6KMX | pdb_00006kmx

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
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6KMX

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 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.

Macromolecule Content 

  • Total Structure Weight: 1,011.73 kDa 
  • Atom Count: 65,112 
  • Modeled Residue Count: 5,919 
  • Deposited Residue Count: 6,591 
  • Unique protein chains: 9

Macromolecules

Find similar proteins by:
|  3D Structure
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)
Explore A0A1Z3HIN6 
Go to UniProtKB:  A0A1Z3HIN6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HIN6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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)
Explore A0A1Z3HIL0 
Go to UniProtKB:  A0A1Z3HIL0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HIL0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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)
Explore A0A1Z3HPE3 
Go to UniProtKB:  A0A1Z3HPE3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HPE3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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)
Explore A0A1Z3HHI7 
Go to UniProtKB:  A0A1Z3HHI7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HHI7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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)
Explore A0A1Z3HI16 
Go to UniProtKB:  A0A1Z3HI16
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HI16
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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)
Explore A0A1Z3HIL5 
Go to UniProtKB:  A0A1Z3HIL5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HIL5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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)
Explore A0A1Z3HR36 
Go to UniProtKB:  A0A1Z3HR36
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HR36
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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)
Explore A0A1Z3HIQ7 
Go to UniProtKB:  A0A1Z3HIQ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HIQ7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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 

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6C

Query on F6C


Download:Ideal Coordinates CCD File
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
CL0

Query on CL0


Download:Ideal Coordinates CCD File
BA [auth aA],
JJ [auth cA],
SE [auth bA]		CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA

Query on CLA


Download:Ideal Coordinates CCD File
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
LMG

Query on LMG


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

Query on LHG


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
BC [auth aA],
JL [auth cA],
SG [auth bA]		DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
EJ [auth bL],
NE [auth aL],
WN [auth cL]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNL

Query on UNL


Download:Ideal Coordinates CCD File
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



View more in-depth experimental data

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