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 7EWK | pdb_00007ewk

Barley photosystem I-LHCI-Lhca6 supercomplex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7EWK

This is version 2.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 505.19 kDa 
  • Atom Count: 32,765 
  • Modeled Residue Count: 3,110 
  • Deposited Residue Count: 3,110 
  • Unique protein chains: 15

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1742Hordeum vulgare subsp. spontaneumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for S4Z1K7 (Hordeum vulgare subsp. spontaneum)
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UniProt GroupS4Z1K7
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2733Hordeum vulgare subsp. spontaneumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for S4Z289 (Hordeum vulgare subsp. spontaneum)
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Reference Sequence
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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 S4YZ47 (Hordeum vulgare subsp. spontaneum)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit D142Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P36213 (Hordeum vulgare)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit E68Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13194 (Hordeum vulgare)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit F158Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13192 (Hordeum vulgare)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit HG [auth H]61Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P20143 (Hordeum vulgare)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIH [auth I]30Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for S4Z1D9 (Hordeum vulgare subsp. spontaneum)
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Reference Sequence
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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 S4Z1E9 (Hordeum vulgare subsp. spontaneum)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit KJ [auth K]84Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P36886 (Hordeum vulgare)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit LK [auth L]146Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23993 (Hordeum vulgare)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein Lhca1L [auth 1]193Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SDM1 (Hordeum vulgare)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein Lhca3M [auth 3]222Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2DAN8 (Hordeum vulgare subsp. vulgare)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 4]197Hordeum vulgareMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9LKC7 (Hordeum vulgare)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein Lhca6O [auth 6]211Hordeum vulgare subsp. spontaneumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2D0D5 (Hordeum vulgare subsp. vulgare)
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Reference Sequence

Small Molecules

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

Query on DGD


Download:Ideal Coordinates CCD File
BE [auth J],
PD [auth B]		DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL


Download:Ideal Coordinates CCD File
AF [auth 1]
AH [auth 6]
CH [auth 6]
DF [auth 1]
GG [auth 4]
AF [auth 1],
AH [auth 6],
CH [auth 6],
DF [auth 1],
GG [auth 4],
HG [auth 4],
JG [auth 4],
QF [auth 3],
XG [auth 6],
YE [auth 1],
YG [auth 6]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AG [auth 4]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AG [auth 4],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BF [auth 1],
BG [auth 4],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CG [auth 4],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth K],
DG [auth 4],
EA [auth A],
EC [auth B],
ED [auth B],
EE [auth K],
EG [auth 4],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FE [auth K],
FG [auth 4],
GA [auth A],
GC [auth B],
GD [auth B],
HA [auth A],
HC [auth B],
HD [auth B],
HE [auth K],
HF [auth 3],
IA [auth A],
IC [auth B],
IF [auth 3],
IG [auth 4],
JA [auth A],
JC [auth B],
JE [auth L],
JF [auth 3],
KA [auth A],
KC [auth B],
KE [auth L],
KF [auth 3],
KG [auth 4],
LA [auth A],
LC [auth B],
LE [auth L],
LF [auth 3],
MA [auth A],
MC [auth B],
MF [auth 3],
NA [auth A],
NC [auth B],
NF [auth 3],
OA [auth A],
OB [auth A],
OC [auth B],
OF [auth 3],
PA [auth A],
PB [auth A],
PC [auth B],
PF [auth 3],
PG [auth 6],
Q [auth A],
QA [auth A],
QC [auth B],
QE [auth 1],
QG [auth 6],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
RE [auth 1],
RF [auth 3],
RG [auth 6],
S [auth A],
SA [auth A],
SC [auth B],
SE [auth 1],
SF [auth 3],
SG [auth 6],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
TE [auth 1],
TF [auth 3],
TG [auth 6],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
UD [auth F],
UE [auth 1],
UG [auth 6],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VE [auth 1],
VG [auth 6],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WE [auth 1],
WG [auth 6],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XE [auth 1],
XF [auth 4],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YD [auth J],
YF [auth 4],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth J],
ZE [auth 1],
ZF [auth 4],
ZG [auth 6]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0


Download:Ideal Coordinates CCD File
P [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG

Query on LMG


Download:Ideal Coordinates CCD File
CE [auth J],
LG [auth 4]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG


Download:Ideal Coordinates CCD File
BH [auth 6],
CF [auth 1],
GB [auth A],
HB [auth A],
QD [auth B]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT

Query on XAT


Download:Ideal Coordinates CCD File
NG [auth 6],
WF [auth 4]		(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


Download:Ideal Coordinates CCD File
EF [auth 3]
FF [auth 3]
MG [auth 6]
NE [auth 1]
OE [auth 1]
EF [auth 3],
FF [auth 3],
MG [auth 6],
NE [auth 1],
OE [auth 1],
VF [auth 4]
(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


Download:Ideal Coordinates CCD File
AE [auth J]
GE [auth K]
GF [auth 3]
IB [auth A]
IE [auth L]
AE [auth J],
GE [auth K],
GF [auth 3],
IB [auth A],
IE [auth L],
JB [auth A],
JD [auth B],
KB [auth A],
KD [auth B],
LB [auth A],
LD [auth B],
MB [auth A],
MD [auth B],
ME [auth L],
NB [auth A],
ND [auth B],
OD [auth B],
OG [auth 6],
PE [auth 1],
QB [auth A],
TD [auth F],
UF [auth 4],
VD [auth F],
WD [auth I],
XD [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
EB [auth A],
ID [auth B]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
RD [auth C],
SB [auth B],
SD [auth C]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

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: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2024-06-05
    Changes: Data collection
  • Version 2.0: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary