[English] 日本語
Yorodumi
- PDB-7wg5: Cyclic electron transport supercomplex NDH-PSI from Arabidopsis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wg5
TitleCyclic electron transport supercomplex NDH-PSI from Arabidopsis
Components
  • (Chlorophyll a-b binding protein ...) x 2
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 13
  • (Photosynthetic NDH subunit of lumenal location ...) x 4
  • (Photosynthetic NDH subunit of subcomplex B ...) x 4
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I chlorophyll a/b-binding protein ...) x 4
  • (Photosystem I reaction center subunit ...) x 9
  • Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, chloroplastic
  • NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
  • NDH dependent flow 6
  • NdhO
  • NdhT
  • Photosystem I iron-sulfur center
KeywordsELECTRON TRANSPORT / Supercomplex / PSI / NDH-PSI / plant / Arabidopsis / cyclic electron transport
Function / homology
Function and homology information


NAD(P)H dehydrogenase complex assembly / nitrite reductase complex [NAD(P)H] / NADH dehydrogenase complex (plastoquinone) assembly / photosystem I antenna complex / NAD(P)H dehydrogenase complex (plastoquinone) / glucose-6-phosphate 1-epimerase activity / photosynthetic NADP+ reduction / photosystem I stabilization / cellular response to sulfate starvation / chloroplast stromal thylakoid ...NAD(P)H dehydrogenase complex assembly / nitrite reductase complex [NAD(P)H] / NADH dehydrogenase complex (plastoquinone) assembly / photosystem I antenna complex / NAD(P)H dehydrogenase complex (plastoquinone) / glucose-6-phosphate 1-epimerase activity / photosynthetic NADP+ reduction / photosystem I stabilization / cellular response to sulfate starvation / chloroplast stromal thylakoid / chloroplast photosystem I / response to low light intensity stimulus / thylakoid lumen / pigment binding / protein histidine kinase binding / chloroplast membrane / response to high light intensity / ubiquinone biosynthetic process / thylakoid membrane / plastoglobule / P450-containing electron transport chain / chloroplast thylakoid / NADPH dehydrogenase activity / chloroplast thylakoid lumen / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / photosystem I reaction center / chloroplast envelope / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / chloroplast stroma / plastid / extrinsic component of membrane / photosynthesis, light reaction / chloroplast thylakoid membrane / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / NADH dehydrogenase activity / defense response to fungus / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / photosynthesis / response to cold / chloroplast / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 2 iron, 2 sulfur cluster binding / NAD binding / protein folding / 4 iron, 4 sulfur cluster binding / carbohydrate binding / response to oxidative stress / carbohydrate metabolic process / electron transfer activity / protein stabilization / oxidoreductase activity / iron ion binding / protein domain specific binding / mRNA binding / calcium ion binding / magnesium ion binding / protein homodimerization activity / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / 4Fe-4S dicluster domain / : / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal ...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 / 4Fe-4S dicluster domain / : / 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 / Mog1/PsbP, alpha/beta/alpha sandwich / NAD(P)H-quinone oxidoreductase subunit 2, N-terminal / NAD(P)H-quinone oxidoreductase subunit 2 N-terminal / 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 / Photosystem I psaG and psaK proteins signature. / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / 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 / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / : / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / 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 / Electron transport accessory-like domain superfamily / Glycoside hydrolase-type carbohydrate-binding / 2Fe-2S iron-sulfur cluster binding domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / 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-quinone oxidoreductase, chain M/4 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / NADH-ubiquinone oxidoreductase chain 4L/K / 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 / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT / NdhO / NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NDH dependent flow 6 / Photosynthetic NDH subunit of lumenal location 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / Chlorophyll a-b binding protein 4, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic / NAD(P)H-quinone oxidoreductase subunit H, chloroplastic / NAD(P)H-quinone oxidoreductase subunit J, chloroplastic / NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / NAD(P)H-quinone oxidoreductase subunit K, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / NAD(P)H-quinone oxidoreductase subunit M, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / Photosystem I chlorophyll a/b-binding protein 6, chloroplastic / Photosynthetic NDH subunit of subcomplex B 2, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / Photosynthetic NDH subunit of lumenal location 5, chloroplastic / Photosystem I chlorophyll a/b-binding protein 5, chloroplastic / NAD(P)H-quinone oxidoreductase subunit L, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of subcomplex B 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit N, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit IV A, chloroplastic / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / Photosystem I reaction center subunit II-2, chloroplastic / Photosynthetic NDH subunit of lumenal location 4, chloroplastic / Photosynthetic NDH subunit of lumenal location 3, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit VI-2, chloroplastic / Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Photosystem I chlorophyll a/b-binding protein 2, chloroplastic / Photosynthetic NDH subunit of lumenal location 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsPan, X.W. / Li, M.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0503702 China
Chinese Academy of SciencesXDB08020106 China
National Natural Science Foundation of China (NSFC)31930064 China
National Natural Science Foundation of China (NSFC)31970264 China
National Natural Science Foundation of China (NSFC)31770778 China
CitationJournal: Mol Plant / Year: 2022
Title: Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana.
Authors: Xiaodong Su / Duanfang Cao / Xiaowei Pan / Lifang Shi / Zhenfeng Liu / Luca Dall'Osto / Roberto Bassi / Xinzheng Zhang / Mei Li /
Abstract: Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane- ...Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane-embedded NADH dehydrogenase-like (NDH) complex that contains at least 29 protein subunits and associates with photosystem I (PSI) to form the NDH-PSI supercomplex. Here, we report the 3.9 Å resolution structure of the Arabidopsis thaliana NDH-PSI (AtNDH-PSI) supercomplex. We constructed structural models for 26 AtNDH subunits, among which 11 are unique to chloroplasts and stabilize the core part of the NDH complex. In the supercomplex, one NDH can bind up to two PSI-light-harvesting complex I (PSI-LHCI) complexes at both sides of its membrane arm. Two minor LHCIs, Lhca5 and Lhca6, each present in one PSI-LHCI, interact with NDH and contribute to supercomplex formation and stabilization. Collectively, our study reveals the structural details of the AtNDH-PSI supercomplex assembly and provides a molecular basis for further investigation of the regulatory mechanism of CEF in plants.
History
DepositionDec 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-32477
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: Photosystem I P700 chlorophyll a apoprotein A1
AB: Photosystem I P700 chlorophyll a apoprotein A2
AC: Photosystem I iron-sulfur center
AD: Photosystem I reaction center subunit II-2, chloroplastic
AE: Photosystem I reaction center subunit IV A, chloroplastic
AF: Photosystem I reaction center subunit III, chloroplastic
AG: Photosystem I reaction center subunit V, chloroplastic
AH: Photosystem I reaction center subunit VI-2, chloroplastic
AI: Photosystem I reaction center subunit VIII
AJ: Photosystem I reaction center subunit IX
AK: Photosystem I reaction center subunit psaK, chloroplastic
AL: Photosystem I reaction center subunit XI, chloroplastic
A1: Chlorophyll a-b binding protein 6, chloroplastic
A3: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
A4: Chlorophyll a-b binding protein 4, chloroplastic
A6: Photosystem I chlorophyll a/b-binding protein 6, chloroplastic
BA: Photosystem I P700 chlorophyll a apoprotein A1
BB: Photosystem I P700 chlorophyll a apoprotein A2
BC: Photosystem I iron-sulfur center
BD: Photosystem I reaction center subunit II-2, chloroplastic
BE: Photosystem I reaction center subunit IV A, chloroplastic
BF: Photosystem I reaction center subunit III, chloroplastic
BG: Photosystem I reaction center subunit V, chloroplastic
BH: Photosystem I reaction center subunit VI-2, chloroplastic
BI: Photosystem I reaction center subunit VIII
BJ: Photosystem I reaction center subunit IX
BK: Photosystem I reaction center subunit psaK, chloroplastic
BL: Photosystem I reaction center subunit XI, chloroplastic
B1: Chlorophyll a-b binding protein 6, chloroplastic
B2: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
B3: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
B5: Photosystem I chlorophyll a/b-binding protein 5, chloroplastic
A: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
B: NAD(P)H-quinone oxidoreductase subunit 2, 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
a: Photosynthetic NDH subunit of subcomplex B 1, chloroplastic
b: Photosynthetic NDH subunit of subcomplex B 2, chloroplastic
c: Photosynthetic NDH subunit of subcomplex B 3, chloroplastic
d: NDH dependent flow 6
e: Photosynthetic NDH subunit of subcomplex B 5, chloroplastic
f: Photosynthetic NDH subunit of lumenal location 1, chloroplastic
g: Photosynthetic NDH subunit of lumenal location 2, chloroplastic
h: Photosynthetic NDH subunit of lumenal location 3, chloroplastic
i: Photosynthetic NDH subunit of lumenal location 4, chloroplastic
j: Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, 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: NdhO
T: NdhT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,963,889481
Polymers1,623,26558
Non-polymers340,625423
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 4 molecules AABAABBB

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


Mass: 83315.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56766, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82555.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56767, photosystem I

+
Protein , 6 types, 7 molecules ACBCDdjOT

#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 9049.509 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62090, photosystem I
#22: Protein NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H dehydrogenase / chain 4 / NADH-plastoquinone oxidoreductase chain 4


Mass: 56992.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: A0A1B1W4Z0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#29: Protein NDH dependent flow 6


Mass: 18699.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: B3H6Z4
#35: Protein Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, chloroplastic / Cyclophilin of 20 kDa 2 / Peptidyl-prolyl cis-trans isomerase CYP20-2 / PPIase CYP20-2 / Rotamase ...Cyclophilin of 20 kDa 2 / Peptidyl-prolyl cis-trans isomerase CYP20-2 / PPIase CYP20-2 / Rotamase CYP20-2 / Thylakoid lumen PPIase of 20 kDa / TLP20


Mass: 27915.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ASS6, peptidylprolyl isomerase
#43: Protein NdhO


Mass: 17679.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178WB24
#44: Protein NdhT


Mass: 10400.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: All Residues in NdhT were modeled as UNK. The real sequence of the entity is: ...Details: All Residues in NdhT were modeled as UNK. The real sequence of the entity is: MAYATSTYARTSCIILPKIQNGAHFTDNTKAFRRITARRVTRISSQGPTKPPKPSPGVDTRIHWESPDEGWIGGRSDPAKSVDEDKTNLLSDEKFAELIKDSFDSHYQFLGVSTDAHLEEIKSAYRRLSKEYHPDTTSLPLKTASEKFMKLREVYNVLSDEETRRFYDWTLAQEVASRQAEKMRMKLEDPKEQDFRGYESIPDMVDRLGGRNMELSDQAMTALTFDILIVLFAVCCIVFVIVFKDPSY
Source: (natural) Arabidopsis thaliana (thale cress)

+
Photosystem I reaction center subunit ... , 9 types, 18 molecules ADBDAEBEAFBFAGBGAHBHAIBIAJBJAKBKALBL

#4: Protein Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I 20 kDa subunit 2 / PSI-D2


Mass: 22336.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SA56
#5: Protein Photosystem I reaction center subunit IV A, chloroplastic / PSI-E A


Mass: 14984.955 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S831
#6: Protein Photosystem I reaction center subunit III, chloroplastic / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 24203.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SHE8
#7: Protein Photosystem I reaction center subunit V, chloroplastic / PSI-G


Mass: 17103.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S7N7
#8: Protein Photosystem I reaction center subunit VI-2, chloroplastic / PSI-H1


Mass: 15291.522 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI6
#9: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 4137.024 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56768
#10: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 5011.897 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56769
#11: Protein Photosystem I reaction center subunit psaK, chloroplastic / PSI-K / Photosystem I subunit X


Mass: 13219.431 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI5
#12: Protein Photosystem I reaction center subunit XI, chloroplastic / PSI-L / PSI subunit V


Mass: 23070.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI4

+
Chlorophyll a-b binding protein ... , 2 types, 3 molecules A1B1A4

#13: Protein Chlorophyll a-b binding protein 6, chloroplastic / LHCI-730 / LHCII type III CAB-6 / Light-harvesting complex protein Lhca1


Mass: 26021.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q01667
#15: Protein Chlorophyll a-b binding protein 4, chloroplastic / LHCI type III CAB-4


Mass: 27760.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P27521

+
Photosystem I chlorophyll a/b-binding protein ... , 4 types, 5 molecules A3B3A6B2B5

#14: Protein Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Lhca3*1 / LHCI type III LHCA3


Mass: 29206.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SY97
#16: Protein Photosystem I chlorophyll a/b-binding protein 6, chloroplastic / LHCI type III LHCA6


Mass: 29969.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LCQ4
#17: Protein Photosystem I chlorophyll a/b-binding protein 2, chloroplastic / Lhca2 / LHCI type III LHCA2


Mass: 27782.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SYW8
#18: Protein Photosystem I chlorophyll a/b-binding protein 5, chloroplastic / Lhca5 / LHCI type III LHCA5


Mass: 27830.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C639

+
NAD(P)H-quinone oxidoreductase subunit ... , 13 types, 13 molecules ABCEFGHIJKLMN

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


Mass: 40041.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q37165, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#20: Protein NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NAD(P)H dehydrogenase / subunit 2 / NADH-plastoquinone oxidoreductase subunit 2


Mass: 57018.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: A0A1B1W4Z4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#21: Protein NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H dehydrogenase subunit 3 / NADH-plastoquinone oxidoreductase subunit 3


Mass: 13846.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56751, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#23: Protein NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H dehydrogenase subunit 4L / NADH-plastoquinone oxidoreductase subunit 4L


Mass: 11297.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P26289, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#24: Protein NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic / NAD(P)H dehydrogenase subunit 5 / NADH-plastoquinone oxidoreductase subunit 5


Mass: 85300.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56752, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#25: Protein NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / NAD(P)H dehydrogenase subunit 6 / NADH-plastoquinone oxidoreductase subunit 6


Mass: 19218.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q95695, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#36: 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: 45553.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56753, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#37: Protein NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / NAD(P)H dehydrogenase subunit I / NDH subunit I / NADH-plastoquinone oxidoreductase subunit I


Mass: 20107.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56755, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#38: Protein NAD(P)H-quinone oxidoreductase subunit J, chloroplastic / NAD(P)H dehydrogenase subunit J / NADH-plastoquinone oxidoreductase subunit J


Mass: 18579.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56754, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#39: Protein NAD(P)H-quinone oxidoreductase subunit K, chloroplastic / NAD(P)H dehydrogenase subunit K / NADH-plastoquinone oxidoreductase subunit K


Mass: 25396.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56756, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#40: Protein NAD(P)H-quinone oxidoreductase subunit L, chloroplastic / NAD(P)H dehydrogenase subunit L / NDH subunit L / NDH-L / NADH-plastoquinone oxidoreductase subunit ...NAD(P)H dehydrogenase subunit L / NDH subunit L / NDH-L / NADH-plastoquinone oxidoreductase subunit L / Protein CHLORORESPIRATORY REDUCTION 23


Mass: 21987.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9CAC5, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#41: Protein NAD(P)H-quinone oxidoreductase subunit M, chloroplastic / NAD(P)H dehydrogenase subunit M / NDH subunit M / NDH-M / NADH-plastoquinone oxidoreductase subunit M


Mass: 24820.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q2V2S7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#42: Protein NAD(P)H-quinone oxidoreductase subunit N, chloroplastic / NAD(P)H dehydrogenase subunit N / NDH subunit N / NDH-N / NADH-plastoquinone oxidoreductase subunit N


Mass: 23430.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9LVM2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

+
Photosynthetic NDH subunit of subcomplex B ... , 4 types, 4 molecules abce

#26: Protein Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / Protein PnsB1 / NAD(P)H DEHYDROGENASE SUBUNIT 48 / NDH-DEPENDENT CYCLIC ELECTRON FLOW 1


Mass: 51080.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S9N6
#27: Protein Photosynthetic NDH subunit of subcomplex B 2, chloroplastic / Protein PnsB2 / NAD(P)H DEHYDROGENASE SUBUNIT 45 / NDH-DEPENDENT CYCLIC ELECTRON FLOW 2


Mass: 38048.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q94AQ8
#28: Protein Photosynthetic NDH subunit of subcomplex B 3, chloroplastic / Protein PnsB3 / NDH-DEPENDENT CYCLIC ELECTRON FLOW 4


Mass: 22448.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LU21
#30: Protein Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Protein PnsB5 / NAD(P)H dehydrogenase 18


Mass: 23767.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FG89

+
Photosynthetic NDH subunit of lumenal location ... , 4 types, 4 molecules fghi

#31: Protein Photosynthetic NDH subunit of lumenal location 1, chloroplastic / PsbP-like protein 2


Mass: 26997.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O80634
#32: Protein Photosynthetic NDH subunit of lumenal location 2, chloroplastic / PsbQ-like protein 1


Mass: 22183.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9XI73
#33: Protein Photosynthetic NDH subunit of lumenal location 3, chloroplastic / PsbQ-like protein 2


Mass: 24811.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SGH4
#34: Protein Photosynthetic NDH subunit of lumenal location 4, chloroplastic / FK506-binding protein 16-2 / AtFKBP16-2 / Immunophilin FKBP16-2 / Peptidyl-prolyl cis-trans ...FK506-binding protein 16-2 / AtFKBP16-2 / Immunophilin FKBP16-2 / Peptidyl-prolyl cis-trans isomerase FKBP16-2 / PPIase FKBP16-2 / Rotamase


Mass: 23282.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SCY3, peptidylprolyl isomerase

+
Sugars , 2 types, 10 molecules

#50: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#51: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15

+
Non-polymers , 11 types, 413 molecules

#45: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 284 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#46: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H46O2
#47: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#48: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C40H56
#49: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#52: 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.: 9 / Source method: obtained synthetically / Formula: C40H56O2
#53: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10
#54: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#55: Chemical
ChemComp-XAT / (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 / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56O4
#56: 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.: 2 / Source method: obtained synthetically / Formula: C41H78O12S
#57: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

+
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cyclic electron transfer supercomplex from Arabidopsis
Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136022 / Symmetry type: POINT

+
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