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- PDB-8hjv: Cryo-EM structure of carotenoid-depleted RC-LH complex from Rosei... -

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Basic information

Entry
Database: PDB / ID: 8hjv
TitleCryo-EM structure of carotenoid-depleted RC-LH complex from Roseiflexus castenholzii at 10,000 lux
Components
  • (Reaction center protein ...) x 2
  • Alpha subunit of light-harvesting 1
  • Beta subunit of light-harvesting 1
  • MULTIHEME_CYTC DOMAIN-CONTAINING PROTEIN
  • SUBUNIT Y
  • SUBUNIT Z
KeywordsPHOTOSYNTHESIS / RC-LH core complex
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C 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, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C 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, L subunit / Multiheme cytochrome 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 / : / PROTOPORPHYRIN IX CONTAINING FE / beta,psi-caroten-4-one / Chem-MQE / Chem-PGV / Uncharacterized protein / Reaction center protein L chain / Alpha subunit of light-harvesting 1 / Beta subunit of light-harvesting 1
Similarity search - Component
Biological speciesRoseiflexus castenholzii DSM 13941 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsXu, X. / Xin, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Elife / Year: 2023
Title: Carotenoid assembly regulates quinone diffusion and the reaction center-light harvesting complex architecture.
Authors: Jiyu Xin / Yang Shi / Xin Zhang / Xinyi Yuan / Yueyong Xin / Huimin He / Jiejie Shen / Robert E Blankenship / Xiaoling Xu /
Abstract: Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships ...Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships between Car depletion in the LH, assembly of the prokaryotic reaction center (RC)-LH complex, and quinone exchange are not fully understood. Here, we analyzed native RC-LH (nRC-LH) and Car-depleted RC-LH (dRC-LH) complexes in , a chlorosome-less filamentous anoxygenic phototroph that forms the deepest branch of photosynthetic bacteria. Newly identified exterior Cars functioned with the bacteriochlorophyll B800 to block the proposed quinone channel between LHαβ subunits in the nRC-LH, forming a sealed LH ring that was disrupted by transmembrane helices from cytochrome and subunit X to allow quinone shuttling. dRC-LH lacked subunit X, leading to an exposed LH ring with a larger opening, which together accelerated the quinone exchange rate. We also assigned amino acid sequences of subunit X and two hypothetical proteins Y and Z that functioned in forming the quinone channel and stabilizing the RC-LH interactions. This study reveals the structural basis by which Cars assembly regulates the architecture and quinone exchange of bacterial RC-LH complexes. These findings mark an important step forward in understanding the evolution and diversity of prokaryotic photosynthetic apparatus.
History
DepositionNov 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.pdbx_aromatic_flag ..._chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.pdbx_aromatic_flag / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Beta subunit of light-harvesting 1
1: Alpha subunit of light-harvesting 1
2: Beta subunit of light-harvesting 1
3: Alpha subunit of light-harvesting 1
4: Beta subunit of light-harvesting 1
5: Alpha subunit of light-harvesting 1
6: Beta subunit of light-harvesting 1
7: Alpha subunit of light-harvesting 1
8: Beta subunit of light-harvesting 1
9: Alpha subunit of light-harvesting 1
A: Alpha subunit of light-harvesting 1
B: Beta subunit of light-harvesting 1
D: Alpha subunit of light-harvesting 1
E: Beta subunit of light-harvesting 1
F: Alpha subunit of light-harvesting 1
G: Beta subunit of light-harvesting 1
H: Alpha subunit of light-harvesting 1
I: Beta subunit of light-harvesting 1
J: Alpha subunit of light-harvesting 1
K: Beta subunit of light-harvesting 1
L: Reaction center protein L chain
M: Reaction center protein M chain
N: Alpha subunit of light-harvesting 1
O: Beta subunit of light-harvesting 1
P: Alpha subunit of light-harvesting 1
Q: Beta subunit of light-harvesting 1
R: Alpha subunit of light-harvesting 1
S: Beta subunit of light-harvesting 1
T: Alpha subunit of light-harvesting 1
U: Beta subunit of light-harvesting 1
V: Alpha subunit of light-harvesting 1
W: Beta subunit of light-harvesting 1
Y: SUBUNIT Y
C: MULTIHEME_CYTC DOMAIN-CONTAINING PROTEIN
Z: SUBUNIT Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,284102
Polymers283,57635
Non-polymers56,70767
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 17 molecules 02468BEGIKOQSUWCZ

#1: Protein
Beta subunit of light-harvesting 1


Mass: 6431.528 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii DSM 13941 (bacteria)
References: UniProt: Q83XD2
#6: Protein MULTIHEME_CYTC DOMAIN-CONTAINING PROTEIN


Mass: 34923.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii DSM 13941 (bacteria)
References: UniProt: A7NQE7
#7: Protein SUBUNIT Z


Mass: 6927.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii DSM 13941 (bacteria)

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Protein/peptide , 2 types, 16 molecules 13579ADFHJNPRTVY

#2: Protein/peptide
Alpha subunit of light-harvesting 1


Mass: 4724.656 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii DSM 13941 (bacteria)
References: UniProt: Q83XD1
#5: Protein/peptide SUBUNIT Y


Mass: 4493.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii DSM 13941 (bacteria)

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

#3: Protein Reaction center protein L chain


Mass: 34844.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: L- AND M-SUBUNITS OF THE RC ARE ENCODED BY A FUSED GENE PUFLM BUT POST-TRANSLATIONAL PROCESSED INTO TWO DISCRETE SUBUNITS EACH CONTAINING SIX AND FIVE TRANSMEMBRANE HELICES
Source: (natural) Roseiflexus castenholzii DSM 13941 (bacteria)
References: UniProt: A7NQE8
#4: Protein Reaction center protein M chain


Mass: 35046.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: L- AND M-SUBUNITS OF THE RC ARE ENCODED BY A FUSED GENE PUFLM BUT POST-TRANSLATIONAL PROCESSED INTO TWO DISCRETE SUBUNITS EACH CONTAINING SIX AND FIVE TRANSMEMBRANE HELICES
Source: (natural) Roseiflexus castenholzii DSM 13941 (bacteria)
References: UniProt: A7NQE8

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Non-polymers , 7 types, 67 molecules

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


Mass: 911.504 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#9: Chemical
ChemComp-KGD / beta,psi-caroten-4-one / Keto-gamma-carotene


Mass: 550.856 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H54O
#10: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H76N4O6
#11: Chemical ChemComp-MQE / 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione / Menaquinone 11


Mass: 921.467 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C66H96O2
#12: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#13: 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.: 3 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#14: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Details

Has ligand of interestN
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: THE CAROTENOID-DEPLETED RC-LH COMPLEX / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Roseiflexus castenholzii DSM 13941 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding 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: 1700 nm / Nominal defocus min: 1100 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1149.65GATAN K3 (6k x 4k)
2149.65GATAN K3 (6k x 4k)
3149.65GATAN K3 (6k x 4k)
4149.65GATAN K3 (6k x 4k)
5149.65GATAN K3 (6k x 4k)
6149.65GATAN K3 (6k x 4k)

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Processing

Image processing
IDImage recording-ID
11
22
33
44
55
66
71
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
33PHASE FLIPPING AND AMPLITUDE CORRECTION
44PHASE FLIPPING AND AMPLITUDE CORRECTION
55PHASE FLIPPING AND AMPLITUDE CORRECTION
66PHASE FLIPPING AND AMPLITUDE CORRECTION
77PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.1FSC 0.143 CUT-OFF8435218HJVPOINT
23.1FSC 0.143 CUT-OFF8435218HJVPOINT
33.1FSC 0.143 CUT-OFF8435218HJVPOINT
43.1FSC 0.143 CUT-OFF8435218HJVPOINT
53.1FSC 0.143 CUT-OFF8435218HJVPOINT
63.1FSC 0.143 CUT-OFF8435218HJVPOINT
73.1FSC 0.143 CUT-OFF8435218HJVPOINT
83.1FSC 0.143 CUT-OFF8435228HJVPOINT
93.1FSC 0.143 CUT-OFF8435228HJVPOINT
103.1FSC 0.143 CUT-OFF8435228HJVPOINT
113.1FSC 0.143 CUT-OFF8435228HJVPOINT
123.1FSC 0.143 CUT-OFF8435228HJVPOINT
133.1FSC 0.143 CUT-OFF8435228HJVPOINT
143.1FSC 0.143 CUT-OFF8435228HJVPOINT
153.1FSC 0.143 CUT-OFF8435238HJVPOINT
163.1FSC 0.143 CUT-OFF8435238HJVPOINT
173.1FSC 0.143 CUT-OFF8435238HJVPOINT
183.1FSC 0.143 CUT-OFF8435238HJVPOINT
193.1FSC 0.143 CUT-OFF8435238HJVPOINT
203.1FSC 0.143 CUT-OFF8435238HJVPOINT
213.1FSC 0.143 CUT-OFF8435238HJVPOINT
223.1FSC 0.143 CUT-OFF8435248HJVPOINT
233.1FSC 0.143 CUT-OFF8435248HJVPOINT
243.1FSC 0.143 CUT-OFF8435248HJVPOINT
253.1FSC 0.143 CUT-OFF8435248HJVPOINT
263.1FSC 0.143 CUT-OFF8435248HJVPOINT
273.1FSC 0.143 CUT-OFF8435248HJVPOINT
283.1FSC 0.143 CUT-OFF8435248HJVPOINT
293.1FSC 0.143 CUT-OFF8435258HJVPOINT
303.1FSC 0.143 CUT-OFF8435258HJVPOINT
313.1FSC 0.143 CUT-OFF8435258HJVPOINT
323.1FSC 0.143 CUT-OFF8435258HJVPOINT
333.1FSC 0.143 CUT-OFF8435258HJVPOINT
343.1FSC 0.143 CUT-OFF8435258HJVPOINT
353.1FSC 0.143 CUT-OFF8435258HJVPOINT
363.1FSC 0.143 CUT-OFF8435268HJVPOINT
373.1FSC 0.143 CUT-OFF8435268HJVPOINT
383.1FSC 0.143 CUT-OFF8435268HJVPOINT
393.1FSC 0.143 CUT-OFF8435268HJVPOINT
403.1FSC 0.143 CUT-OFF8435268HJVPOINT
413.1FSC 0.143 CUT-OFF8435268HJVPOINT
423.1FSC 0.143 CUT-OFF8435268HJVPOINT
433.1FSC 0.143 CUT-OFF8435278HJVPOINT
443.1FSC 0.143 CUT-OFF8435278HJVPOINT
453.1FSC 0.143 CUT-OFF8435278HJVPOINT
463.1FSC 0.143 CUT-OFF8435278HJVPOINT
473.1FSC 0.143 CUT-OFF8435278HJVPOINT
483.1FSC 0.143 CUT-OFF8435278HJVPOINT
493.1FSC 0.143 CUT-OFF8435278HJVPOINT
RefinementHighest resolution: 3.1 Å

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