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 7Y3F | pdb_00007y3f

Structure of the Anabaena PSI-monomer-IsiA supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history. 

Literature

Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120.

Nagao, R., Kato, K., Hamaguchi, T., Ueno, Y., Tsuboshita, N., Shimizu, S., Furutani, M., Ehira, S., Nakajima, Y., Kawakami, K., Suzuki, T., Dohmae, N., Akimoto, S., Yonekura, K., Shen, J.R.

(2023) Nat Commun 14: 920-920

  • DOI: https://doi.org/10.1038/s41467-023-36504-1
  • Primary Citation Related Structures: 
    7Y3F

  • PubMed Abstract: 

    Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.


  • Organizational Affiliation: 
    • Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan. nagao.ryo@shizuoka.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 617.16 kDa 
  • Atom Count: 39,463 
  • Modeled Residue Count: 4,112 
  • Deposited Residue Count: 4,347 
  • Unique protein chains: 14

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1752Nostoc sp.Mutation(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))
Explore P58576 
Go to UniProtKB:  P58576
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UniProt GroupP58576
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2 1741Nostoc sp.Mutation(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))
Explore P58565 
Go to UniProtKB:  P58565
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UniProt GroupP58565
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Nostoc sp.Mutation(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))
Explore P0A410 
Go to UniProtKB:  P0A410
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UniProt GroupP0A410
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II139Nostoc sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58573 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P58573 
Go to UniProtKB:  P58573
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UniProt GroupP58573
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV70Nostoc sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58575 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P58575 
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UniProt GroupP58575
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III164Nostoc sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58564 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P58564 
Go to UniProtKB:  P58564
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UniProt GroupP58564
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]46Nostoc sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58560 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P58560 
Go to UniProtKB:  P58560
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UniProt GroupP58560
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]49Nostoc sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58568 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P58568 
Go to UniProtKB:  P58568
Entity Groups
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UniProt GroupP58568
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
UnknownI [auth K]82Nostoc sp.Mutation(s): 0 
Sequence Annotations
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaMJ [auth M]40Nostoc sp.Mutation(s): 0 
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I 4.8 kDa proteinK [auth X]44Nostoc sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P58566 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P58566 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIL [auth 1]476Nostoc sp.Mutation(s): 0 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
IsiAM [auth 2],
N [auth 3],
Q [auth 6]
325Nostoc sp.Mutation(s): 0 
Sequence Annotations
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Iron stress-induced chlorophyll-binding proteinO [auth 4],
P [auth 5]
344Nostoc sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8YQ35 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YQ35 
Go to UniProtKB:  Q8YQ35
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AF [auth 1]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AF [auth 1],
AG [auth 4],
AH [auth 5],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BF [auth 1],
BG [auth 4],
BH [auth 6],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CG [auth 4],
CH [auth 6],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth J],
DG [auth 4],
DH [auth 6],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth J],
EG [auth 4],
EH [auth 6],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FF [auth 1],
FH [auth 6],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GF [auth 1],
GH [auth 6],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth K],
HF [auth 1],
HG [auth 5],
HH [auth 6],
IA [auth A],
IC [auth B],
IG [auth 5],
IH [auth 6],
JA [auth A],
JC [auth B],
JE [auth K],
JG [auth 5],
JH [auth 6],
KA [auth A],
KC [auth B],
KG [auth 5],
LA [auth A],
LC [auth B],
LF [auth 1],
LG [auth 5],
MA [auth A],
MC [auth B],
ME [auth X],
MF [auth 1],
MG [auth 5],
NA [auth A],
NC [auth B],
NE [auth 1],
NF [auth 2],
NG [auth 5],
OA [auth A],
OC [auth B],
OE [auth 1],
OF [auth 2],
OG [auth 5],
PA [auth A],
PC [auth B],
PE [auth 1],
PF [auth 2],
PG [auth 5],
QA [auth A],
QC [auth B],
QE [auth 1],
QF [auth 2],
QG [auth 5],
RA [auth A],
RC [auth B],
RE [auth 1],
RF [auth 2],
RG [auth 5],
S [auth A],
SA [auth A],
SC [auth B],
SE [auth 1],
SF [auth 2],
SG [auth 5],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
TE [auth 1],
TF [auth 3],
TG [auth 5],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
UE [auth 1],
UG [auth 5],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VE [auth 1],
VF [auth 4],
VG [auth 5],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WD [auth F],
WE [auth 1],
WF [auth 4],
WG [auth 5],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XE [auth 1],
XF [auth 4],
XG [auth 5],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YE [auth 1],
YF [auth 4],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth F],
ZE [auth 1],
ZF [auth 4],
ZG [auth 5]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0



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

Query on LMG



Download:Ideal Coordinates CCD File
PD [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
QB [auth A],
QD [auth B],
RB [auth A],
YD [auth F]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AE [auth F]
BE [auth I]
CE [auth I]
CF [auth 1]
DF [auth 1]
AE [auth F],
BE [auth I],
CE [auth I],
CF [auth 1],
DF [auth 1],
EF [auth 1],
FE [auth J],
GE [auth J],
GG [auth 5],
IE [auth K],
IF [auth 1],
JD [auth B],
JF [auth 1],
KB [auth A],
KD [auth B],
LB [auth A],
LD [auth B],
LE [auth M],
MB [auth A],
MD [auth B],
NB [auth A],
ND [auth B],
OB [auth A],
OD [auth B],
PB [auth A],
TD [auth B],
UF [auth 4],
XD [auth F],
YG [auth 5]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
FG [auth 5]
KE [auth M]
KF [auth 1]
RD [auth B]
SB [auth A]
FG [auth 5],
KE [auth M],
KF [auth 1],
RD [auth B],
SB [auth A],
SD [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN



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

Query on SF4



Download:Ideal Coordinates CCD File
JB [auth A],
UD [auth C],
VD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UNK
Query on UNK
I [auth K]L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTREFMAC5.8.0267
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP20H02914

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 2.0: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2026-09-16
    Changes: Data collection, Structure summary
  • Version 2.2: 2026-09-23
    Changes: Data collection