5V8K

Homodimeric reaction center of H. modesticaldum

PDB DOI: https://doi.org/10.2210/pdb5V8K/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Heliomicrobium modesticaldum, Heliomicrobium modesticaldum Ice1
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2017-03-22 Released: 2017-09-06
Deposition Author(s): Gisriel, C., Sarrou, I., Ferlez, B., Golbeck, J., Redding, K.E., Fromme, R.
Funding Organization(s): Department of Energy (DOE, United States)

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

wwPDB Validation 3D Report Full Report

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

PubMed: 28751471 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 97.9 kDa
Atom Count: 6,958
Modelled Residue Count: 625
Deposited Residue Count: 625
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
p800 reaction center core protein	A	600	Heliomicrobium modesticaldum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q1MX24 (Heliomicrobium modesticaldum) Explore Q1MX24 Go to UniProtKB: Q1MX24
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1MX24
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
proteinsubunit pshX	B	25	Heliomicrobium modesticaldum Ice1	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B0TAT4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AOH Query on AOH Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	8(1)-OH-Chlorophyll aF C₅₀ H₆₀ Mg N₄ O₆ RSDQAIDZUXTOBN-UZWLNIDASA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GBF Query on GBF Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain D [auth A] SDF format, chain DA [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	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		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
GB0 Query on GB0 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A]	C [auth A], G [auth A]	Bacteriochlorophyll g' C₅₀ H₅₈ Mg N₄ O₅ LRFAKGNZCOQNAG-QUMYBLOASA-M		Interactions Focus chain C [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain G [auth A]
DGG Query on DGG Download Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain GA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A]	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		Interactions Focus chain FA [auth A] Focus chain GA [auth A] Interactions & Density Focus chain FA [auth A] Focus chain GA [auth A]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain JA [auth A] SDF format, chain KA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A]	JA [auth A], KA [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain JA [auth A] Focus chain KA [auth A] Interactions & Density Focus chain JA [auth A] Focus chain KA [auth A]
C4D Query on C4D Download Ideal Coordinates CCD File SDF format, chain LA [auth B] MOL2 format, chain LA [auth B] mmCIF format, chain LA [auth B]	LA [auth B]	4,4'-Diaponeurosporene C₃₀ H₄₂ FPSYVUBUILNSRF-MQMKOTMBSA-N		Interactions Focus chain LA [auth B] Interactions & Density Focus chain LA [auth B]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain EA [auth A] MOL2 format, chain EA [auth A] mmCIF format, chain EA [auth A]	EA [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Interactions & Density Focus chain EA [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain IA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A]	HA [auth A], IA [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Focus chain IA [auth A] Interactions & Density Focus chain HA [auth A] Focus chain IA [auth A]

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 = 131.358	α = 90
b = 89.714	β = 108.15
c = 111.637	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
BUCCANEER	model building
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing
SHELXE	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-09-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-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