7EW6

Barley photosystem I-LHCI-Lhca5 supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare.

Shen, L.Tang, K.Wang, W.Wang, C.Wu, H.Mao, Z.An, S.Chang, S.Kuang, T.Shen, J.R.Han, G.Zhang, X.

(2022) Nature 601: 649-654

  • DOI: https://doi.org/10.1038/s41586-021-04277-6
  • Primary Citation of Related Structures:  
    7EU3, 7EW6, 7EWK, 7F9O

  • PubMed Abstract: 

    The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET) 1-3 . The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET.


  • Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1750Hordeum vulgare subsp. spontaneumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A1E9J1 (Hordeum vulgare)
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UniProt GroupA1E9J1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2734Hordeum vulgare subsp. spontaneumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A1E9J0 (Hordeum vulgare)
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UniProt GroupA1E9J0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Hordeum vulgare subsp. spontaneumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P69416 (Hordeum vulgare)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplastic205Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P36213 (Hordeum vulgare)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV, chloroplastic147Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13194 (Hordeum vulgare)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplastic235Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13192 (Hordeum vulgare)
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UniProt GroupP13192
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplasticG [auth H]143Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P20143 (Hordeum vulgare)
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UniProt GroupP20143
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIH [auth I]36Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13165 (Hordeum vulgare)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXI [auth J]42Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1E9L0 (Hordeum vulgare)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplasticJ [auth K]131Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P36886 (Hordeum vulgare)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplasticK [auth L]209Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23993 (Hordeum vulgare)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein Lhca1L [auth 1]247Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SDM1 (Hordeum vulgare)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticM [auth 2]255Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q43485 (Hordeum vulgare)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 3]269Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2DAN8 (Hordeum vulgare subsp. vulgare)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein Lhca5O [auth 5]257Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2CW18 (Hordeum vulgare subsp. vulgare)
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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BE [auth J],
ND [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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AF [auth 1]
CH [auth 5]
DF [auth 1]
DH [auth 5]
FH [auth 5]
AF [auth 1],
CH [auth 5],
DF [auth 1],
DH [auth 5],
FH [auth 5],
LG [auth 3],
PF [auth 2],
QF [auth 2],
SF [auth 2],
TF [auth 2],
YE [auth 1],
YF [auth 3]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AH [auth 5]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AH [auth 5],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BF [auth 1],
BH [auth 5],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth K],
CG [auth 3],
DA [auth A],
DC [auth B],
DD [auth B],
DE [auth K],
DG [auth 3],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth K],
EG [auth 3],
EH [auth 5],
FA [auth A],
FC [auth B],
FD [auth B],
FG [auth 3],
GA [auth A],
GC [auth B],
GE [auth K],
GG [auth 3],
HA [auth A],
HC [auth B],
HE [auth L],
HF [auth 2],
HG [auth 3],
IA [auth A],
IC [auth B],
IE [auth L],
IF [auth 2],
IG [auth 3],
JA [auth A],
JC [auth B],
JE [auth L],
JF [auth 2],
JG [auth 3],
KA [auth A],
KC [auth B],
KE [auth L],
KF [auth 2],
KG [auth 3],
LA [auth A],
LC [auth B],
LF [auth 2],
MA [auth A],
MC [auth B],
MF [auth 2],
MG [auth 3],
NA [auth A],
NC [auth B],
NF [auth 2],
NG [auth 3],
OA [auth A],
OB [auth A],
OC [auth B],
OF [auth 2],
OG [auth 3],
PA [auth A],
PC [auth B],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
QE [auth 1],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
RE [auth 1],
RF [auth 2],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
SE [auth 1],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
TD [auth F],
TE [auth 1],
TG [auth 5],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
UD [auth F],
UE [auth 1],
UG [auth 5],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VE [auth 1],
VG [auth 5],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WE [auth 1],
WG [auth 5],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XE [auth 1],
XF [auth 3],
XG [auth 5],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YG [auth 5],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth J],
ZE [auth 1],
ZG [auth 5]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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P [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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PG [auth 5],
VF [auth 2],
WD [auth F],
WF [auth 2],
XD [auth F]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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CF [auth 1],
FB [auth A],
GB [auth A],
OD [auth B],
UF [auth 2]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT

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FF [auth 2],
SG [auth 5]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT
Query on LUT

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AG [auth 3]
EF [auth 2]
NE [auth 1]
OE [auth 1]
RG [auth 5]
AG [auth 3],
EF [auth 2],
NE [auth 1],
OE [auth 1],
RG [auth 5],
ZF [auth 3]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
Query on BCR

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AE [auth J]
BG [auth 3]
FE [auth K]
GF [auth 2]
HB [auth A]
AE [auth J],
BG [auth 3],
FE [auth K],
GF [auth 2],
HB [auth A],
HD [auth B],
IB [auth A],
ID [auth B],
JB [auth A],
JD [auth B],
KB [auth A],
KD [auth B],
LB [auth A],
LD [auth B],
LE [auth L],
MD [auth B],
ME [auth L],
NB [auth A],
PB [auth A],
PD [auth B],
PE [auth 1],
QG [auth 5],
SD [auth F],
VD [auth F],
YD [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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DB [auth A],
GD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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MB [auth A],
QD [auth C],
RD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaQYZDY-SSW-SMC003

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary