6YXR | pdb_00006yxr

Dunaliella Minimal Photosystem I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history

Literature

Structure and energy transfer pathways of the Dunaliella Salina photosystem I supercomplex.

Caspy, I.Malavath, T.Klaiman, D.Fadeeva, M.Shkolnisky, Y.Nelson, N.

(2020) Biochim Biophys Acta Bioenerg 1861: 148253-148253

  • DOI: https://doi.org/10.1016/j.bbabio.2020.148253
  • Primary Citation Related Structures: 
    6SL5, 6YXR

  • PubMed Abstract: 

    Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained for the complexes that were isolated from various organisms, ranging from cyanobacteria to plants. These complexes are all evolutionarily linked. In this paper, the researchers have uncovered the increased complexity of PSI in a single organism demonstrated by the coexistance of two distinct PSI compositions. The Large Dunaliella PSI contains eight additional subunits, six in PSI core and two light harvesting complexes. Two additional chlorophyll a molecules pertinent for efficient excitation energy transfer in state II transition were identified in PsaL and PsaO. Short distances between these newly identified chlorophylls correspond with fast excitation transfer rates previously reported during state II transition. The apparent PSI conformations could be a coping mechanism for the high salinity.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

Macromolecule Content 

  • Total Structure Weight: 466.24 kDa 
  • Atom Count: 31,910 
  • Modeled Residue Count: 2,783 
  • Deposited Residue Count: 2,783 
  • Unique protein chains: 11

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth 1]197Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for C1K003 (Dunaliella salina)
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Go to UniProtKB:  C1K003
Entity Groups
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UniProt GroupC1K003
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca2B [auth 2]208Dunaliella salinaMutation(s): 0 
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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)
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Go to UniProtKB:  C1K004
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UniProt GroupC1K004
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca4D [auth 4]211Dunaliella salinaMutation(s): 0 
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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)
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UniProt GroupD0FXV2
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]730Dunaliella salinaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for D0FXZ0 (Dunaliella salina)
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UniProt GroupD0FXZ0
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Reference Sequence
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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)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaDH [auth D]141Dunaliella salinaMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaEI [auth E]64Dunaliella salinaMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaFJ [auth F]163Dunaliella salinaMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXK [auth J]40Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXW0 (Dunaliella salina)
Explore D0FXW0 
Go to UniProtKB:  D0FXW0
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UniProt GroupD0FXW0
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Reference Sequence

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
MG [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL



Download:Ideal Coordinates CCD File
FB [auth 3]
FC [auth 4]
GC [auth 4]
IC [auth 4]
OA [auth 2]
FB [auth 3],
FC [auth 4],
GC [auth 4],
IC [auth 4],
OA [auth 2],
PA [auth 2],
QA [auth 2],
SA [auth 2],
W [auth 1],
X [auth 1]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth 1]
AC [auth 4]
AD [auth A]
AE [auth A]
AF [auth B]
AA [auth 1],
AC [auth 4],
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],
CC [auth 4],
CD [auth A],
CE [auth A],
CF [auth B],
CG [auth B],
DB [auth 3],
DC [auth 4],
DD [auth A],
DF [auth B],
DG [auth B],
EB [auth 3],
EC [auth 4],
ED [auth A],
EF [auth B],
FD [auth A],
FF [auth B],
GA [auth 2],
GB [auth 3],
GD [auth A],
GF [auth B],
HA [auth 2],
HB [auth 3],
HC [auth 4],
HD [auth A],
HF [auth B],
IA [auth 2],
IB [auth 3],
ID [auth A],
IF [auth B],
JA [auth 2],
JB [auth 3],
JC [auth 4],
JD [auth A],
JF [auth B],
KA [auth 2],
KB [auth 3],
KD [auth A],
KF [auth B],
LA [auth 2],
LB [auth 3],
LD [auth A],
LF [auth B],
MA [auth 2],
MB [auth 3],
MC [auth A],
MD [auth A],
MF [auth B],
NA [auth 2],
NB [auth 3],
NC [auth A],
ND [auth A],
NF [auth B],
O [auth 1],
OB [auth 3],
OC [auth A],
OD [auth A],
OE [auth B],
OF [auth B],
P [auth 1],
PB [auth 3],
PC [auth A],
PD [auth A],
PE [auth B],
PF [auth B],
Q [auth 1],
QB [auth 3],
QC [auth A],
QD [auth A],
QE [auth B],
QF [auth B],
QG [auth F],
R [auth 1],
RA [auth 2],
RC [auth A],
RD [auth A],
RE [auth B],
RF [auth B],
RG [auth F],
S [auth 1],
SC [auth A],
SD [auth A],
SE [auth B],
SF [auth B],
T [auth 1],
TA [auth 2],
TC [auth A],
TD [auth A],
TE [auth B],
TF [auth B],
U [auth 1],
UC [auth A],
UD [auth A],
UE [auth B],
UF [auth B],
UG [auth J],
V [auth 1],
VC [auth A],
VD [auth A],
VE [auth B],
VF [auth B],
WB [auth 4],
WC [auth A],
WD [auth A],
WE [auth B],
WF [auth B],
XB [auth 4],
XC [auth A],
XD [auth A],
XE [auth B],
XF [auth B],
Y [auth 1],
YB [auth 4],
YC [auth A],
YD [auth A],
YE [auth B],
YF [auth B],
Z [auth 1],
ZB [auth 4],
ZC [auth A],
ZD [auth A],
ZE [auth B],
ZF [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0



Download:Ideal Coordinates CCD File
LC [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
KC [auth 4],
NG [auth B],
VA [auth 2],
WA [auth 2],
XA [auth 2]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
CA [auth 1]
LG [auth B]
ME [auth A]
NE [auth A]
RB [auth 3]
CA [auth 1],
LG [auth B],
ME [auth A],
NE [auth A],
RB [auth 3],
UA [auth 2]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH

Query on 3PH



Download:Ideal Coordinates CCD File
SB [auth 3]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
XAT

Query on XAT



Download:Ideal Coordinates CCD File
EA [auth 2],
M [auth 1],
UB [auth 4],
ZA [auth 3]
(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
DA [auth 2],
L [auth 1],
TB [auth 4],
YA [auth 3]
(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
AB [auth 3]
BB [auth 3]
CB [auth 3]
FA [auth 2]
FE [auth A]
AB [auth 3],
BB [auth 3],
CB [auth 3],
FA [auth 2],
FE [auth A],
FG [auth B],
GE [auth A],
GG [auth B],
HE [auth A],
HG [auth B],
IE [auth A],
IG [auth B],
JE [auth A],
JG [auth B],
KE [auth A],
KG [auth B],
LE [auth A],
N [auth 1],
SG [auth F],
TG [auth F],
VB [auth 4],
VG [auth J],
WG [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
DE [auth A],
EG [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
EE [auth A],
OG [auth C],
PG [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0.7

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael569/17
European Research Council (ERC)Belgium723991

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 2.0: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary