6KMX

Structure of PSI from H. hongdechloris grown under far-red light condition


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis for the adaptation and function of chlorophyll f in photosystem I.

Kato, K.Shinoda, T.Nagao, R.Akimoto, S.Suzuki, T.Dohmae, N.Chen, M.Allakhverdiev, S.I.Shen, J.R.Akita, F.Miyazaki, N.Tomo, T.

(2020) Nat Commun 11: 238-238

  • DOI: https://doi.org/10.1038/s41467-019-13898-5
  • Primary Citation of Related Structures:  
    6KMW, 6KMX

  • PubMed Abstract: 

    Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth aA],
J [auth bA],
S [auth cA]
784Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HIN6 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HIN6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth aB],
K [auth bB],
T [auth cB]
743Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HIL0 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HIL0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC [auth aC],
L [auth bC],
U [auth cC]
81Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HPE3 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HPE3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID [auth aD],
M [auth bD],
V [auth cD]
142Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for A0A1Z3HHI7 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HHI7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVE [auth aE],
N [auth bE],
W [auth cE]
68Halomicronema hongdechloris C2206Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HI16 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HI16
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIF [auth aI],
O [auth bI],
X [auth cI]
63Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HIL5 (Halomicronema hongdechloris C2206)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKG [auth aK],
P [auth bK],
Y [auth cK]
96Halomicronema hongdechloris C2206Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HR36 (Halomicronema hongdechloris C2206)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIH [auth aL],
Q [auth bL],
Z [auth cL]
189Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HIQ7 (Halomicronema hongdechloris C2206)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIAA [auth cM],
I [auth aM],
R [auth bM]
31Halomicronema hongdechloris C2206Mutation(s): 0 
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6C
Query on F6C

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AB [auth aA]
AL [auth cA]
BB [auth aA]
EB [auth aA]
GB [auth aA]
AB [auth aA],
AL [auth cA],
BB [auth aA],
EB [auth aA],
GB [auth aA],
GE [auth aL],
HM [auth cB],
IK [auth cA],
JG [auth bA],
JK [auth cA],
MK [auth cA],
OK [auth cA],
PN [auth cL],
QH [auth bB],
RF [auth bA],
SB [auth aA],
SF [auth bA],
VF [auth bA],
XF [auth bA],
XI [auth bL],
ZC [auth aB]
Chlorophyll F
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
CLA
Query on CLA

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AD [auth aB]
AF [auth bA]
AG [auth bA]
AH [auth bB]
AI [auth bB]
AD [auth aB],
AF [auth bA],
AG [auth bA],
AH [auth bB],
AI [auth bB],
AJ [auth bL],
AK [auth cA],
AM [auth cB],
BD [auth aB],
BF [auth bA],
BG [auth bA],
BH [auth bB],
BI [auth bB],
BJ [auth bL],
BK [auth cA],
BM [auth cB],
CA [auth aA],
CB [auth aA],
CC [auth aB],
CD [auth aB],
CE [auth aK],
CF [auth bA],
CG [auth bA],
CH [auth bB],
CI [auth bB],
CK [auth cA],
CM [auth cB],
DA [auth aA],
DB [auth aA],
DC [auth aB],
DD [auth aB],
DF [auth bA],
DG [auth bA],
DH [auth bB],
DI [auth bB],
DK [auth cA],
DM [auth cB],
EA [auth aA],
EC [auth aB],
ED [auth aB],
EE [auth aK],
EF [auth bA],
EG [auth bA],
EH [auth bB],
EI [auth bB],
EK [auth cA],
EM [auth cB],
FA [auth aA],
FB [auth aA],
FC [auth aB],
FD [auth aB],
FF [auth bA],
FG [auth bA],
FH [auth bB],
FI [auth bB],
FK [auth cA],
FM [auth cB],
GA [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],
HF [auth bA],
HG [auth bA],
HH [auth bB],
HK [auth cA],
IA [auth aA],
IB [auth aA],
IC [auth aB],
ID [auth aB],
IE [auth aL],
IF [auth bA],
IG [auth bA],
IH [auth bB],
IM [auth cB],
JA [auth aA],
JB [auth aA],
JC [auth aB],
JD [auth aB],
JE [auth aL],
JF [auth bA],
JH [auth bB],
JM [auth cB],
KA [auth aA],
KB [auth aA],
KC [auth aB],
KD [auth aB],
KE [auth aL],
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],
LN [auth cK],
MA [auth aA],
MB [auth aA],
MC [auth aB],
MD [auth aB],
MF [auth bA],
MH [auth bB],
MJ [auth cA],
ML [auth cB],
MM [auth cB],
NA [auth aA],
NB [auth aA],
NC [auth aB],
ND [auth aB],
NF [auth bA],
NH [auth bB],
NJ [auth cA],
NK [auth cA],
NL [auth cB],
NM [auth cB],
NN [auth cK],
OA [auth aA],
OB [auth aA],
OC [auth aB],
OD [auth aB],
OF [auth bA],
OH [auth bB],
OJ [auth cA],
OL [auth cB],
OM [auth cB],
PA [auth aA],
PB [auth aA],
PC [auth aB],
PD [auth aB],
PF [auth bA],
PH [auth bB],
PJ [auth cA],
PK [auth cA],
PL [auth cB],
PM [auth cB],
QA [auth aA],
QB [auth aA],
QC [auth aB],
QF [auth bA],
QJ [auth cA],
QK [auth cA],
QL [auth cB],
QM [auth cB],
RA [auth aA],
RB [auth aA],
RC [auth aB],
RH [auth bB],
RJ [auth cA],
RK [auth cA],
RL [auth cB],
RM [auth cB],
RN [auth cL],
SA [auth aA],
SC [auth aB],
SH [auth bB],
SJ [auth cA],
SK [auth cA],
SL [auth cB],
SM [auth cB],
SN [auth cL],
TA [auth aA],
TC [auth aB],
TE [auth bA],
TF [auth bA],
TG [auth bB],
TH [auth bB],
TI [auth bK],
TJ [auth cA],
TK [auth cA],
TL [auth cB],
TM [auth cB],
TN [auth cL],
UA [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],
VC [auth aB],
VE [auth bA],
VG [auth bB],
VH [auth bB],
VI [auth bK],
VJ [auth cA],
VK [auth cA],
VL [auth cB],
VM [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],
WM [auth cB],
XA [auth aA],
XC [auth aB],
XE [auth bA],
XG [auth bB],
XH [auth bB],
XJ [auth cA],
XK [auth cA],
XL [auth cB],
XM [auth cB],
YA [auth aA],
YC [auth aB],
YE [auth bA],
YF [auth bA],
YG [auth bB],
YH [auth bB],
YJ [auth cA],
YK [auth cA],
YL [auth cB],
ZA [auth aA],
ZE [auth bA],
ZF [auth bA],
ZG [auth bB],
ZH [auth bB],
ZI [auth bL],
ZJ [auth cA],
ZK [auth cA],
ZL [auth cB]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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BA [auth aA],
JJ [auth cA],
SE [auth bA]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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EN [auth cB],
NI [auth bB],
WD [auth aB]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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AC [auth aA],
IL [auth cA],
RG [auth bA]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

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AE [auth aI]
AN [auth cB]
BN [auth cB]
CJ [auth bL]
CN [auth cB]
AE [auth aI],
AN [auth cB],
BN [auth cB],
CJ [auth bL],
CN [auth cB],
DE [auth aK],
DJ [auth bL],
DL [auth cA],
DN [auth cB],
EL [auth cA],
FL [auth cA],
FN [auth cB],
GL [auth cA],
HE [auth aL],
HL [auth cA],
II [auth bB],
IJ [auth bM],
JI [auth bB],
KI [auth bB],
KN [auth cI],
LE [auth aL],
LI [auth bB],
ME [auth aL],
MG [auth bA],
MI [auth bB],
MN [auth cK],
NG [auth bA],
OG [auth bA],
OI [auth bB],
PG [auth bA],
QG [auth bA],
QN [auth cL],
RD [auth aB],
RE [auth aM],
RI [auth bI],
SD [auth aB],
TD [auth aB],
UD [auth aB],
UI [auth bK],
UN [auth cL],
VB [auth aA],
VD [auth aB],
VN [auth cL],
WB [auth aA],
XB [auth aA],
XD [auth aB],
YB [auth aA],
YI [auth bL],
ZB [auth aA],
ZM [auth cB],
ZN [auth cM]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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BC [auth aA],
JL [auth cA],
SG [auth bA]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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BL [auth cA]
HI [auth bB]
KG [auth bA]
QD [auth aB]
TB [auth aA]
BL [auth cA],
HI [auth bB],
KG [auth bA],
QD [auth aB],
TB [auth aA],
YM [auth cB]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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CL [auth cA]
GN [auth cC]
HN [auth cC]
LG [auth bA]
PI [auth bC]
CL [auth cA],
GN [auth cC],
HN [auth cC],
LG [auth bA],
PI [auth bC],
QI [auth bC],
UB [auth aA],
YD [auth aC],
ZD [auth aC]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA

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EJ [auth bL],
NE [auth aL],
WN [auth cL]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNL
Query on UNL

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BE [auth aI]
FE [auth aL]
FJ [auth bL]
GJ [auth bL]
HJ [auth bL]
BE [auth aI],
FE [auth aL],
FJ [auth bL],
GJ [auth bL],
HJ [auth bL],
IN [auth cI],
JN [auth cI],
OE [auth aL],
ON [auth cL],
PE [auth aL],
QE [auth aL],
SI [auth bI],
WI [auth bL],
XN [auth cL],
YN [auth cL]
Unknown ligand
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Data collection, Database references
  • Version 2.0: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description