7F4V | pdb_00007f4v

Cryo-EM structure of a primordial cyanobacterial photosystem I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI

Kato, K.Hamaguchi, T.Nagao, R.Kawakami, K.Ueno, Y.Suzuki, T.Uchida, H.Murakami, A.Nakajima, Y.Yokono, M.Akimoto, S.Dohmae, N.Yonekura, K.Shen, J.R.

(2022) bioRxiv 

Macromolecule Content 

  • Total Structure Weight: 1,067.07 kDa 
  • Atom Count: 67,641 
  • Modeled Residue Count: 6,435 
  • Deposited Residue Count: 7,125 
  • Unique protein chains: 10

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth aA],
K [auth bA],
U [auth cA]
783Gloeobacter violaceus PCC 7421Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q7NFT6 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NFT6 
Go to UniProtKB:  Q7NFT6
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UniProt GroupQ7NFT6
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth aB],
L [auth bB],
V [auth cB]
872Gloeobacter violaceus PCC 7421Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q7NFT5 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC [auth aC],
M [auth bC],
W [auth cC]
81Gloeobacter violaceus PCC 7421Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q7NG86 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID [auth aD],
N [auth bD],
X [auth cD]
144Gloeobacter violaceus PCC 7421Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7NF26 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVE [auth aE],
O [auth bE],
Y [auth cE]
65Gloeobacter violaceus PCC 7421Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7NFW6 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NFW6 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIF [auth aF],
P [auth bF],
Z [auth cF]
181Gloeobacter violaceus PCC 7421Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7NH05 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit ZAA [auth cI],
G [auth aI],
Q [auth bI]
35Gloeobacter violaceus PCC 7421Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C029 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown proteinBA [auth cJ],
H [auth aJ],
R [auth bJ]
33Gloeobacter violaceus PCC 7421Mutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XICA [auth cL],
I [auth aL],
S [auth bL]
147Gloeobacter violaceus PCC 7421Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7NIE7 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIDA [auth cM],
J [auth aM],
T [auth bM]
34Gloeobacter violaceus PCC 7421Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7NHY3 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NHY3 
Go to UniProtKB:  Q7NHY3
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AB [auth aA]
AD [auth aB]
AF [auth bA]
AG [auth bA]
AH [auth bB]
AB [auth aA],
AD [auth aB],
AF [auth bA],
AG [auth bA],
AH [auth bB],
AI [auth bB],
AK [auth cA],
AM [auth cB],
BB [auth aA],
BD [auth aB],
BF [auth bA],
BG [auth bA],
BH [auth bB],
BI [auth bB],
BJ [auth bL],
BK [auth cA],
BM [auth cB],
CB [auth aA],
CD [auth aB],
CE [auth aB],
CF [auth bA],
CG [auth bA],
CH [auth bB],
CI [auth bB],
CJ [auth bL],
CK [auth cA],
CM [auth cB],
DB [auth aA],
DD [auth aB],
DE [auth aB],
DF [auth bA],
DG [auth bA],
DH [auth bB],
DI [auth bB],
DJ [auth bL],
DK [auth cA],
DM [auth cB],
EB [auth aA],
ED [auth aB],
EF [auth bA],
EG [auth bA],
EH [auth bB],
EI [auth bB],
EK [auth cA],
EM [auth cB],
EN [auth cB],
FA [auth aA],
FB [auth aA],
FC [auth aA],
FD [auth aB],
FF [auth bA],
FG [auth bA],
FH [auth bB],
FI [auth bB],
FK [auth cA],
FM [auth cB],
GA [auth aA],
GB [auth aA],
GC [auth aB],
GD [auth aB],
GF [auth bA],
GG [auth bA],
GH [auth bB],
GI [auth bB],
GK [auth cA],
GM [auth cB],
HA [auth aA],
HB [auth aA],
HC [auth aB],
HD [auth aB],
HE [auth aF],
HF [auth bA],
HG [auth bA],
HH [auth bB],
HK [auth cA],
HL [auth cA],
HM [auth cB],
IA [auth aA],
IB [auth aA],
IC [auth aB],
ID [auth aB],
IF [auth bA],
IG [auth bA],
IH [auth bB],
IJ [auth cA],
IK [auth cA],
IL [auth cB],
IM [auth cB],
IN [auth cF],
JA [auth aA],
JB [auth aA],
JC [auth aB],
JD [auth aB],
JF [auth bA],
JG [auth bA],
JH [auth bB],
JJ [auth cA],
JK [auth cA],
JL [auth cB],
JM [auth cB],
KA [auth aA],
KB [auth aA],
KC [auth aB],
KD [auth aB],
KF [auth bA],
KH [auth bB],
KJ [auth cA],
KK [auth cA],
KL [auth cB],
KM [auth cB],
LA [auth aA],
LB [auth aA],
LC [auth aB],
LD [auth aB],
LF [auth bA],
LH [auth bB],
LJ [auth cA],
LK [auth cA],
LL [auth cB],
LM [auth cB],
MA [auth aA],
MB [auth aA],
MC [auth aB],
MD [auth aB],
MF [auth bA],
MH [auth bB],
MJ [auth cA],
MK [auth cA],
ML [auth cB],
MM [auth cB],
NA [auth aA],
NB [auth aA],
NC [auth aB],
ND [auth aB],
NE [auth aL],
NF [auth bA],
NH [auth bB],
NJ [auth cA],
NK [auth cA],
NL [auth cB],
NM [auth cB],
OA [auth aA],
OB [auth aA],
OC [auth aB],
OD [auth aB],
OE [auth aL],
OF [auth bA],
OH [auth bB],
OJ [auth cA],
OK [auth cA],
OL [auth cB],
OM [auth cB],
ON [auth cL],
PA [auth aA],
PB [auth aA],
PC [auth aB],
PD [auth aB],
PE [auth aL],
PF [auth bA],
PH [auth bB],
PJ [auth cA],
PK [auth cA],
PL [auth cB],
PM [auth cB],
PN [auth cL],
QA [auth aA],
QB [auth aA],
QC [auth aB],
QD [auth aB],
QF [auth bA],
QH [auth bB],
QI [auth bB],
QJ [auth cA],
QK [auth cA],
QL [auth cB],
QM [auth cB],
QN [auth cL],
RA [auth aA],
RB [auth aA],
RC [auth aB],
RD [auth aB],
RF [auth bA],
RH [auth bB],
RI [auth bB],
RJ [auth cA],
RK [auth cA],
RL [auth cB],
RM [auth cB],
SA [auth aA],
SB [auth aA],
SC [auth aB],
SD [auth aB],
SF [auth bA],
SH [auth bB],
SJ [auth cA],
SK [auth cA],
SL [auth cB],
SM [auth cB],
TA [auth aA],
TB [auth aA],
TC [auth aB],
TF [auth bA],
TG [auth bA],
TH [auth bB],
TJ [auth cA],
TK [auth cA],
TL [auth cB],
TM [auth cB],
UA [auth aA],
UB [auth aA],
UC [auth aB],
UE [auth bA],
UF [auth bA],
UG [auth bB],
UH [auth bB],
UJ [auth cA],
UK [auth cA],
UL [auth cB],
UM [auth cB],
VA [auth aA],
VB [auth aA],
VC [auth aB],
VE [auth bA],
VF [auth bA],
VG [auth bB],
VH [auth bB],
VI [auth bF],
VJ [auth cA],
VK [auth cA],
VL [auth cB],
WA [auth aA],
WC [auth aB],
WE [auth bA],
WF [auth bA],
WG [auth bB],
WH [auth bB],
WJ [auth cA],
WK [auth cA],
WL [auth cB],
XA [auth aA],
XC [auth aB],
XE [auth bA],
XF [auth bA],
XG [auth bB],
XH [auth bB],
XJ [auth cA],
XK [auth cA],
XL [auth cB],
YA [auth aA],
YC [auth aB],
YE [auth bA],
YF [auth bA],
YG [auth bB],
YH [auth bB],
YJ [auth cA],
YL [auth cB],
ZA [auth aA],
ZC [auth aB],
ZE [auth bA],
ZF [auth bA],
ZG [auth bB],
ZH [auth bB],
ZJ [auth cA],
ZL [auth cB]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0



Download:Ideal Coordinates CCD File
EA [auth aA],
HJ [auth cA],
TE [auth bA]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
AE [auth aB],
CN [auth cB],
OI [auth bB]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
BE [auth aB]
DC [auth aA]
DN [auth cB]
EC [auth aA]
FL [auth cA]
BE [auth aB],
DC [auth aA],
DN [auth cB],
EC [auth aA],
FL [auth cA],
GL [auth cA],
PI [auth bB],
RG [auth bA],
SG [auth bA]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AC [auth aA]
AJ [auth bL]
AL [auth cA]
AN [auth cB]
BC [auth aA]
AC [auth aA],
AJ [auth bL],
AL [auth cA],
AN [auth cB],
BC [auth aA],
BL [auth cA],
BN [auth cB],
CC [auth aA],
CL [auth cA],
DL [auth cA],
EJ [auth bL],
EL [auth cA],
FJ [auth bL],
GE [auth aF],
GJ [auth bM],
HN [auth cF],
IE [auth aF],
II [auth bB],
JE [auth aF],
JI [auth bB],
JN [auth cF],
KE [auth aI],
KI [auth bB],
KN [auth cF],
LE [auth aJ],
LI [auth bB],
LN [auth cI],
ME [auth aL],
MG [auth bA],
MI [auth bB],
MN [auth cJ],
NG [auth bA],
NI [auth bB],
NN [auth cL],
OG [auth bA],
PG [auth bA],
QE [auth aL],
QG [auth bA],
RE [auth aL],
RN [auth cL],
SE [auth aM],
SN [auth cL],
TN [auth cM],
UD [auth aB],
UI [auth bF],
VD [auth aB],
WD [auth aB],
WI [auth bF],
WM [auth cB],
XD [auth aB],
XI [auth bF],
XM [auth cB],
YB [auth aA],
YD [auth aB],
YI [auth bI],
YM [auth cB],
ZB [auth aA],
ZD [auth aB],
ZI [auth bJ],
ZM [auth cB]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
1L3

Query on 1L3



Download:Ideal Coordinates CCD File
HI [auth bB]
KG [auth bA]
TD [auth aB]
VM [auth cB]
WB [auth aA]
HI [auth bB],
KG [auth bA],
TD [auth aB],
VM [auth cB],
WB [auth aA],
YK [auth cA]
Menaquinone-4
C31 H40 O2
DKHGMERMDICWDU-GHDNBGIDSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
EE [auth aC]
FE [auth aC]
FN [auth cC]
GN [auth cC]
LG [auth bA]
EE [auth aC],
FE [auth aC],
FN [auth cC],
GN [auth cC],
LG [auth bA],
SI [auth bC],
TI [auth bC],
XB [auth aA],
ZK [auth cA]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13_2998
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary