5Y5S

Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Structure of photosynthetic LH1-RC supercomplex at 1.9 angstrom resolution.

Yu, L.-J.Suga, M.Wang-Otomo, Z.-Y.Shen, J.R.

(2018) Nature 556: 209-213

  • DOI: https://doi.org/10.1038/s41586-018-0002-9
  • Primary Citation of Related Structures:  
    5Y5S

  • PubMed Abstract: 

    Light-harvesting complex 1 (LH1) and the reaction centre (RC) form a membrane-protein supercomplex that performs the primary reactions of photosynthesis in purple photosynthetic bacteria. The structure of the LH1-RC complex can provide information on the arrangement of protein subunits and cofactors; however, so far it has been resolved only at a relatively low resolution. Here we report the crystal structure of the calcium-ion-bound LH1-RC supercomplex of Thermochromatium tepidum at a resolution of 1.9 Å. This atomic-resolution structure revealed several new features about the organization of protein subunits and cofactors. We describe the loop regions of RC in their intact states, the interaction of these loop regions with the LH1 subunits, the exchange route for the bound quinone Q B with free quinone molecules, the transport of free quinones between the inside and outside of the LH1 ring structure, and the detailed calcium-ion-binding environment. This structure provides a solid basis for the detailed examination of the light reactions that occur during bacterial photosynthesis.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]404Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P5 (Thermochromatium tepidum)
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UniProt GroupD2Z0P5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center L subunitB [auth L]281Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P3 (Thermochromatium tepidum)
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UniProt GroupD2Z0P3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center M subunitC [auth M]325Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A8ASG6 (Thermochromatium tepidum)
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UniProt GroupA8ASG6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitD [auth H]259Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P9 (Thermochromatium tepidum)
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UniProt GroupD2Z0P9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
LH1 alpha polypeptide61Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P2 (Thermochromatium tepidum)
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UniProt GroupD2Z0P2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
LH1 beta polypeptide47Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P1 (Thermochromatium tepidum)
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UniProt GroupD2Z0P1
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Small Molecules
Ligands 18 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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DD [auth K]
JC [auth D]
NE [auth Y]
OE [auth Y]
RB [auth M]
DD [auth K],
JC [auth D],
NE [auth Y],
OE [auth Y],
RB [auth M],
RD [auth Q],
WD [auth S],
XB [auth H],
ZB [auth H]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
Query on BCL

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AC [auth A]
AE [auth U]
BD [auth K]
BF [auth 3]
CC [auth A]
AC [auth A],
AE [auth U],
BD [auth K],
BF [auth 3],
CC [auth A],
CD [auth K],
CF [auth 3],
DB [auth M],
EB [auth M],
FB [auth M],
HC [auth D],
HD [auth O],
HE [auth W],
HF [auth 5],
IC [auth D],
ID [auth O],
IE [auth W],
IF [auth 5],
ME [auth Y],
NC [auth F],
NF [auth 7],
OC [auth F],
OD [auth Q],
OF [auth 7],
PD [auth Q],
QE [auth Z],
TA [auth L],
TC [auth I],
TE [auth 1],
UC [auth I],
UD [auth S],
UE [auth 1],
UF [auth 9],
VD [auth S],
WF [auth 0],
ZD [auth U]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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GB [auth M],
UA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
PGV
Query on PGV

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EC [auth A]
EF [auth 3]
KC [auth D]
PB [auth M]
QB [auth M]
EC [auth A],
EF [auth 3],
KC [auth D],
PB [auth M],
QB [auth M],
SA [auth C],
XA [auth L],
XE [auth 1],
YA [auth L],
YB [auth H]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
UQ8
Query on UQ8

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AB [auth L],
BB [auth L],
PF [auth 7],
TB [auth M],
VA [auth L]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
LHG
Query on LHG

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RA [auth C]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
MQ8
Query on MQ8

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HB [auth M]MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
PEF
Query on PEF

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CE [auth U]
DE [auth U]
DF [auth 3]
ED [auth K]
JB [auth M]
CE [auth U],
DE [auth U],
DF [auth 3],
ED [auth K],
JB [auth M],
JE [auth W],
JF [auth 5],
KB [auth M],
LB [auth M],
MB [auth M],
UB [auth M],
VC [auth I],
WE [auth 1]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
HEC
Query on HEC

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KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
CRT
Query on CRT

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BE [auth U]
DC [auth A]
EE [auth V]
FD [auth N]
IB [auth M]
BE [auth U],
DC [auth A],
EE [auth V],
FD [auth N],
IB [auth M],
JD [auth O],
KF [auth 6],
LD [auth P],
PE [auth Z],
QC [auth G],
QD [auth Q],
SF [auth 9],
TF [auth 9],
VE [auth 1],
VF [auth 0],
XC [auth J],
YE [auth 2]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
LMT
Query on LMT

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PC [auth F],
VB [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LDA
Query on LDA

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FE [auth V],
KD [auth O],
NB [auth M],
WC [auth I],
YC [auth J]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
SO4
Query on SO4

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OB [auth M],
QA [auth C],
WA [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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PA [auth C],
WB [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE
Query on FE

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CB [auth L]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA
Query on CA

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AD [auth J]
AF [auth 2]
BC [auth A]
GC [auth B]
GD [auth N]
AD [auth J],
AF [auth 2],
BC [auth A],
GC [auth B],
GD [auth N],
GE [auth V],
GF [auth 4],
LE [auth X],
MC [auth E],
MF [auth 6],
ND [auth P],
RF [auth 8],
SC [auth G],
SE [auth Z],
TD [auth R],
YD [auth T]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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OA [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL

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FC [auth B]
FF [auth 4]
KE [auth X]
LC [auth E]
LF [auth 6]
FC [auth B],
FF [auth 4],
KE [auth X],
LC [auth E],
LF [auth 6],
MD [auth P],
QF [auth 8],
RC [auth G],
RE [auth Z],
SB [auth M],
SD [auth R],
XD [auth T],
XF [auth 0],
ZA [auth L],
ZC [auth J],
ZE [auth 2]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.28α = 90
b = 143.81β = 90.74
c = 210.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2019-10-02
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary