6QPH

Dunaliella minimal PSI complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.337 
  • R-Value Observed: 0.338 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structure of a minimal photosystem I from the green alga Dunaliella salina.

Perez-Boerema, A.Klaiman, D.Caspy, I.Netzer-El, S.Y.Amunts, A.Nelson, N.

(2020) Nat Plants 6: 321-327

  • DOI: https://doi.org/10.1038/s41477-020-0611-9
  • Primary Citation of Related Structures:  
    6QPH, 6RHZ

  • PubMed Abstract: 

    Solar energy harnessed by oxygenic photosynthesis supports most of the life forms on Earth. In eukaryotes, photosynthesis occurs in chloroplasts and is achieved by membrane-embedded macromolecular complexes that contain core and peripheral antennae with multiple pigments. The structure of photosystem I (PSI) comprises the core and light-harvesting (LHCI) complexes, which together form PSI-LHCI. Here we determined the structure of PSI-LHCI from the salt-tolerant green alga Dunaliella salina using X-ray crystallography and electron cryo-microscopy. Our results reveal a previously undescribed configuration of the PSI core. It is composed of only 7 subunits, compared with 14-16 subunits in plants and the alga Chlamydomonas reinhardtii, and forms the smallest known PSI. The LHCI is poorly conserved at the sequence level and binds to pigments that form new energy pathways, and the interactions between the individual Lhca1-4 proteins are weakened. Overall, the data indicate the PSI of D. salina represents a different type of the molecular organization that provides important information for reconstructing the plasticity and evolution of PSI.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth 1]195Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for C1K003 (Dunaliella salina)
Explore C1K003 
Go to UniProtKB:  C1K003
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1K003
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lhc2B [auth 2]211Dunaliella salinaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticC [auth 3]210Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for C1K004 (Dunaliella salina)
Explore C1K004 
Go to UniProtKB:  C1K004
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1K004
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Lhc4D [auth 4]211Dunaliella salinaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]739Dunaliella salinaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for D0FXV2 (Dunaliella salina)
Explore D0FXV2 
Go to UniProtKB:  D0FXV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXV2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]734Dunaliella salinaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for D0FXZ0 (Dunaliella salina)
Explore D0FXZ0 
Go to UniProtKB:  D0FXZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXZ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]80Dunaliella salinaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for D0FXW7 (Dunaliella salina)
Explore D0FXW7 
Go to UniProtKB:  D0FXW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXW7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PsaDH [auth D]142Dunaliella salinaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PsaEI [auth E]64Dunaliella salinaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PsaFJ [auth F]163Dunaliella salinaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXK [auth J]41Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXW0 (Dunaliella salina)
Explore D0FXW0 
Go to UniProtKB:  D0FXW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXW0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
DB [auth 2],
FH [auth J],
PC [auth 4],
TG [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

Download Ideal Coordinates CCD File 
KC [auth 4]
LB [auth 3]
LC [auth 4]
NC [auth 4]
UA [auth 2]
KC [auth 4],
LB [auth 3],
LC [auth 4],
NC [auth 4],
UA [auth 2],
VA [auth 2],
WA [auth 2],
X [auth 1],
Y [auth 1],
YA [auth 2]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0
Query on CL0

Download Ideal Coordinates CCD File 
TC [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth 1]
AD [auth A]
AE [auth A]
AF [auth B]
AG [auth B]
AA [auth 1],
AD [auth A],
AE [auth A],
AF [auth B],
AG [auth B],
BA [auth 1],
BC [auth 4],
BD [auth A],
BE [auth A],
BF [auth B],
BG [auth B],
BH [auth J],
CA [auth 1],
CC [auth 4],
CD [auth A],
CE [auth A],
CF [auth B],
CG [auth B],
DC [auth 4],
DD [auth A],
DE [auth A],
DF [auth B],
DG [auth B],
EC [auth 4],
ED [auth A],
EE [auth A],
EF [auth B],
EG [auth B],
FC [auth 4],
FD [auth A],
FE [auth A],
FF [auth B],
FG [auth B],
GC [auth 4],
GD [auth A],
GE [auth A],
GF [auth B],
GG [auth B],
HC [auth 4],
HD [auth A],
HE [auth A],
HF [auth B],
HG [auth B],
IC [auth 4],
ID [auth A],
IE [auth A],
IF [auth B],
IG [auth B],
JB [auth 3],
JC [auth 4],
JD [auth A],
JE [auth A],
JF [auth B],
JG [auth B],
KB [auth 3],
KD [auth A],
KE [auth A],
KF [auth B],
KG [auth B],
LD [auth A],
LF [auth B],
MA [auth 2],
MB [auth 3],
MC [auth 4],
MD [auth A],
MF [auth B],
NA [auth 2],
NB [auth 3],
ND [auth A],
NF [auth B],
OA [auth 2],
OB [auth 3],
OC [auth 4],
OD [auth A],
OF [auth B],
P [auth 1],
PA [auth 2],
PB [auth 3],
PD [auth A],
PF [auth B],
Q [auth 1],
QA [auth 2],
QB [auth 3],
QD [auth A],
QF [auth B],
R [auth 1],
RA [auth 2],
RB [auth 3],
RD [auth A],
RF [auth B],
S [auth 1],
SA [auth 2],
SB [auth 3],
SD [auth A],
SF [auth B],
T [auth 1],
TA [auth 2],
TB [auth 3],
TD [auth A],
TF [auth B],
U [auth 1],
UB [auth 3],
UC [auth A],
UD [auth A],
UF [auth B],
V [auth 1],
VC [auth A],
VD [auth A],
VE [auth B],
VF [auth B],
W [auth 1],
WC [auth A],
WD [auth A],
WE [auth B],
WF [auth B],
XA [auth 2],
XC [auth A],
XD [auth A],
XE [auth B],
XF [auth B],
YC [auth A],
YD [auth A],
YE [auth B],
YF [auth B],
YG [auth F],
Z [auth 1],
ZA [auth 2],
ZC [auth A],
ZD [auth A],
ZE [auth B],
ZF [auth B],
ZG [auth F]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
Query on SQD

Download Ideal Coordinates CCD File 
GA [auth 1]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

Download Ideal Coordinates CCD File 
BB [auth 2],
CB [auth 2],
EA [auth 1],
FA [auth 1]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
AB [auth 2],
DA [auth 1],
SG [auth B],
TE [auth A],
UE [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT

Download Ideal Coordinates CCD File 
GB [auth 3],
KA [auth 2],
M [auth 1],
YB [auth 4]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT
Query on LUT

Download Ideal Coordinates CCD File 
FB [auth 3],
JA [auth 2],
L [auth 1],
XB [auth 4]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
Query on BCR

Download Ideal Coordinates CCD File 
AC [auth 4]
AH [auth F]
CH [auth J]
DH [auth J]
EH [auth J]
AC [auth 4],
AH [auth F],
CH [auth J],
DH [auth J],
EH [auth J],
HB [auth 3],
IB [auth 3],
LA [auth 2],
MG [auth B],
N [auth 1],
NE [auth A],
NG [auth B],
O [auth 1],
OE [auth A],
OG [auth B],
PE [auth A],
PG [auth B],
QE [auth A],
QG [auth B],
RE [auth A],
RG [auth B],
SE [auth A],
ZB [auth 4]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
EB [auth 2]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

Download Ideal Coordinates CCD File 
LE [auth A],
LG [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
ME [auth A],
WG [auth C],
XG [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
GSH
Query on GSH

Download Ideal Coordinates CCD File 
QC [auth 4],
UG [auth B]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
CAC
Query on CAC

Download Ideal Coordinates CCD File 
HA [auth 1]
IA [auth 1]
RC [auth 4]
SC [auth 4]
VB [auth 3]
HA [auth 1],
IA [auth 1],
RC [auth 4],
SC [auth 4],
VB [auth 3],
WB [auth 3]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
VG [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.337 
  • R-Value Observed: 0.338 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.881α = 90
b = 100.506β = 91.73
c = 191.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael569/17
Israel Science FoundationIsrael2716/17

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2020-03-25
    Changes: Database references
  • Version 2.0: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary