5V8K

Homodimeric reaction center of H. modesticaldum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structure of a symmetric photosynthetic reaction center-photosystem.

Gisriel, C.Sarrou, I.Ferlez, B.Golbeck, J.H.Redding, K.E.Fromme, R.

(2017) Science 357: 1021-1025

  • DOI: https://doi.org/10.1126/science.aan5611
  • Primary Citation of Related Structures:  
    5V8K

  • PubMed Abstract: 

    Reaction centers are pigment-protein complexes that drive photosynthesis by converting light into chemical energy. It is believed that they arose once from a homodimeric protein. The symmetry of a homodimer is broken in heterodimeric reaction-center structures, such as those reported previously. The 2.2-angstrom resolution x-ray structure of the homodimeric reaction center-photosystem from the phototroph Heliobacterium modesticaldum exhibits perfect C 2 symmetry. The core polypeptide dimer and two small subunits coordinate 54 bacteriochlorophylls and 2 carotenoids that capture and transfer energy to the electron transfer chain at the center, which performs charge separation and consists of 6 (bacterio)chlorophylls and an iron-sulfur cluster; unlike other reaction centers, it lacks a bound quinone. This structure preserves characteristics of the ancestral reaction center, providing insight into the evolution of photosynthesis.


  • Organizational Affiliation

    School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
p800 reaction center core protein600Heliomicrobium modesticaldumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q1MX24 (Heliomicrobium modesticaldum)
Explore Q1MX24 
Go to UniProtKB:  Q1MX24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1MX24
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
proteinsubunit pshX25Heliomicrobium modesticaldum Ice1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0TAT4 (Heliobacterium modesticaldum (strain ATCC 51547 / Ice1))
Explore B0TAT4 
Go to UniProtKB:  B0TAT4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0TAT4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AOH
Query on AOH

Download Ideal Coordinates CCD File 
E [auth A]8(1)-OH-Chlorophyll aF
C50 H60 Mg N4 O6
RSDQAIDZUXTOBN-UZWLNIDASA-M
GBF
Query on GBF

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AA [auth A]
BA [auth A]
CA [auth A]
D [auth A]
DA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
D [auth A],
DA [auth A],
F [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
Bacteriochlorophyll g
C50 H58 Mg N4 O5
LRFAKGNZCOQNAG-QZHKZBCOSA-M
GB0
Query on GB0

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C [auth A],
G [auth A]
Bacteriochlorophyll g'
C50 H58 Mg N4 O5
LRFAKGNZCOQNAG-QUMYBLOASA-M
DGG
Query on DGG

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FA [auth A],
GA [auth A]
1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL
C39 H75 O10 P
JWIOKCJPLNKYBQ-JIZALCTLSA-N
LMT
Query on LMT

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JA [auth A],
KA [auth A]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
C4D
Query on C4D

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LA [auth B]4,4'-Diaponeurosporene
C30 H42
FPSYVUBUILNSRF-MQMKOTMBSA-N
SF4
Query on SF4

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EA [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
HA [auth A],
IA [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.358α = 90
b = 89.714β = 108.15
c = 111.637γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
BUCCANEERmodel building
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
SHELXEmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references, Derived calculations, Experimental preparation, Structure summary
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references, Derived calculations