6SL5 | pdb_00006sl5

Dunaliella Photosystem I Supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 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: 644.18 kDa 
  • Atom Count: 43,789 
  • Modeled Residue Count: 3,744 
  • Deposited Residue Count: 3,745 
  • Unique protein chains: 19

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1740Dunaliella 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
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2733Dunaliella 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
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Dunaliella 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
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaD144Dunaliella salinaMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaE64Dunaliella salinaMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaF162Dunaliella salinaMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXG [auth J]41Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXW0 (Dunaliella salina)
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Go to UniProtKB:  D0FXW0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0FXW0
Sequence Annotations
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaGH [auth G]101Dunaliella salinaMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaHI [auth H]92Dunaliella salinaMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaIJ [auth I]39Dunaliella salinaMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaK84Dunaliella salinaMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaL155Dunaliella salinaMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaOM [auth O]86Dunaliella salinaMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 1]197Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for C1K003 (Dunaliella salina)
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Entity Groups
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UniProt GroupC1K003
Sequence Annotations
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca2O [auth 2]208Dunaliella salinaMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticP [auth 3]228Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for C1K004 (Dunaliella salina)
Explore C1K004 
Go to UniProtKB:  C1K004
Entity Groups
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UniProt GroupC1K004
Sequence Annotations
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca4Q [auth 4]211Dunaliella salinaMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca5R [auth 5]202Dunaliella salinaMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca6S [auth 6]178Dunaliella salinaMutation(s): 0 

Small Molecules

Ligands 20 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
GI [auth 3],
HH [auth 2],
HI [auth 3],
XD [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL



Download:Ideal Coordinates CCD File
AG [auth 1]
AH [auth 2]
AJ [auth 4]
RK [auth 6]
SH [auth 3]
AG [auth 1],
AH [auth 2],
AJ [auth 4],
RK [auth 6],
SH [auth 3],
TJ [auth 5],
UJ [auth 5],
WG [auth 2],
XG [auth 2],
XI [auth 4],
YG [auth 2],
YI [auth 4],
ZF [auth 1]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AI [auth 3]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AI [auth 3],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BF [auth L],
BG [auth 1],
BH [auth 2],
BI [auth 3],
BJ [auth 4],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CF [auth L],
CG [auth 1],
CI [auth 3],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth F],
DF [auth L],
DG [auth 1],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth F],
EF [auth L],
EG [auth 1],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IK [auth 6],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth O],
JK [auth 6],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KE [auth J],
KF [auth O],
KK [auth 6],
LA [auth A],
LC [auth B],
LD [auth B],
LF [auth O],
LJ [auth 5],
LK [auth 6],
MA [auth A],
MC [auth B],
MD [auth B],
MJ [auth 5],
MK [auth 6],
NA [auth A],
NC [auth B],
ND [auth B],
NE [auth G],
NJ [auth 5],
NK [auth 6],
OA [auth A],
OC [auth B],
OD [auth B],
OE [auth G],
OG [auth 2],
OI [auth 4],
OJ [auth 5],
OK [auth 6],
PA [auth A],
PC [auth B],
PE [auth G],
PG [auth 2],
PH [auth 3],
PI [auth 4],
PJ [auth 5],
PK [auth 6],
QA [auth A],
QC [auth B],
QG [auth 2],
QH [auth 3],
QI [auth 4],
QJ [auth 5],
QK [auth 6],
RA [auth A],
RC [auth B],
RE [auth H],
RF [auth 1],
RG [auth 2],
RH [auth 3],
RI [auth 4],
RJ [auth 5],
SA [auth A],
SC [auth B],
SE [auth H],
SF [auth 1],
SG [auth 2],
SI [auth 4],
SJ [auth 5],
SK [auth 6],
TA [auth A],
TC [auth B],
TF [auth 1],
TG [auth 2],
TH [auth 3],
TI [auth 4],
TK [auth 6],
U [auth A],
UA [auth A],
UC [auth B],
UF [auth 1],
UG [auth 2],
UH [auth 3],
UI [auth 4],
V [auth A],
VA [auth A],
VC [auth B],
VF [auth 1],
VG [auth 2],
VH [auth 3],
VI [auth 4],
VJ [auth 5],
W [auth A],
WA [auth A],
WC [auth B],
WE [auth K],
WF [auth 1],
WH [auth 3],
WI [auth 4],
WJ [auth 5],
X [auth A],
XA [auth A],
XC [auth B],
XE [auth K],
XF [auth 1],
XH [auth 3],
XJ [auth 5],
Y [auth A],
YA [auth A],
YC [auth B],
YE [auth K],
YF [auth 1],
YH [auth 3],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZE [auth K],
ZG [auth 2],
ZH [auth 3],
ZI [auth 4]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0



Download:Ideal Coordinates CCD File
T [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
4RF

Query on 4RF



Download:Ideal Coordinates CCD File
CK [auth 5],
HF [auth L]
Tripalmitoylglycerol
C51 H98 O6
PVNIQBQSYATKKL-UHFFFAOYSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
GH [auth 2],
II [auth 3],
WK [auth 6]
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
DJ [auth 4]
EI [auth 3]
EJ [auth 4]
FH [auth 2]
FI [auth 3]
DJ [auth 4],
EI [auth 3],
EJ [auth 4],
FH [auth 2],
FI [auth 3],
IE [auth F],
IG [auth 1],
VK [auth 6]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LMK

Query on LMK



Download:Ideal Coordinates CCD File
GJ [auth 4],
IH [auth 2]
trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium
C46 H94 N O7
BUXLRCGOLVGJEI-LHQLQFMZSA-O
PTY

Query on PTY



Download:Ideal Coordinates CCD File
AK [auth 5]
FJ [auth 4]
IF [auth L]
JG [auth 1]
JI [auth 3]
AK [auth 5],
FJ [auth 4],
IF [auth L],
JG [auth 1],
JI [auth 3],
KG [auth 1],
KI [auth 3],
NF [auth O],
XK [auth 6]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
CH [auth 2]
CJ [auth 4]
DH [auth 2]
DI [auth 3]
EH [auth 2]
CH [auth 2],
CJ [auth 4],
DH [auth 2],
DI [auth 3],
EH [auth 2],
FG [auth 1],
GG [auth 1],
HE [auth F],
HG [auth 1],
UB [auth A],
UK [auth 6],
VB [auth A],
WD [auth B],
YJ [auth 5],
ZJ [auth 5]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
P3H

Query on P3H



Download:Ideal Coordinates CCD File
DK [auth 5],
JH [auth 2]
[(2~{R})-1-nonanoyloxy-3-[oxidanyl-[(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z})-heptadeca-5,8-dienoate
C35 H63 O13 P
YESDZPSNSSEMJX-BCWHKXFCSA-N
3PH

Query on 3PH



Download:Ideal Coordinates CCD File
BK [auth 5],
EK [auth 5],
JE [auth F],
YD [auth B]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
XAT

Query on XAT



Download:Ideal Coordinates CCD File
GK [auth 6]
HK [auth 6]
LH [auth 3]
MG [auth 2]
MI [auth 4]
GK [auth 6],
HK [auth 6],
LH [auth 3],
MG [auth 2],
MI [auth 4],
PF [auth 1]
(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
FK [auth 6]
HJ [auth 5]
IJ [auth 5]
JJ [auth 5]
KH [auth 3]
FK [auth 6],
HJ [auth 5],
IJ [auth 5],
JJ [auth 5],
KH [auth 3],
KJ [auth 5],
LG [auth 2],
LI [auth 4],
OF [auth 1]
(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
AF [auth K]
FE [auth F]
FF [auth L]
GE [auth F]
GF [auth L]
AF [auth K],
FE [auth F],
FF [auth L],
GE [auth F],
GF [auth L],
LE [auth J],
ME [auth J],
MF [auth O],
MH [auth 3],
NB [auth A],
NG [auth 2],
NH [auth 3],
NI [auth 4],
OB [auth A],
OH [auth 3],
PB [auth A],
QB [auth A],
QD [auth B],
QE [auth G],
QF [auth 1],
RB [auth A],
RD [auth B],
SB [auth A],
SD [auth B],
TB [auth A],
TD [auth B],
TE [auth H],
UD [auth B],
UE [auth I],
VD [auth B],
VE [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU

Query on LMU



Download:Ideal Coordinates CCD File
XB [auth A],
YB [auth A],
YK [auth 6],
ZD [auth B]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN

Query on PQN



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

Query on SF4



Download:Ideal Coordinates CCD File
BE [auth C],
CE [auth C],
MB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
OCD

Query on OCD



Download:Ideal Coordinates CCD File
WB [auth A]octadecanal
C18 H36 O
FWWQKRXKHIRPJY-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AE [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
RECONSTRUCTIONRELION3

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: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 1.2: 2020-07-15
    Changes: Database references
  • Version 2.0: 2024-05-22
    Changes: Data collection, Database references, Derived calculations, Non-polymer description