5Y5S | pdb_00005y5s

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 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 425.93 kDa 
  • Atom Count: 27,981 
  • Modeled Residue Count: 2,726 
  • Deposited Residue Count: 2,997 
  • Unique protein chains: 6

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)
Explore D2Z0P5 
Go to UniProtKB:  D2Z0P5
Entity Groups
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UniProt GroupD2Z0P5
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Reference Sequence
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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)
Explore D2Z0P3 
Go to UniProtKB:  D2Z0P3
Entity Groups
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UniProt GroupD2Z0P3
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Reference Sequence
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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)
Explore A8ASG6 
Go to UniProtKB:  A8ASG6
Entity Groups
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UniProt GroupA8ASG6
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Reference Sequence
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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)
Explore D2Z0P9 
Go to UniProtKB:  D2Z0P9
Entity Groups
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UniProt GroupD2Z0P9
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Reference Sequence
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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)
Explore D2Z0P2 
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Entity Groups
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UniProt GroupD2Z0P2
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Reference Sequence
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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)
Explore D2Z0P1 
Go to UniProtKB:  D2Z0P1
Entity Groups
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UniProt GroupD2Z0P1
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Reference Sequence

Small Molecules

Ligands 18 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
GB [auth M],
UA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
PGV

Query on PGV



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
PC [auth F],
VB [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LDA

Query on LDA



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
OB [auth M],
QA [auth C],
WA [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
PA [auth C],
WB [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
CB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AD [auth K]
AF [auth 3]
BC [auth A]
GC [auth D]
GD [auth O]
AD [auth K],
AF [auth 3],
BC [auth A],
GC [auth D],
GD [auth O],
GE [auth W],
GF [auth 5],
LE [auth Y],
MC [auth F],
MF [auth 7],
ND [auth Q],
RF [auth 9],
SC [auth I],
SE [auth 1],
TD [auth S],
YD [auth U]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
OA [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL

Query on UNL



Download:Ideal Coordinates CCD File
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 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
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
  • Version 3.0: 2025-09-17
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary