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- PDB-5yq7: Cryo-EM structure of the RC-LH core complex from Roseiflexus cast... -

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Entry
Database: PDB / ID: 5yq7
TitleCryo-EM structure of the RC-LH core complex from Roseiflexus castenholzii
Components
  • (Precursor for ...) x 2
  • Alpha subunit of light-harvesting 1
  • Beta subunit of light-harvesting 1
  • Cytochrome subunit of photosynthetic reaction center
  • Peptide from Precursor for L and M subunits of photosynthetic reaction center
  • Subunit X
KeywordsPHOTOSYNTHESIS / Photosynthetic core complex
Function / homology
Function and homology information


organelle inner 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 ...organelle inner 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, 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 / Cytochrome subunit of photosynthetic reaction center / Reaction center protein L chain / Alpha subunit of light-harvesting 1 / Beta subunit of light-harvesting 1
Similarity search - Component
Biological speciesRoseiflexus castenholzii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsShi, Y. / Xin, Y.Y. / Niu, T.X. / Wang, Q.Q. / Niu, W.Q. / Huang, X.J. / Ding, W. / Blankenship, R.E. / Xu, X.L. / Sun, F.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08030202 China
Ministry of Science and Technology of China2014CB910700 China
CitationJournal: Nat Commun / Year: 2018
Title: Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote.
Authors: Yueyong Xin / Yang Shi / Tongxin Niu / Qingqiang Wang / Wanqiang Niu / Xiaojun Huang / Wei Ding / Lei Yang / Robert E Blankenship / Xiaoling Xu / Fei Sun /
Abstract: Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important ...Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important early branching photosynthetic bacteria in understanding the origin and evolution of photosynthesis. How their photosynthetic machinery assembles for efficient energy transfer is yet to be elucidated. Here, we report the 4.1 Å structure of photosynthetic core complex from Roseiflexus castenholzii by cryo-electron microscopy. The RC-LH complex has a tetra-heme cytochrome c bound RC encompassed by an elliptical LH ring that is assembled from 15 LHαβ subunits. An N-terminal transmembrane helix of cytochrome c inserts into the LH ring, not only yielding a tightly bound cytochrome c for rapid electron transfer, but also opening a slit in the LH ring, which is further flanked by a transmembrane helix from a newly discovered subunit X. These structural features suggest an unusual quinone exchange model of prokaryotic photosynthetic machinery.
History
DepositionNov 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / struct_conn / struct_conn_type
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.0Jun 25, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / em_software ...atom_site / em_software / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _em_software.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id

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Structure visualization

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Assembly

Deposited unit
E: Beta subunit of light-harvesting 1
B: Beta subunit of light-harvesting 1
0: Beta subunit of light-harvesting 1
L: Precursor for L subunits of photosynthetic reaction center
8: Beta subunit of light-harvesting 1
6: Beta subunit of light-harvesting 1
4: Beta subunit of light-harvesting 1
2: Beta subunit of light-harvesting 1
K: Beta subunit of light-harvesting 1
C: Cytochrome subunit of photosynthetic reaction center
I: Beta subunit of light-harvesting 1
G: Beta subunit of light-harvesting 1
W: Beta subunit of light-harvesting 1
U: Beta subunit of light-harvesting 1
T: Alpha subunit of light-harvesting 1
S: Beta subunit of light-harvesting 1
Q: Beta subunit of light-harvesting 1
O: Beta subunit of light-harvesting 1
V: Alpha subunit of light-harvesting 1
R: Alpha subunit of light-harvesting 1
P: Alpha subunit of light-harvesting 1
N: Alpha subunit of light-harvesting 1
J: Alpha subunit of light-harvesting 1
H: Alpha subunit of light-harvesting 1
F: Alpha subunit of light-harvesting 1
D: Alpha subunit of light-harvesting 1
A: Alpha subunit of light-harvesting 1
9: Alpha subunit of light-harvesting 1
7: Alpha subunit of light-harvesting 1
5: Alpha subunit of light-harvesting 1
3: Alpha subunit of light-harvesting 1
1: Alpha subunit of light-harvesting 1
Y: Peptide from Precursor for L and M subunits of photosynthetic reaction center
X: Subunit X
M: Precursor for M subunits of photosynthetic reaction center
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,265107
Polymers275,76935
Non-polymers58,49772
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area145190 Å2
ΔGint-1290 kcal/mol
Surface area122320 Å2

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Components

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Protein , 2 types, 16 molecules EB08642KIGWUSQOC

#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 (bacteria) / References: UniProt: Q83XD2
#3: Protein Cytochrome subunit of photosynthetic reaction center


Mass: 34923.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XC9

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Precursor for ... , 2 types, 2 molecules LM

#2: Protein Precursor for L subunits of photosynthetic reaction center


Mass: 34432.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XD0
#7: Protein Precursor for M subunits of photosynthetic reaction center


Mass: 34948.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XD0

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Protein/peptide , 3 types, 17 molecules TVRPNJHFDA97531YX

#4: 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 (bacteria) / References: UniProt: Q83XD1
#5: Protein/peptide Peptide from Precursor for L and M subunits of photosynthetic reaction center


Mass: 2145.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The peptide could be either an unidentified new gene product or a proteolytic fragment of the pufLM gene product that is cleaved twice during processing.
Source: (natural) Roseiflexus castenholzii (bacteria)
#6: Protein/peptide Subunit X


Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Subunit X with its flexible transmembrane helix is flanking the gap of light harvesting complex.
Source: (natural) Roseiflexus castenholzii (bacteria)

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Non-polymers , 6 types, 72 molecules

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


Mass: 911.504 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: C55H74MgN4O6
#9: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H76N4O6
#10: 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.: 2 / Source method: obtained synthetically / Formula: C66H96O2
#11: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#12: Chemical
ChemComp-KGD / beta,psi-caroten-4-one / Keto-gamma-carotene


Mass: 550.856 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C40H54O
#13: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

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Details

Has protein modificationN

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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 core complex / Type: COMPLEX / Entity ID: #1-#2, #7, #3-#5 / Source: NATURAL
Molecular weightValue: 0.33 MDa / Experimental value: NO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Buffer solutionpH: 8.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in.
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 magnification: 75000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 50 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2330

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 148618
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256903 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.03521059
ELECTRON MICROSCOPYf_angle_d1.38729497
ELECTRON MICROSCOPYf_dihedral_angle_d9.49610471
ELECTRON MICROSCOPYf_chiral_restr0.0473112
ELECTRON MICROSCOPYf_plane_restr0.0133416

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