7Y3F

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


This is version 1.0 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58576
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58565
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A410
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58573
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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 
Go to UniProtKB:  P58575
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58575
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58564
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58560
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58568
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
UnknownI [auth K]82Nostoc sp.Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PsaMJ [auth M]40Nostoc sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8YNB0 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YNB0 
Go to UniProtKB:  Q8YNB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YNB0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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 
Go to UniProtKB:  P58566
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58566
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIL [auth 1]476Nostoc sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8YQ34 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YQ34 
Go to UniProtKB:  Q8YQ34
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YQ34
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
IsiAM [auth 2],
N [auth 3],
Q [auth 6]
325Nostoc sp.Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YQ35
Sequence Annotations
Expand
  • 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
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