Otomo, Z.-Y.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101116 Japan
Japan Society for the Promotion of Science (JSPS)JP16H04174 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05153 Japan
Japan Society for the Promotion of Science (JSPS)20H05086 Japan
Japan Society for the Promotion of Science (JSPS)20H02856 Japan
CitationJournal: Biochemistry / Year: 2025
Title: Structure and Biochemistry of the LH1-RC Photocomplex from the Halophilic Purple Bacterium, .
Authors: Kazutoshi Tani / Ryo Kanno / Miyu Inami / Takumi Ooya / Ryo Matsushita / Kazuki Inada / Shinji Takenaka / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / Toshiaki Mochizuki / Long- ...Authors: Kazutoshi Tani / Ryo Kanno / Miyu Inami / Takumi Ooya / Ryo Matsushita / Kazuki Inada / Shinji Takenaka / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / Toshiaki Mochizuki / Long-Jiang Yu / Akira Mizoguchi / Bruno M Humbel / Michael T Madigan / Yukihiro Kimura / Zheng-Yu Wang-Otomo /
Abstract: is a moderately halophilic purple nonsulfur bacterium whose unique cell wall composition and phylogeny are distinct from those of all other purple phototrophs. Here we present a cryo-EM structure ... is a moderately halophilic purple nonsulfur bacterium whose unique cell wall composition and phylogeny are distinct from those of all other purple phototrophs. Here we present a cryo-EM structure and biochemical analysis of the light-harvesting 1-reaction center (LH1-RC) complex from at 2.29 Å resolution. The LH1 complex forms a closed ring structure with 16 αβ-polypeptides surrounding the RC and contains 16 phosphatidylglycerols regularly positioned between the β-polypeptides. Extensive interactions were observed between the C-terminal domains of LH1 α-and β-polypeptides and between the regularly arranged phosphatidylglycerols and β-polypeptides, supporting the hypothesis that LH1 C-terminal interactions define the post-translational truncation sites of αβ-polypeptides in phototrophic purple bacteria. Multiple insertions were identified in the membrane-extruded RC cytochrome- and H-subunits of . Insertions in the periplasm-exposed cytochrome subunit contain high proportions of Gly, Asp, and Glu, contributing to an overall negatively charged surface of this subunit. The cytoplasm-exposed H-subunit contained an unusually long 57-residue insert rich in Pro and Ala that was invisible in the cryo-EM density map, indicating its highly flexible nature. The extensive Pro-Ala repetitive motifs in this insertion points to a regulatory role in assemblies of the RC and LH1-RC complexes. The structural features of LH1-RC are also discussed in relation to differences in the physiological environment between the periplasmic and cytoplasmic sides of membranes in halophiles, necessary for maintaining cellular activities under the high ionic strength conditions of hypersaline environments.
History
DepositionMar 12, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)460,624159
Polymers372,98736
Non-polymers87,637123
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Photosynthetic reaction center ... , 2 types, 2 molecules CH

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 42110.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothalassium salexigens DSM 2132 (bacteria)
References: UniProt: A0A4R2PKR2
#4: Protein Photosynthetic reaction center subunit H


Mass: 35239.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothalassium salexigens DSM 2132 (bacteria)
References: UniProt: A0A4R2PIK4

-
Reaction center protein ... , 2 types, 2 molecules LM

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


Mass: 30681.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothalassium salexigens DSM 2132 (bacteria)
References: UniProt: A0A2L1K3Q4
#3: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 35887.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodothalassium salexigens DSM 2132 (bacteria)
References: UniProt: A0A2L1K3U8

-
Light-harvesting complex 1 ... , 2 types, 32 molecules ADFIKOQSUWY13579BEGJNPRTVXZ24680

#5: Protein
Light-harvesting complex 1 alpha chain


Mass: 6978.299 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Rhodothalassium salexigens DSM 2132 (bacteria)
References: UniProt: A0A4R2PMJ4
#6: Protein
Light-harvesting complex 1 beta chain


Mass: 7338.393 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Rhodothalassium salexigens DSM 2132 (bacteria)
References: UniProt: A0A4R2PKF8

-
Sugars , 1 types, 21 molecules

#16: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 14 types, 201 molecules

#7: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#8: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#9: Chemical ChemComp-Z41 / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate


Mass: 568.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68O5
#10: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#12: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#13: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#15: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C59H90O4
#17: Chemical...
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#18: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#19: Chemical ChemComp-A1L8Q / Menaquinone 10 / menaquinone-10


Mass: 853.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C61H88O2
#20: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C42H60O2
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Photosynthetic LH1-RC complex of Rhodothalassium salexigens
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rhodothalassium salexigens DSM 2132 (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 5.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 377574
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229234 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementHighest resolution: 2.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00628711
ELECTRON MICROSCOPYf_angle_d2.68139304
ELECTRON MICROSCOPYf_dihedral_angle_d18.9356581
ELECTRON MICROSCOPYf_chiral_restr0.0713884
ELECTRON MICROSCOPYf_plane_restr0.0044710

+
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