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- PDB-9j2f: Structure of photosynthetic LH1-RC complex from the purple bacter... -

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Basic information

Entry
Database: PDB / ID: 9j2f
TitleStructure of photosynthetic LH1-RC complex from the purple bacterium Blastochloris tepida
Components
  • (Antenna complex alpha/beta subunit domain-containing ...) x 2
  • (Light-harvesting protein ...) 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 B / BACTERIOPHEOPHYTIN B / CARDIOLIPIN / DIACYL GLYCEROL / : / HEME C / MENAQUINONE-7 / all-trans-1,2-dihydroneurosporene / 15-cis-1,2-dihydroneurosporene / Chem-PGV ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / CARDIOLIPIN / DIACYL GLYCEROL / : / HEME C / MENAQUINONE-7 / all-trans-1,2-dihydroneurosporene / 15-cis-1,2-dihydroneurosporene / Chem-PGV / Ubiquinone-8 / Photosynthetic reaction center subunit H / Antenna complex alpha/beta subunit domain-containing protein / Antenna complex alpha/beta subunit domain-containing protein / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit / Uncharacterized protein / Light-harvesting protein B-1015 gamma chain
Similarity search - Component
Biological speciesBlastochloris tepida (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsKimura, Y. / Kanno, R. / Mori, K. / Matsuda, Y. / Seto, R. / Takenaka, S. / Mino, H. / Ohkubo, T. / Honda, M. / Sasaki, Y.C. ...Kimura, Y. / Kanno, R. / Mori, K. / Matsuda, Y. / Seto, R. / Takenaka, S. / Mino, H. / Ohkubo, T. / Honda, M. / Sasaki, Y.C. / Kishikawa, J. / Mitsuoka, K. / Mio, K. / Hall, M. / Purba, E.R. / Mochizuki, T. / Mizoguchi, A. / Humbel, B.M. / Madigan, M.T. / Wang-Otomo, Z.-Y. / Tani, K.
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: The Thermal-Stable LH1-RC Complex of a Hot Spring Purple Bacterium Powers Photosynthesis with Extremely Low-Energy Near-Infrared Light.
Authors: Yukihiro Kimura / Ryo Kanno / Kaisei Mori / Yoshiki Matsuda / Ryuta Seto / Shinji Takenaka / Hiroyuki Mino / Tatsunari Ohkubo / Mai Honda / Yuji C Sasaki / Jun-Ichi Kishikawa / Kaoru ...Authors: Yukihiro Kimura / Ryo Kanno / Kaisei Mori / Yoshiki Matsuda / Ryuta Seto / Shinji Takenaka / Hiroyuki Mino / Tatsunari Ohkubo / Mai Honda / Yuji C Sasaki / Jun-Ichi Kishikawa / Kaoru Mitsuoka / Kazuhiro Mio / Malgorzata Hall / Endang R Purba / Toshiaki Mochizuki / Akira Mizoguchi / Bruno M Humbel / Michael T Madigan / Zheng-Yu Wang-Otomo / Kazutoshi Tani /
Abstract: is a hot spring purple nonsulfur phototrophic bacterium that contains bacteriochlorophyll (BChl) . Here, we present a 2.21 Å cryo-EM structure of the thermostable light-harvesting 1-reaction center ... is a hot spring purple nonsulfur phototrophic bacterium that contains bacteriochlorophyll (BChl) . Here, we present a 2.21 Å cryo-EM structure of the thermostable light-harvesting 1-reaction center (LH1-RC) complex from . The LH1 ring comprises 16 circularly arranged αβγ-subunits plus one αβ-subunit that surround the RC complex composed of C-, H-, L-, and M-subunits. In a comparative study, the LH1-RC showed numerous electrostatic and hydrophobic interactions both within the LH1 complex itself and between the LH1 and the RC complexes that are absent from the LH1-RC complex of its mesophilic counterpart, . These additional interactions result in a tightly packed LH1-RC architecture with a reduced accessible surface area per volume that enhances the thermal stability of the complex and allows the light reactions of photosynthesis to proceed at hot spring temperatures. Moreover, based on high-resolution structural information combined with spectroscopic evidence, the unique photosynthetic property of the LH1-RC─absorption of energy-poor near-infrared light beyond 1000 nm─can be attributed to strong hydrogen-bonding interactions between the C3-acetyl C═O of the LH1 BChl and two LH1 α-Trp residues, structural rigidity of the LH1, and the enhanced exciton coupling of the LH1 BChls of this thermophile.
History
DepositionAug 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: Antenna complex alpha/beta subunit domain-containing protein
B: Antenna complex alpha/beta subunit domain-containing protein
G: Light-harvesting protein gamma1
D: Antenna complex alpha/beta subunit domain-containing protein
E: Antenna complex alpha/beta subunit domain-containing protein
F: Light-harvesting protein B-1015 gamma chain
I: Antenna complex alpha/beta subunit domain-containing protein
J: Antenna complex alpha/beta subunit domain-containing protein
K: Light-harvesting protein B-1015 gamma chain
N: Antenna complex alpha/beta subunit domain-containing protein
O: Antenna complex alpha/beta subunit domain-containing protein
P: Light-harvesting protein B-1015 gamma chain
Q: Antenna complex alpha/beta subunit domain-containing protein
R: Antenna complex alpha/beta subunit domain-containing protein
S: Light-harvesting protein B-1015 gamma chain
T: Antenna complex alpha/beta subunit domain-containing protein
U: Antenna complex alpha/beta subunit domain-containing protein
V: Light-harvesting protein B-1015 gamma chain
W: Antenna complex alpha/beta subunit domain-containing protein
X: Antenna complex alpha/beta subunit domain-containing protein
Y: Light-harvesting protein B-1015 gamma chain
Z: Antenna complex alpha/beta subunit domain-containing protein
1: Antenna complex alpha/beta subunit domain-containing protein
2: Light-harvesting protein B-1015 gamma chain
3: Antenna complex alpha/beta subunit domain-containing protein
4: Antenna complex alpha/beta subunit domain-containing protein
5: Light-harvesting protein B-1015 gamma chain
6: Antenna complex alpha/beta subunit domain-containing protein
7: Antenna complex alpha/beta subunit domain-containing protein
8: Light-harvesting protein B-1015 gamma chain
9: Antenna complex alpha/beta subunit domain-containing protein
0: Antenna complex alpha/beta subunit domain-containing protein
a: Light-harvesting protein B-1015 gamma chain
b: Antenna complex alpha/beta subunit domain-containing protein
c: Antenna complex alpha/beta subunit domain-containing protein
d: Light-harvesting protein B-1015 gamma chain
e: Antenna complex alpha/beta subunit domain-containing protein
f: Antenna complex alpha/beta subunit domain-containing protein
g: Light-harvesting protein B-1015 gamma chain
h: Antenna complex alpha/beta subunit domain-containing protein
i: Antenna complex alpha/beta subunit domain-containing protein
j: Light-harvesting protein B-1015 gamma chain
k: Antenna complex alpha/beta subunit domain-containing protein
l: Antenna complex alpha/beta subunit domain-containing protein
m: Light-harvesting protein B-1015 gamma chain
n: Antenna complex alpha/beta subunit domain-containing protein
o: Antenna complex alpha/beta subunit domain-containing protein
p: Light-harvesting protein B-1015 gamma chain
q: Antenna complex alpha/beta subunit domain-containing protein
r: Antenna complex alpha/beta subunit domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)562,610143
Polymers493,71754
Non-polymers68,89389
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 39181.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris tepida (bacteria) / References: UniProt: A0A348FW74
#4: Protein Photosynthetic reaction center subunit H


Mass: 28839.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris tepida (bacteria) / References: UniProt: A0A348FW44

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

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


Mass: 30406.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris tepida (bacteria) / References: UniProt: A0A348FW72
#3: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 37068.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris tepida (bacteria) / References: UniProt: A0A348FW73

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Antenna complex alpha/beta subunit domain-containing ... , 2 types, 34 molecules ADINQTWZ369behknqBEJORUX1470cf...

#5: Protein
Antenna complex alpha/beta subunit domain-containing protein


Mass: 7834.260 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Blastochloris tepida (bacteria) / References: UniProt: A0A348FW71
#6: Protein
Antenna complex alpha/beta subunit domain-containing protein


Mass: 7653.907 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Blastochloris tepida (bacteria) / References: UniProt: A0A348FW70

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Light-harvesting protein ... , 2 types, 16 molecules GFKPSVY258adgjmp

#7: Protein Light-harvesting protein gamma1


Mass: 5927.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris tepida (bacteria) / References: UniProt: A0A348G0X9
#8: Protein
Light-harvesting protein B-1015 gamma chain


Mass: 5933.010 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Blastochloris tepida (bacteria) / References: UniProt: A0A348G0Y0

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Sugars , 1 types, 8 molecules

#19: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 13 types, 504 molecules

#9: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#11: 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.: 5 / Source method: obtained synthetically / Formula: C49H74O4
#12: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#13: Chemical...
ChemComp-BCB / BACTERIOCHLOROPHYLL B


Mass: 909.488 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C55H72MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#15: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#16: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#17: Chemical ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H64O2
#18: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#20: 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.: 6 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#21: Chemical
ChemComp-NS0 / all-trans-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H60
#22: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Photosynthetic LH1-RC complex of Blastochloris tepida / Type: COMPLEX / Entity ID: #1-#5, #7-#8, #6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Blastochloris tepida (bacteria)
Buffer solutionpH: 8.5
SpecimenConc.: 3.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 2700 nm / Nominal defocus min: 900 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)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 373104
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 294012 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00733771
ELECTRON MICROSCOPYf_angle_d2.70446551
ELECTRON MICROSCOPYf_dihedral_angle_d17.38612729
ELECTRON MICROSCOPYf_chiral_restr0.1894896
ELECTRON MICROSCOPYf_plane_restr0.0085402

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