[English] 日本語
Yorodumi
- PDB-9grx: NDH-PSI-LHCI supercomplex from S. oleracea -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9grx
TitleNDH-PSI-LHCI supercomplex from S. oleracea
Components
  • (Chlorophyll a-b binding protein, ...) x 4
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 15
  • (Photosynthetic NDH subunit of lumenal location ...) x 3
  • (Photosynthetic NDH subunit of subcomplex B ...) x 5
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
  • PSI-K
  • Peptidyl-prolyl cis-trans isomerase
  • Photosystem I iron-sulfur center
  • peptidylprolyl isomerase
KeywordsELECTRON TRANSPORT / NDH / PSI / Supercomplex / photosynthesis / electron transport chain / lipids / proton translocation / plastoquinone
Function / homology
Function and homology information


NAD(P)H dehydrogenase complex (plastoquinone) / glucose-6-phosphate 1-epimerase activity / P450-containing electron transport chain / thylakoid / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / photosystem II oxygen evolving complex / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center ...NAD(P)H dehydrogenase complex (plastoquinone) / glucose-6-phosphate 1-epimerase activity / P450-containing electron transport chain / thylakoid / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / photosystem II oxygen evolving complex / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / photosystem II / extrinsic component of membrane / chlorophyll binding / cyclosporin A binding / photosynthesis, light reaction / chloroplast thylakoid membrane / : / ubiquinone binding / electron transport coupled proton transport / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / photosynthesis / chloroplast / aerobic respiration / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / peptidylprolyl isomerase / 2 iron, 2 sulfur cluster binding / NAD binding / protein folding / 4 iron, 4 sulfur cluster binding / carbohydrate binding / molecular adaptor activity / response to oxidative stress / carbohydrate metabolic process / electron transfer activity / oxidoreductase activity / iron ion binding / calcium ion binding / magnesium ion binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
NAD(P)H-quinone oxidoreductase subunit U, chloroplastic / Photosynthetic NDH subunit of subcomplex B 4, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of lumenal location 4-like / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / : / PsbP, C-terminal / PsbP / : / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal ...NAD(P)H-quinone oxidoreductase subunit U, chloroplastic / Photosynthetic NDH subunit of subcomplex B 4, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of lumenal location 4-like / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / : / PsbP, C-terminal / PsbP / : / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NAD(P)H-quinone oxidoreductase subunit O / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / Cyanobacterial and plant NDH-1 subunit O / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase, subunit N / NADH-quinone oxidoreductase chain 4 / Cyanobacterial and plastid NDH-1 subunit M / NADH dehydrogenase transmembrane subunit / NADH-quinone oxidoreductase cyanobacterial subunit N / NADH-plastoquinone oxidoreductase, subunit I / NAD(P)H-quinone oxidoreductase subunit 2, N-terminal / NAD(P)H-quinone oxidoreductase subunit 2 N-terminal / Mog1/PsbP, alpha/beta/alpha sandwich / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Adrenodoxin / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / Photosystem I reaction centre subunit PsaK superfamily / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaD / Chlorophyll A-B binding protein / Photosystem I, reaction centre subunit PsaD superfamily / Chlorophyll A-B binding protein / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Glycoside hydrolase-type carbohydrate-binding / Electron transport accessory-like domain superfamily / Chaperone J-domain superfamily / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / Galactose mutarotase-like domain superfamily / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH dehydrogenase, subunit C / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature.
Similarity search - Domain/homology
: / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-PGT / Chem-PQ9 ...: / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-PGT / Chem-PQ9 / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I reaction center subunit IX / Photosynthetic NDH subunit of lumenal location 2, chloroplastic / Peptidyl-prolyl cis-trans isomerase / PSI-K / peptidylprolyl isomerase / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosynthetic NDH subunit of subcomplex B 4, chloroplastic / NAD(P)H-quinone oxidoreductase subunit N, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosynthetic NDH subunit of subcomplex B 3, chloroplastic / Photosynthetic NDH subunit of lumenal location 3, chloroplastic / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit L, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosynthetic NDH subunit of lumenal location 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit M, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / NAD(P)H-quinone oxidoreductase subunit U, chloroplastic / NAD(P)H-quinone oxidoreductase subunit O, chloroplastic / Photosynthetic NDH subunit of subcomplex B 2, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / NAD(P)H-quinone oxidoreductase subunit H, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit K, chloroplastic / NAD(P)H-quinone oxidoreductase subunit J, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsIntroini, B. / Hahn, A. / Kuehlbrandt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other private Germany
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Cryo-EM structure of the NDH-PSI-LHCI supercomplex from Spinacia oleracea.
Authors: Bianca Introini / Alexander Hahn / Werner Kühlbrandt /
Abstract: The nicotinamide adenine dinucleotide phosphate (NADPH) dehydrogenase (NDH) complex is crucial for photosynthetic cyclic electron flow and respiration, transferring electrons from ferredoxin to ...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.
History
DepositionSep 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: Photosynthetic NDH subunit of lumenal location 1, chloroplastic
1: Photosynthetic NDH subunit of subcomplex B 1, chloroplastic
2: Photosynthetic NDH subunit of subcomplex B 2, chloroplastic
3: Photosynthetic NDH subunit of subcomplex B 3, chloroplastic
4: Photosynthetic NDH subunit of subcomplex B 4, chloroplastic
5: Photosynthetic NDH subunit of subcomplex B 5, chloroplastic
6: Photosynthetic NDH subunit of lumenal location 2, chloroplastic
7: Photosynthetic NDH subunit of lumenal location 3, chloroplastic
8: peptidylprolyl isomerase
9: Peptidyl-prolyl cis-trans isomerase
A: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
B: NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic
C: NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic
D: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
E: NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic
F: NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic
G: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic
H: NAD(P)H-quinone oxidoreductase subunit H, chloroplastic
I: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
J: NAD(P)H-quinone oxidoreductase subunit J, chloroplastic
K: NAD(P)H-quinone oxidoreductase subunit K, chloroplastic
L: NAD(P)H-quinone oxidoreductase subunit L, chloroplastic
M: NAD(P)H-quinone oxidoreductase subunit M, chloroplastic
N: NAD(P)H-quinone oxidoreductase subunit N, chloroplastic
O: NAD(P)H-quinone oxidoreductase subunit O, chloroplastic
U: NAD(P)H-quinone oxidoreductase subunit U, chloroplastic
a: Photosystem I P700 chlorophyll a apoprotein A1
b: Photosystem I P700 chlorophyll a apoprotein A2
c: Photosystem I iron-sulfur center
d: Photosystem I reaction center subunit II, chloroplastic
e: Photosystem I reaction center subunit IV, chloroplastic
f: Photosystem I reaction center subunit III, chloroplastic
g: Photosystem I reaction center subunit V, chloroplastic
h: Photosystem I reaction center subunit VI, chloroplastic
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
k: PSI-K
l: Photosystem I reaction center subunit XI, chloroplastic
w: Chlorophyll a-b binding protein, chloroplastic
x: Chlorophyll a-b binding protein, chloroplastic
y: Chlorophyll a-b binding protein, chloroplastic
z: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,246,903290
Polymers1,048,45342
Non-polymers198,449248
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Photosynthetic NDH subunit of lumenal location ... , 3 types, 3 molecules 067

#1: Protein Photosynthetic NDH subunit of lumenal location 1, chloroplastic


Mass: 18606.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JJI5
#7: Protein Photosynthetic NDH subunit of lumenal location 2, chloroplastic


Mass: 14875.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0I5E4
#8: Protein Photosynthetic NDH subunit of lumenal location 3, chloroplastic


Mass: 16451.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JBH0

-
Photosynthetic NDH subunit of subcomplex B ... , 5 types, 5 molecules 12345

#2: Protein Photosynthetic NDH subunit of subcomplex B 1, chloroplastic


Mass: 44622.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JDZ5
#3: Protein Photosynthetic NDH subunit of subcomplex B 2, chloroplastic


Mass: 40259.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0KAG7
#4: Protein Photosynthetic NDH subunit of subcomplex B 3, chloroplastic


Mass: 15614.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0J911
#5: Protein Photosynthetic NDH subunit of subcomplex B 4, chloroplastic


Mass: 10763.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0J426
#6: Protein Photosynthetic NDH subunit of subcomplex B 5, chloroplastic


Mass: 17772.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JS52

-
Protein , 5 types, 5 molecules 89Dck

#9: Protein peptidylprolyl isomerase


Mass: 15352.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0IC28, peptidylprolyl isomerase
#10: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 18900.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0IB03, peptidylprolyl isomerase
#14: Protein NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H dehydrogenase / chain 4 / NADH-plastoquinone oxidoreductase chain 4


Mass: 55980.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: Q9M3J0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#29: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 9035.483 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P10098, photosystem I
#37: Protein PSI-K / Photosystem I subunit X


Mass: 13229.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0IBB5

-
NAD(P)H-quinone oxidoreductase subunit ... , 15 types, 15 molecules ABCEFGHIJKLMNOU

#11: Protein NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / NAD(P)H dehydrogenase subunit 1 / NDH subunit 1 / NADH-plastoquinone oxidoreductase subunit 1


Mass: 38985.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: Q9M3I6, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#12: Protein NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic / NAD(P)H dehydrogenase / subunit 2 A / NADH-plastoquinone oxidoreductase subunit 2 A


Mass: 54026.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P0CD52, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#13: Protein NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H dehydrogenase subunit 3 / NADH-plastoquinone oxidoreductase subunit 3


Mass: 13270.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: Q9M3L9, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#15: Protein NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H dehydrogenase subunit 4L / NADH-plastoquinone oxidoreductase subunit 4L


Mass: 11085.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: Q9M3I9, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#16: Protein NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic / NAD(P)H dehydrogenase subunit 5 / NADH-plastoquinone oxidoreductase subunit 5


Mass: 84590.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: Q9M3J4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#17: Protein NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / NAD(P)H dehydrogenase subunit 6 / NADH-plastoquinone oxidoreductase subunit 6


Mass: 19193.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: Q9M3I8, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#18: Protein NAD(P)H-quinone oxidoreductase subunit H, chloroplastic / NAD(P)H dehydrogenase subunit H / NADH-plastoquinone oxidoreductase 49 kDa subunit / NADH- ...NAD(P)H dehydrogenase subunit H / NADH-plastoquinone oxidoreductase 49 kDa subunit / NADH-plastoquinone oxidoreductase subunit H


Mass: 45172.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: Q9M3I5, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#19: Protein NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / NAD(P)H dehydrogenase subunit I / NDH subunit I / NADH-plastoquinone oxidoreductase subunit I


Mass: 19004.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: Q9M3I7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#20: Protein NAD(P)H-quinone oxidoreductase subunit J, chloroplastic / NAD(P)H dehydrogenase subunit J / NADH-plastoquinone oxidoreductase subunit J


Mass: 18687.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: Q9M3M1, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#21: Protein NAD(P)H-quinone oxidoreductase subunit K, chloroplastic / NAD(P)H dehydrogenase subunit K / NADH-plastoquinone oxidoreductase subunit K


Mass: 22789.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: Q9M3M0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#22: Protein NAD(P)H-quinone oxidoreductase subunit L, chloroplastic


Mass: 13194.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JHB5
#23: Protein NAD(P)H-quinone oxidoreductase subunit M, chloroplastic / NAD(P)H dehydrogenase subunit M / NADH-plastoquinone oxidoreductase subunit M


Mass: 16702.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JNY9
#24: Protein NAD(P)H-quinone oxidoreductase subunit N, chloroplastic


Mass: 18727.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0J7P2
#25: Protein NAD(P)H-quinone oxidoreductase subunit O, chloroplastic


Mass: 11127.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0K504
#26: Protein NAD(P)H-quinone oxidoreductase subunit U, chloroplastic


Mass: 27127.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0K267

-
Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules ab

#27: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 82144.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06511, photosystem I
#28: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82377.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06512, photosystem I

-
Photosystem I reaction center subunit ... , 8 types, 8 molecules defghijl

#30: Protein Photosystem I reaction center subunit II, chloroplastic / Photosystem I 20 kDa subunit / PSI-D


Mass: 16053.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12353
#31: Protein Photosystem I reaction center subunit IV, chloroplastic / PSI-E


Mass: 7736.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12354
#32: Protein Photosystem I reaction center subunit III, chloroplastic / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 17151.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12355
#33: Protein Photosystem I reaction center subunit V, chloroplastic / PSI-G / Photosystem I 9 kDa protein


Mass: 10719.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12357
#34: Protein Photosystem I reaction center subunit VI, chloroplastic / PSI-H / Light-harvesting complex I 11 kDa protein


Mass: 10391.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P22179
#35: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3458.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17228
#36: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4845.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A6B9Q8A1
#38: Protein Photosystem I reaction center subunit XI, chloroplastic / PSI-L / PSI subunit V


Mass: 16988.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q41385

-
Chlorophyll a-b binding protein, ... , 4 types, 4 molecules wxyz

#39: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23947.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0JIF6
#40: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22135.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0J335
#41: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24168.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0IPK6
#42: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 21184.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A9R0J8B1

-
Sugars , 1 types, 3 molecules

#51: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 12 types, 245 molecules

#43: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#44: Chemical...
ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H79O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#45: Chemical ChemComp-A1H1M / 4-trans-(4-trans-Propylcyclohexyl)-cyclohexyl alpha-maltoside / (2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[(2R,3S,4R,5R,6R)-2-(hydroxymethyl)-4,5-bis(oxidanyl)-6-[4-(4-propylcyclohexyl)cyclohexyl]oxy-oxan-3-yl]oxy-oxane-3,4,5-triol


Mass: 548.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H48O11 / Feature type: SUBJECT OF INVESTIGATION
#46: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#47: Chemical ChemComp-PQ9 / 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


Mass: 612.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H64O2 / Feature type: SUBJECT OF INVESTIGATION
#48: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#49: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#50: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 144 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#52: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#53: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#54: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#55: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: NDH-PSI-LHCI supercomplex from Spinacia oleracea / Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Spinacia oleracea (spinach)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Titan Krios G3i microscope at 300 kV, equipped with a K3 (Gatan) detector operating in electron counting mode, Bioquantum energy filter (Gatan)
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.19 Å / Resolution method: OTHER / Num. of particles: 38385 / Details: This is a composite map / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDSource nameTypeAccession codeInitial refinement model-ID
11AlphaFoldin silico model
24y28

4y28

1PDBexperimental model4y282
36khj

6khj

1PDBexperimental model6khj3

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more