9GRX

NDH-PSI-LHCI supercomplex from S. oleracea


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of the NDH-PSI-LHCI supercomplex from Spinacia oleracea.

Introini, B.Hahn, A.Kuhlbrandt, W.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01478-1
  • Primary Citation of Related Structures:  
    9GRX

  • PubMed Abstract: 

    The nicotinamide adenine dinucleotide phosphate (NADPH) dehydrogenase (NDH) complex is crucial for photosynthetic cyclic electron flow and respiration, transferring electrons from ferredoxin to plastoquinone while transporting H + across the chloroplast membrane. This process boosts adenosine triphosphate production, regardless of NADPH levels. In flowering plants, NDH forms a supercomplex with photosystem I, enhancing its stability under high light. We report the cryo-electron microscopy structure of the NDH supercomplex in Spinacia oleracea at a resolution of 3.0-3.3 Å. The supercomplex consists of 41 protein subunits, 154 chlorophylls and 38 carotenoids. Subunit interactions are reinforced by 46 distinct lipids. The structure of NDH resembles that of mitochondrial complex I closely, including the quinol-binding site and an extensive internal aqueous passage for proton translocation. A well-resolved catalytic plastoquinone (PQ) occupies the PQ channel. The pronounced structural similarity to complex I sheds light on electron transfer and proton translocation within the NDH supercomplex.


  • Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of lumenal location 1, chloroplasticA [auth 0]157Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 1, chloroplasticB [auth 1]403Spinacia oleraceaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 2, chloroplasticC [auth 2]372Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 3, chloroplasticD [auth 3]139Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0J911 (Spinacia oleracea)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 4, chloroplasticE [auth 4]93Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 5, chloroplasticF [auth 5]154Spinacia oleraceaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of lumenal location 2, chloroplasticG [auth 6]125Spinacia oleraceaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of lumenal location 3, chloroplasticH [auth 7]144Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
peptidylprolyl isomeraseI [auth 8]143Spinacia oleraceaMutation(s): 0 
EC: 5.2.1.8
UniProt
Find proteins for A0A9R0IC28 (Spinacia oleracea)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseJ [auth 9]174Spinacia oleraceaMutation(s): 0 
EC: 5.2.1.8
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 1, chloroplasticK [auth A]350Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplasticL [auth B]488Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 3, chloroplasticM [auth C]115Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase chain 4, chloroplasticN [auth D]498Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 4L, chloroplasticO [auth E]100Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 5, chloroplasticP [auth F]742Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 6, chloroplasticQ [auth G]176Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit H, chloroplasticR [auth H]389Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit I, chloroplasticS [auth I]163Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit J, chloroplasticT [auth J]158Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit K, chloroplasticU [auth K]202Spinacia oleraceaMutation(s): 0 
EC: 7.1.1
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit L, chloroplasticV [auth L]109Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for A0A9R0JHB5 (Spinacia oleracea)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit M, chloroplasticW [auth M]141Spinacia oleraceaMutation(s): 0 
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Find proteins for A0A9R0JNY9 (Spinacia oleracea)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit N, chloroplasticX [auth N]165Spinacia oleraceaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit O, chloroplasticY [auth O]95Spinacia oleraceaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit U, chloroplasticZ [auth U]240Spinacia oleraceaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1AA [auth a]742Spinacia oleraceaMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2BA [auth b]733Spinacia oleraceaMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerCA [auth c]81Spinacia oleraceaMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplasticDA [auth d]143Spinacia oleraceaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV, chloroplasticEA [auth e]68Spinacia oleraceaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticFA [auth f]153Spinacia oleraceaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticGA [auth g]97Spinacia oleraceaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplasticHA [auth h]95Spinacia oleraceaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIIA [auth i]31Spinacia oleraceaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXJA [auth j]42Spinacia oleraceaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-KKA [auth k]130Spinacia oleraceaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplasticLA [auth l]160Spinacia oleraceaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticMA [auth w]215Spinacia oleraceaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticNA [auth x]198Spinacia oleraceaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticOA [auth y]221Spinacia oleraceaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticPA [auth z]193Spinacia oleraceaMutation(s): 0 
UniProt
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9R0J8B1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

Download Ideal Coordinates CCD File 
OI [auth x],
UE [auth b],
WB [auth a]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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CI [auth x]
HH [auth w]
II [auth x]
MH [auth w]
MJ [auth z]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

Download Ideal Coordinates CCD File 
AC [auth a]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AD [auth a]
AE [auth b]
AI [auth x]
AJ [auth y]
BC [auth a]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

Download Ideal Coordinates CCD File 
CB [auth B]
HB [auth F]
LB [auth F]
SG [auth j]
UH [auth w]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG (Subject of Investigation/LOI)
Query on LMG

Download Ideal Coordinates CCD File 
DB [auth B]
FB [auth D]
GG [auth f]
IB [auth F]
MB [auth H]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PGT (Subject of Investigation/LOI)
Query on PGT

Download Ideal Coordinates CCD File 
AB [auth B]
BB [auth B]
CF [auth b]
DF [auth b]
EB [auth B]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
PQ9 (Subject of Investigation/LOI)
Query on PQ9

Download Ideal Coordinates CCD File 
YA [auth A]5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE
C43 H64 O2
JXUCGUASMMLSBH-HOHOQCMASA-N
LUT (Subject of Investigation/LOI)
Query on LUT

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CK [auth z]
DK [auth z]
HJ [auth y]
IJ [auth y]
RI [auth x]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
A1H1M (Subject of Investigation/LOI)
Query on A1H1M

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KB [auth F],
SA [auth 5]
4-trans-(4-trans-Propylcyclohexyl)-cyclohexyl alpha-maltoside
C27 H48 O11
ZESBUFKOCABQIP-YJUXXZBVSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

Download Ideal Coordinates CCD File 
AH [auth l]
AK [auth z]
BH [auth l]
CC [auth a]
EF [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

Download Ideal Coordinates CCD File 
AF [auth b],
RC [auth a]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
AG [auth c]
NB [auth I]
OB [auth I]
QB [auth K]
YC [auth a]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release