5B5M

Crystal structure of the Sr-substituted LH1-RC complex from Tch. tepidum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural Basis for the Unusual Qy Red-Shift and Enhanced Thermostability of the LH1 Complex from Thermochromatium tepidum.

Yu, L.J.Kawakami, T.Kimura, Y.Wang-Otomo, Z.Y.

(2016) Biochemistry 55: 6495-6504

  • DOI: https://doi.org/10.1021/acs.biochem.6b00742
  • Primary Citation of Related Structures:  
    5B5M, 5B5N

  • PubMed Abstract: 

    While the majority of the core light-harvesting complexes (LH1) in purple photosynthetic bacteria exhibit a Q y absorption band in the range of 870-890 nm, LH1 from the thermophilic bacterium Thermochromatium tepidum displays the Q y band at 915 nm with an enhanced thermostability. These properties are regulated by Ca 2+ ions. Substitution of the Ca 2+ with other divalent metal ions results in a complex with the Q y band blue-shifted to 880-890 nm and a reduced thermostability. Following the recent publication of the structure of the Ca-bound LH1-reaction center (RC) complex [Niwa, S., et al. (2014) Nature 508, 228], we have determined the crystal structures of the Sr- and Ba-substituted LH1-RC complexes with the LH1 Q y band at 888 nm. Sixteen Sr 2+ and Ba 2+ ions are identified in the LH1 complexes. Both Sr 2+ and Ba 2+ are located at the same positions, and these are clearly different from, though close to, the Ca 2+ -binding sites. Conformational rearrangement induced by the substitution is limited to the metal-binding sites. Unlike the Ca-LH1-RC complex, only the α-polypeptides are involved in the Sr and Ba coordinations in LH1. The difference in the thermostability between these complexes can be attributed to the different patterns of the network formed by metal binding. The Sr- and Ba-LH1-RC complexes form a single-ring network by the LH1 α-polypeptides only, in contrast to the double-ring network composed of both α- and β-polypeptides in the Ca-LH1-RC complex. On the basis of the structural information, a combined effect of hydrogen bonding, structural integrity, and charge distribution is considered to influence the spectral properties of the core antenna complex.


  • Organizational Affiliation

    Faculty of Science, Ibaraki University , Mito 310-8512, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C],
KA [auth o]
333Thermochromatium tepidumMutation(s): 0 
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],
LA [auth x]
281Thermochromatium tepidumMutation(s): 0 
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],
MA [auth y]
319Thermochromatium tepidumMutation(s): 0 
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],
NA [auth t]
259Thermochromatium tepidumMutation(s): 0 
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 
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 
UniProt
Find proteins for D2Z0P1 (Thermochromatium tepidum)
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UniProt GroupD2Z0P1
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

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AD [auth D]
AF [auth 7]
BC [auth L]
BE [auth T]
BI [auth AL]
AD [auth D],
AF [auth 7],
BC [auth L],
BE [auth T],
BI [auth AL],
CE [auth U],
CH [auth z],
CI [auth d],
DC [auth L],
DD [auth F],
DF [auth 8],
DH [auth AA],
FE [auth V],
FH [auth AB],
FI [auth e],
GD [auth G],
GE [auth W],
GF [auth 9],
GI [auth f],
HD [auth I],
HF [auth 0],
HH [auth AC],
IC [auth M],
IG [auth m],
JE [auth X],
JG [auth m],
JH [auth AD],
JI [auth g],
KD [auth J],
KE [auth Y],
KI [auth h],
LD [auth K],
MH [auth AE],
NE [auth Z],
NF [auth x],
NG [auth p],
NI [auth i],
OD [auth N],
OE [auth 1],
OH [auth AE],
OI [auth j],
PD [auth O],
PE [auth 1],
PF [auth x],
PG [auth p],
QH [auth AH],
RD [auth P],
RF [auth x],
RG [auth r],
RI [auth k],
SE [auth 3],
SH [auth AH],
SI [auth l],
TD [auth Q],
TH [auth AI],
UE [auth 4],
UG [auth s],
VC [auth A],
VE [auth 5],
VG [auth u],
VI [auth c],
WD [auth R],
WE [auth 5],
WF [auth y],
XG [auth v],
XH [auth AJ],
YC [auth B],
YD [auth S],
YG [auth w],
YH [auth AK],
ZB [auth L],
ZC [auth D]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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AC [auth L],
JC [auth M],
OF [auth x],
XF [auth y]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
PGW
Query on PGW

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LH [auth AE],
XD [auth S]
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
C40 H77 O10 P
PAZGBAOHGQRCBP-HGWHEPCSSA-N
UQ8
Query on UQ8

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CC [auth L],
QF [auth x]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
MQ8
Query on MQ8

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KC [auth M],
YF [auth y]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
PEF
Query on PEF

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BG [auth y]
CG [auth y]
DG [auth y]
EC [auth L]
EG [auth t]
BG [auth y],
CG [auth y],
DG [auth y],
EC [auth L],
EG [auth t],
GG [auth t],
HG [auth m],
MG [auth p],
NC [auth M],
OC [auth M],
PC [auth M],
QC [auth H],
SC [auth H],
SF [auth x],
TC [auth H],
UC [auth A]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
HEM
Query on HEM

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IF [auth o]
JF [auth o]
KF [auth o]
LF [auth o]
UB [auth C]
IF [auth o],
JF [auth o],
KF [auth o],
LF [auth o],
UB [auth C],
VB [auth C],
WB [auth C],
XB [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CRT
Query on CRT

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AE [auth T]
AI [auth AL]
BH [auth z]
CD [auth E]
CF [auth 8]
AE [auth T],
AI [auth AL],
BH [auth z],
CD [auth E],
CF [auth 8],
DE [auth U],
EI [auth e],
FD [auth G],
FF [auth 9],
GH [auth AC],
HI [auth f],
IE [auth X],
JD [auth J],
KH [auth AD],
LC [auth M],
LG [auth n],
ME [auth Z],
MI [auth i],
ND [auth N],
NH [auth AE],
OG [auth p],
QI [auth k],
RE [auth 2],
RH [auth AH],
SD [auth P],
TE [auth 4],
TG [auth s],
UI [auth c],
VD [auth R],
WC [auth A],
WG [auth v],
WH [auth AJ],
ZE [auth 6],
ZF [auth y]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
PO4
Query on PO4

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AG [auth y],
FG [auth t],
MC [auth M],
RC [auth H]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
SR
Query on SR

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AH [auth w]
BD [auth D]
BF [auth 7]
DI [auth d]
ED [auth F]
AH [auth w],
BD [auth D],
BF [auth 7],
DI [auth d],
ED [auth F],
EE [auth U],
EF [auth 9],
EH [auth AA],
FC [auth L],
GC [auth L],
HE [auth W],
ID [auth I],
IH [auth AC],
II [auth f],
KG [auth m],
LE [auth Y],
LI [auth h],
MD [auth K],
MF [auth o],
PH [auth AE],
PI [auth j],
QD [auth O],
QE [auth 1],
QG [auth p],
SG [auth r],
TF [auth x],
TI [auth l],
UD [auth Q],
UF [auth x],
UH [auth AI],
VH [auth AI],
XC [auth A],
XE [auth 5],
YB [auth C],
YE [auth 5],
ZD [auth S],
ZG [auth w],
ZH [auth AK]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
FE
Query on FE

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HC [auth L],
VF [auth x]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.888α = 90
b = 148.946β = 108.18
c = 210.226γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.3: 2024-03-20
    Changes: Source and taxonomy