6K61 | pdb_00006k61

Cryo-EM structure of the tetrameric photosystem I from a heterocyst-forming cyanobacterium Anabaena sp. PCC7120

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: HELICAL ARRAY 
  • 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

Structural and functional insights into the tetrameric photosystem I from heterocyst-forming cyanobacteria.

Zheng, L., Li, Y., Li, X., Zhong, Q., Li, N., Zhang, K., Zhang, Y., Chu, H., Ma, C., Li, G., Zhao, J., Gao, N.

(2019) Nat Plants 5: 1087-1097

  • DOI: https://doi.org/10.1038/s41477-019-0525-6
  • Primary Citation Related Structures: 
    6K61

  • PubMed Abstract: 

    Two large protein-cofactor complexes, photosystem I and photosystem II, are the central components of photosynthesis in the thylakoid membranes. Here, we report the 2.37-Å structure of a tetrameric photosystem I complex from a heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Four photosystem I monomers, organized in a dimer of dimer, form two distinct interfaces that are largely mediated by specifically orientated polar lipids, such as sulfoquinovosyl diacylglycerol. The structure depicts a more closely connected network of chlorophylls across monomer interfaces than those seen in trimeric PSI from thermophilic cyanobacteria, possibly allowing a more efficient energy transfer between monomers. Our physiological data also revealed a functional link of photosystem I oligomerization to cyclic electron flow and thylakoid membrane organization.

    • Organizational Affiliation: 
    • State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 733.16 kDa 
  • Atom Count: 49,283 
  • Modeled Residue Count: 4,542 
  • Deposited Residue Count: 4,752 
  • Unique protein chains: 12

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
M [auth a]		752Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P58576 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I 4.8 kDa proteinB [auth X],
N [auth x]		44Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58566 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2 1C [auth B],
O [auth b]		741Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P58565 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerD [auth C],
P [auth c]		81Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A410 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIE [auth D],
Q [auth d]		139Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58573 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVF [auth E],
R [auth e]		70Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58575 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIG [auth F],
S [auth f]		164Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58564 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J],
T [auth j]		49Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58568 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 1I [auth K],
U [auth k]		86Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58583 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIJ [auth I],
V [auth i]		46Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58560 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIK [auth L],
W [auth l]		172Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58577 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIL [auth M],
X [auth m]		32Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8YNB0 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
(Subject of Investigation/LOI)

Query on CLA


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AD [auth B]
AF [auth a]
AG [auth a]
AA [auth A],
AB [auth A],
AD [auth B],
AF [auth a],
AG [auth a],
AH [auth b],
AI [auth b],
AJ [auth f],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BF [auth a],
BG [auth a],
BH [auth b],
BI [auth b],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CF [auth a],
CG [auth a],
CH [auth b],
CI [auth b],
CJ [auth j],
DA [auth A],
DB [auth A],
DD [auth B],
DE [auth F],
DF [auth a],
DG [auth a],
DH [auth b],
DI [auth b],
DJ [auth j],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EF [auth a],
EG [auth a],
EH [auth b],
EI [auth b],
EJ [auth j],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FE [auth F],
FF [auth a],
FG [auth a],
FH [auth b],
FI [auth b],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GF [auth a],
GG [auth a],
GH [auth b],
GI [auth b],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth J],
HF [auth a],
HG [auth a],
HH [auth b],
HI [auth b],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth J],
IF [auth a],
IG [auth a],
IH [auth b],
II [auth b],
IJ [auth k],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth a],
JG [auth a],
JH [auth b],
JI [auth b],
JJ [auth k],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KF [auth a],
KG [auth a],
KH [auth b],
KI [auth b],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LF [auth a],
LH [auth b],
LI [auth b],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth K],
MF [auth a],
MH [auth b],
MI [auth b],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth K],
NF [auth a],
NH [auth b],
NI [auth b],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OF [auth a],
OH [auth b],
PA [auth A],
PC [auth B],
PD [auth B],
PF [auth a],
PH [auth b],
QA [auth A],
QC [auth B],
QD [auth B],
QF [auth a],
QH [auth b],
QJ [auth l],
RA [auth A],
RC [auth B],
RD [auth B],
RE [auth L],
RF [auth a],
RH [auth b],
RJ [auth l],
SA [auth A],
SC [auth B],
SE [auth L],
SF [auth a],
SH [auth b],
SJ [auth l],
TA [auth A],
TC [auth B],
TE [auth L],
TF [auth a],
TH [auth b],
UA [auth A],
UC [auth B],
UF [auth a],
UH [auth b],
VA [auth A],
VC [auth B],
VF [auth a],
VG [auth x],
VH [auth b],
VJ [auth m],
WA [auth A],
WC [auth B],
WF [auth a],
WH [auth b],
XA [auth A],
XC [auth B],
XE [auth a],
XF [auth a],
XH [auth b],
YA [auth A],
YC [auth B],
YE [auth a],
YF [auth a],
YG [auth b],
YH [auth b],
YI [auth f],
Z [auth A],
ZA [auth A],
ZB [auth X],
ZC [auth B],
ZE [auth a],
ZF [auth a],
ZG [auth b],
ZH [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
(Subject of Investigation/LOI)

Query on CL0


Download:Ideal Coordinates CCD File
WE [auth a],
Y [auth A]		CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
SQD
(Subject of Investigation/LOI)

Query on SQD


Download:Ideal Coordinates CCD File
AC [auth X],
PJ [auth l],
WG [auth x],
XG [auth b]		1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
(Subject of Investigation/LOI)

Query on LMG


Download:Ideal Coordinates CCD File
DC [auth B],
VI [auth b],
ZD [auth B]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG


Download:Ideal Coordinates CCD File
CE [auth F]
NJ [auth i]
TG [auth a]
UG [auth a]
XB [auth A]
CE [auth F],
NJ [auth i],
TG [auth a],
UG [auth a],
XB [auth A],
YB [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
(Subject of Investigation/LOI)

Query on BCR


Download:Ideal Coordinates CCD File
BJ [auth f]
EE [auth F]
FJ [auth j]
GE [auth F]
GJ [auth j]
BJ [auth f],
EE [auth F],
FJ [auth j],
GE [auth F],
GJ [auth j],
HJ [auth j],
JE [auth J],
KE [auth J],
KJ [auth k],
LE [auth J],
LJ [auth i],
MJ [auth i],
NG [auth a],
OE [auth K],
OG [auth a],
OJ [auth l],
PE [auth I],
PG [auth a],
PI [auth b],
QE [auth I],
QG [auth a],
QI [auth b],
RB [auth A],
RG [auth a],
RI [auth b],
SB [auth A],
SG [auth a],
SI [auth b],
TB [auth A],
TD [auth B],
TI [auth b],
TJ [auth l],
UB [auth A],
UD [auth B],
UE [auth L],
UI [auth b],
UJ [auth l],
VB [auth A],
VD [auth B],
VE [auth M],
WB [auth A],
WD [auth B],
WJ [auth m],
XD [auth B],
YD [auth B],
ZI [auth f]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
(Subject of Investigation/LOI)

Query on PQN


Download:Ideal Coordinates CCD File
LG [auth a],
OI [auth b],
PB [auth A],
SD [auth B]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
(Subject of Investigation/LOI)

Query on SF4


Download:Ideal Coordinates CCD File
AE [auth C]
BE [auth C]
MG [auth a]
QB [auth A]
WI [auth c]
AE [auth C],
BE [auth C],
MG [auth a],
QB [auth A],
WI [auth c],
XI [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (China)--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 2.0: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description