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- PDB-6khi: Supercomplex for cylic electron transport in cyanobacteria -

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Entry
Database: PDB / ID: 6khi
TitleSupercomplex for cylic electron transport in cyanobacteria
Components
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 12
  • (proton-translocating NADH-quinone dehydrogenase subunit ...) x 2
  • Ferredoxin-1
  • NAD(P)H-quinone oxidoreductase chain 4 1
  • NADH dehydrogenase subunit 5
  • NADH-quinone oxidoreductase subunit J
  • Tlr0472 protein
  • Tlr0636 protein
KeywordsELECTRON TRANSPORT / Cylic electron transport / photosynthetic NDH complex / Cyanobacteria
Function / homology
Function and homology information


: / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / photosynthesis, light reaction / plasma membrane-derived thylakoid membrane / NADH dehydrogenase activity / respiratory chain complex I ...: / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / photosynthesis, light reaction / plasma membrane-derived thylakoid membrane / NADH dehydrogenase activity / respiratory chain complex I / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / aerobic respiration / electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Protein of unknown function DUF2996 / Protein of unknown function (DUF2996) / Helix Hairpins - #3510 / NADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / 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 ...Protein of unknown function DUF2996 / Protein of unknown function (DUF2996) / Helix Hairpins - #3510 / NADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / 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 / Ferredoxin [2Fe-2S], plant / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / SH3 type barrels. - #140 / 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 / 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. / NADH:ubiquinone oxidoreductase / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Beta-grasp domain superfamily / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / SH3 type barrels. / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER / Chem-SQD / Ferredoxin-1 / NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit 3 ...BETA-CAROTENE / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER / Chem-SQD / Ferredoxin-1 / NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit 3 / NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H-quinone oxidoreductase subunit N / NADH dehydrogenase subunit 5 / NAD(P)H-quinone oxidoreductase chain 4 1 / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H-quinone oxidoreductase subunit 4L / NADH-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit I / NAD(P)H-quinone oxidoreductase subunit 1 / Tlr0636 protein / Tlr0472 protein / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit O / Proton-translocating NADH-quinone dehydrogenase subunit P NdhP / Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
Thermosynechococcus elongatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsPan, X. / Cao, D. / Xie, F. / Zhang, X. / Li, M.
Funding support China, 9items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFA0503702 China
Ministry of Science and Technology (China)2017YFA0504700 China
Ministry of Science and Technology (China)2016YFA0502900 China
Chinese Academy of SciencesXDB08020302 China
Chinese Academy of SciencesXDB08030204 China
Chinese Academy of SciencesXDB27020106 China
Chinese Academy of SciencesQYZDB-SSW-SMC005 China
National Natural Science Foundation of China31770778 China
National Natural Science Foundation of China31600609 China
Citation
Journal: Nat Commun / Year: 2020
Title: Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase.
Authors: Xiaowei Pan / Duanfang Cao / Fen Xie / Fang Xu / Xiaodong Su / Hualing Mi / Xinzheng Zhang / Mei Li /
Abstract: NAD(P)H dehydrogenase-like (NDH) complex NDH-1L of cyanobacteria plays a crucial role in cyclic electron flow (CEF) around photosystem I and respiration processes. NDH-1L couples the electron ...NAD(P)H dehydrogenase-like (NDH) complex NDH-1L of cyanobacteria plays a crucial role in cyclic electron flow (CEF) around photosystem I and respiration processes. NDH-1L couples the electron transport from ferredoxin (Fd) to plastoquinone (PQ) and proton pumping from cytoplasm to the lumen that drives the ATP production. NDH-1L-dependent CEF increases the ATP/NADPH ratio, and is therefore pivotal for oxygenic phototrophs to function under stress. Here we report two structures of NDH-1L from Thermosynechococcus elongatus BP-1, in complex with one Fd and an endogenous PQ, respectively. Our structures represent the complete model of cyanobacterial NDH-1L, revealing the binding manner of NDH-1L with Fd and PQ, as well as the structural elements crucial for proper functioning of the NDH-1L complex. Together, our data provides deep insights into the electron transport from Fd to PQ, and its coupling with proton translocation in NDH-1L.
#1: Journal: To Be Published
Title: Structure of photosystem from green alga.
Authors: Su, X. / Ma, J. / Pan, X. / Zhao, X. / Chang, W. / Liu, Z. / Zhang, X. / Li, M.
History
DepositionJul 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: NAD(P)H-quinone oxidoreductase subunit 1
B: NAD(P)H-quinone oxidoreductase subunit 2
C: NAD(P)H-quinone oxidoreductase subunit 3
D: NAD(P)H-quinone oxidoreductase chain 4 1
E: NAD(P)H-quinone oxidoreductase subunit 4L
F: NADH dehydrogenase subunit 5
G: NADH-quinone oxidoreductase subunit J
H: NAD(P)H-quinone oxidoreductase subunit H
I: NAD(P)H-quinone oxidoreductase subunit I
J: NAD(P)H-quinone oxidoreductase subunit J
K: NAD(P)H-quinone oxidoreductase subunit K
L: NAD(P)H-quinone oxidoreductase subunit L
M: NAD(P)H-quinone oxidoreductase subunit M
N: NAD(P)H-quinone oxidoreductase subunit N
O: NAD(P)H-quinone oxidoreductase subunit O
P: proton-translocating NADH-quinone dehydrogenase subunit P
Q: proton-translocating NADH-quinone dehydrogenase subunit Q
S: Tlr0636 protein
V: Tlr0472 protein
1: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)493,45239
Polymers480,95220
Non-polymers12,50119
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NAD(P)H-quinone oxidoreductase subunit ... , 12 types, 12 molecules ABCEHIJKLMNO

#1: Protein NAD(P)H-quinone oxidoreductase subunit 1 / NAD(P)H dehydrogenase I subunit 1 / NDH-1 subunit 1 / NDH-A


Mass: 40565.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DL32, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H dehydrogenase subunit 2 / NADH-plastoquinone oxidoreductase subunit 2 / NDH-1 / subunit 2


Mass: 55168.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DMR6, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#3: Protein NAD(P)H-quinone oxidoreductase subunit 3 / NAD(P)H dehydrogenase subunit 3 / NADH-plastoquinone oxidoreductase subunit 3 / NDH-1 subunit 3 / NDH-C


Mass: 15013.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DJ02, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#5: Protein NAD(P)H-quinone oxidoreductase subunit 4L / NAD(P)H dehydrogenase subunit 4L / NADH-plastoquinone oxidoreductase subunit 4L / NDH-1 / subunit 4L / NDH-E


Mass: 11140.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DL29, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#8: Protein NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H dehydrogenase subunit H / NADH-plastoquinone oxidoreductase subunit H / NDH-1 subunit H / NDH-H


Mass: 45271.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DJD9, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#9: Protein NAD(P)H-quinone oxidoreductase subunit I / NAD(P)H dehydrogenase I subunit I / NDH-1 subunit I / NDH-I


Mass: 22444.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DL31, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#10: Protein NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H dehydrogenase subunit J / NADH-plastoquinone oxidoreductase subunit J / NDH-1 subunit J / NDH-J


Mass: 19363.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DJ01, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#11: Protein NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H dehydrogenase I subunit K / NDH-1 subunit K / NDH-K


Mass: 25766.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DKZ4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#12: Protein NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H dehydrogenase I subunit L / NDH-1 subunit L / NDH-L


Mass: 8575.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DKZ3, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#13: Protein NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H dehydrogenase I subunit M / NDH-M


Mass: 12584.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DLN5, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#14: Protein NAD(P)H-quinone oxidoreductase subunit N / NAD(P)H dehydrogenase I subunit N / NDH-N


Mass: 16656.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DJU2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#15: Protein NAD(P)H-quinone oxidoreductase subunit O / NAD(P)H dehydrogenase I subunit O / NDH-1 subunit O / NDH-O


Mass: 7877.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1
References: UniProt: Q8DMU4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Protein , 6 types, 6 molecules DFGSV1

#4: Protein NAD(P)H-quinone oxidoreductase chain 4 1 / NAD(P)H dehydrogenase I / chain 4 1 / NDH-1


Mass: 57847.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1
References: UniProt: Q8DKY0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein NADH dehydrogenase subunit 5


Mass: 72025.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: Q8DKX9
#7: Protein NADH-quinone oxidoreductase subunit J


Mass: 21580.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1
References: UniProt: Q8DL30, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#18: Protein Tlr0636 protein


Mass: 12462.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DL61
#19: Protein Tlr0472 protein


Mass: 16016.489 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DLL4
#20: Protein Ferredoxin-1 / Ferredoxin I


Mass: 10853.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / Gene: petF1, petF / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3C9

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Proton-translocating NADH-quinone dehydrogenase subunit ... , 2 types, 2 molecules PQ

#16: Protein/peptide proton-translocating NADH-quinone dehydrogenase subunit P


Mass: 4878.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: V5V507*PLUS
#17: Protein/peptide proton-translocating NADH-quinone dehydrogenase subunit Q


Mass: 4858.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: V5V791*PLUS

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Sugars , 1 types, 2 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 6 types, 17 molecules

#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#23: 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.: 3 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Electron transport complex NDH-Fd from cyanobacteria / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152003 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00633468
ELECTRON MICROSCOPYf_angle_d0.94445485
ELECTRON MICROSCOPYf_dihedral_angle_d16.70519525
ELECTRON MICROSCOPYf_chiral_restr0.0565225
ELECTRON MICROSCOPYf_plane_restr0.0085603

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