5YQ7

Cryo-EM structure of the RC-LH core complex from Roseiflexus castenholzii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote.

Xin, Y.Y.Shi, Y.Niu, T.X.Wang, Q.Q.Niu, W.Q.Huang, X.J.Ding, W.Yang, L.Blankenship, R.E.Xu, X.L.Sun, F.

(2018) Nat Commun 9: 1568-1568

  • DOI: https://doi.org/10.1038/s41467-018-03881-x
  • Primary Citation of Related Structures:  
    5YQ7

  • PubMed 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 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.


  • Organizational Affiliation

    Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou, 311121, Zhejiang Province, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta subunit of light-harvesting 155Roseiflexus castenholziiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q83XD2 (Roseiflexus castenholzii)
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Go to UniProtKB:  Q83XD2
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UniProt GroupQ83XD2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Precursor for L subunits of photosynthetic reaction centerD [auth L]310Roseiflexus castenholziiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q83XD0 (Roseiflexus castenholzii)
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Go to UniProtKB:  Q83XD0
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UniProt GroupQ83XD0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome subunit of photosynthetic reaction centerJ [auth C]320Roseiflexus castenholziiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q83XC9 (Roseiflexus castenholzii)
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Go to UniProtKB:  Q83XC9
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UniProt GroupQ83XC9
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha subunit of light-harvesting 142Roseiflexus castenholziiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q83XD1 (Roseiflexus castenholzii)
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UniProt GroupQ83XD1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Precursor for L and M subunits of photosynthetic reaction centerGA [auth Y]25Roseiflexus castenholziiMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit XHA [auth X]23Roseiflexus castenholziiMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Precursor for M subunits of photosynthetic reaction centerIA [auth M]306Roseiflexus castenholziiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q83XD0 (Roseiflexus castenholzii)
Explore Q83XD0 
Go to UniProtKB:  Q83XD0
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UniProt GroupQ83XD0
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MQE
Query on MQE

Download Ideal Coordinates CCD File 
SA [auth L],
ZC [auth M]
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
C66 H96 O2
YYDMANIEKFAEJC-RYZSZPJESA-N
BCL
Query on BCL

Download Ideal Coordinates CCD File 
AB [auth 2]
AD [auth M]
BB [auth 2]
BC [auth R]
CB [auth K]
AB [auth 2],
AD [auth M],
BB [auth 2],
BC [auth R],
CB [auth K],
CC [auth P],
DB [auth K],
FC [auth N],
HC [auth J],
IB [auth I],
IC [auth H],
JA [auth E],
JB [auth I],
KA [auth E],
KB [auth G],
LA [auth B],
LB [auth G],
LC [auth F],
MA [auth B],
MB [auth W],
MC [auth D],
NA [auth 0],
NB [auth W],
OA [auth 0],
OB [auth U],
OC [auth A],
PA [auth L],
PB [auth U],
QA [auth L],
RC [auth 9],
SB [auth T],
SC [auth 7],
TB [auth S],
UA [auth 8],
UB [auth S],
UC [auth 5],
VA [auth 8],
VB [auth Q],
WA [auth 6],
WB [auth Q],
WC [auth 3],
XA [auth 6],
XB [auth O],
YA [auth 4],
YB [auth O],
YC [auth 1],
ZA [auth 4],
ZB [auth V]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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BD [auth M],
CD [auth M],
RA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
HEM
Query on HEM

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EB [auth C],
FB [auth C],
GB [auth C],
HB [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
KGD
Query on KGD

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AC [auth R]
DC [auth N]
EC [auth N]
GC [auth J]
JC [auth H]
AC [auth R],
DC [auth N],
EC [auth N],
GC [auth J],
JC [auth H],
KC [auth F],
NC [auth A],
PC [auth 9],
QB [auth T],
QC [auth 9],
RB [auth T],
TC [auth 5],
VC [auth 3],
XC [auth 3]
beta,psi-caroten-4-one
C40 H54 O
BRKQDNOGSHYATK-HNNISBQLSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
TA [auth L]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB08030202
Ministry of Science and Technology of ChinaChina2014CB910700

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release