5Y5S

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosynthetic reaction center cytochrome c subunit
C
404Thermochromatium tepidumMutation(s): 0 
Gene Names: pufC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for D2Z0P5 (Thermochromatium tepidum)
Go to UniProtKB:  D2Z0P5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosynthetic reaction center L subunit
L
281Thermochromatium tepidumMutation(s): 0 
Gene Names: pufL
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for D2Z0P3 (Thermochromatium tepidum)
Go to UniProtKB:  D2Z0P3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosynthetic reaction center M subunit
M
325Thermochromatium tepidumMutation(s): 0 
Gene Names: pufM
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for A8ASG6 (Thermochromatium tepidum)
Go to UniProtKB:  A8ASG6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosynthetic reaction center H subunit
H
259Thermochromatium tepidumMutation(s): 0 
Gene Names: puhA
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for D2Z0P9 (Thermochromatium tepidum)
Go to UniProtKB:  D2Z0P9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
LH1 alpha polypeptide
A, D, F, I, K, O, Q, S, U, W, Y, 1, 3, 5, 7, 9
61Thermochromatium tepidumMutation(s): 0 
Gene Names: pufA
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for D2Z0P2 (Thermochromatium tepidum)
Go to UniProtKB:  D2Z0P2
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
LH1 beta polypeptide
B, E, G, J, N, P, R, T, V, X, Z, 2, 4, 6, 8, 0
47Thermochromatium tepidumMutation(s): 0 
Gene Names: pufB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Light-Harvesting+Reaction Center Complexes
Protein: 
LH1-RC complex, P21 crystal form
Find proteins for D2Z0P1 (Thermochromatium tepidum)
Go to UniProtKB:  D2Z0P1
Small Molecules
Ligands 17 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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D, H, K, M, Q, S, Y
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
SO4
Query on SO4

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C, L, M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PEF
Query on PEF

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1, 3, 5, I, K, M, U, W
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
GOL
Query on GOL

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C, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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2, 4, 6, 8, A, B, E, G, J, N, P, R, T, V, X, Z
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BCL
Query on BCL

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0, 1, 3, 5, 7, 9, A, D, F, I, K, L, M, O, Q, S, U, W, Y, Z
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
LDA
Query on LDA

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I, J, M, O, V
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
CRT
Query on CRT

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0, 1, 2, 6, 9, A, G, J, M, N, O, P, Q, U, V, Z
SPIRILLOXANTHIN
RHODOVIOLASCIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
 Ligand Interaction
UQ8
Query on UQ8

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7, L, M
Ubiquinone-8
2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl]cyclohexa-2,5-diene-1,4-dione
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
 Ligand Interaction
MG
Query on MG

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C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FE
Query on FE

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L
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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F, M
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
BPH
Query on BPH

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L, M
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
MQ8
Query on MQ8

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M
MENAQUINONE 8
2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
 Ligand Interaction
PGV
Query on PGV

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1, 3, A, C, D, H, L, M
(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
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
 Ligand Interaction
LHG
Query on LHG

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C
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 145.280α = 90.00
b = 143.810β = 90.74
c = 210.280γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection, Database references, Structure summary