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- PDB-6hum: Structure of the photosynthetic complex I from Thermosynechococcu... -

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Entry
Database: PDB / ID: 6hum
TitleStructure of the photosynthetic complex I from Thermosynechococcus elongatus
Components
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 12
  • (NADH dehydrogenase subunit ...) x 2
  • (Proton-translocating NADH-quinone dehydrogenase subunit ...) x 2
  • NAD(P)H-quinone oxidoreductase chain 4 1
  • Tlr0636 protein
KeywordsPROTON TRANSPORT / Respiratory Complex / Ferredoxin / Cyclic electron flow / Complex I / Membrane protein complex
Function / homologyNADH-quinone oxidoreductase chain 4 / Cyanobacterial and plastid NDH-1 subunit M / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site ...NADH-quinone oxidoreductase chain 4 / Cyanobacterial and plastid NDH-1 subunit M / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase, subunit N / NAD(P)H-quinone oxidoreductase subunit O / NADH dehydrogenase-like complex, subunit S / NAD(P)H-quinone oxidoreductase subunit D/H / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NADH-quinone oxidoreductase, chain I / [NiFe]-hydrogenase, large subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Proton-conducting membrane transporter / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, chain M/4 / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, 20 Kd subunit / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S dicluster domain / Cyanobacterial and plant NDH-1 subunit O / NADH-quinone oxidoreductase cyanobacterial subunit N / NAD(P)H dehydrogenase subunit S / NADH dehydrogenase transmembrane subunit / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, subunit D / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH:ubiquinone oxidoreductase / NADH-plastoquinone oxidoreductase, chain 5 / NADH-plastoquinone oxidoreductase, subunit I / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / Translocases, Catalysing the translocation of hydrons, Linked to oxidoreductase reactions / Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor / NADH dehydrogenase (quinone) / NADH dehydrogenase (ubiquinone) activity / photosynthetic electron transport chain / ATP synthesis coupled electron transport / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / thylakoid membrane / photosynthesis, light reaction / quinone binding / 4 iron, 4 sulfur cluster binding / NAD binding / iron ion binding / integral component of membrane / plasma membrane / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit 4L / NAD(P)H-quinone oxidoreductase subunit M / Tlr0636 protein / NAD(P)H-quinone oxidoreductase subunit 1 / NAD(P)H-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit 3 / NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase chain 4 1 / NADH dehydrogenase subunit 5 / NAD(P)H-quinone oxidoreductase subunit N / NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit O
Function and homology information
Specimen sourceThermosynechococcus elongatus BP-1 (Cyanobacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.34 Å resolution
AuthorsSchuller, J.M. / Schuller, S.K. / Kurisu, G. / Engel, B.D. / Nowaczyk, M.M.
CitationJournal: Science / Year: 2018
Title: Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer.
Authors: Jan M Schuller / James A Birrell / Hideaki Tanaka / Tsuyoshi Konuma / Hannes Wulfhorst / Nicholas Cox / Sandra K Schuller / Jacqueline Thiemann / Wolfgang Lubitz / Pierre Sétif / Takahisa Ikegami / Benjamin D Engel / Genji Kurisu / Marc M Nowaczyk
Abstract: Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-Å resolution cryo-EM structure of ...Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-Å resolution cryo-EM structure of photosynthetic complex I from the cyanobacterium The model reveals structural adaptations that facilitate binding and electron transfer from the photosynthetic electron carrier ferredoxin. By mimicking cyclic electron flow with isolated components in vitro, we demonstrate that ferredoxin directly mediates electron transfer between photosystem I and complex I, instead of using intermediates such as NADPH. A large rate constant for association of ferredoxin to complex I indicates efficient recognition, with the protein subunit NdhS being the key component in this process.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 9, 2018 / Release: Jan 9, 2019

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Assembly

Deposited unit
A: NAD(P)H-quinone oxidoreductase subunit 1
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
B: NAD(P)H-quinone oxidoreductase subunit 2
G: NADH dehydrogenase subunit 6
J: NAD(P)H-quinone oxidoreductase subunit J
P: Proton-translocating NADH-quinone dehydrogenase subunit P NdhP
H: NAD(P)H-quinone oxidoreductase subunit H
I: NAD(P)H-quinone oxidoreductase subunit I
K: NAD(P)H-quinone oxidoreductase subunit K
L: NAD(P)H-quinone oxidoreductase subunit L
F: NADH dehydrogenase subunit 5
N: NAD(P)H-quinone oxidoreductase subunit N
M: NAD(P)H-quinone oxidoreductase subunit M
S: Tlr0636 protein
O: NAD(P)H-quinone oxidoreductase subunit O
Q: Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,56023
Polyers453,18118
Non-polymers2,3795
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)96820
ΔGint (kcal/M)-765
Surface area (Å2)118600
MethodPISA

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Components

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

#1: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DL32, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#2: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DJ02, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#4: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DL29, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#5: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DMR6, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#7: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DJ01, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#9: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DJD9, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#10: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DL31, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#11: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DKZ4, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#12: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DKZ3, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#14: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DJU2, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#15: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DLN5, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#17: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DMU4, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor

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Protein/peptide , 2 types, 2 molecules DS

#3: Protein/peptide 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: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DKY0, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#16: Protein/peptide Tlr0636 protein


Mass: 12462.559 Da / Num. of mol.: 1
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DL61

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NADH dehydrogenase subunit ... , 2 types, 2 molecules GF

#6: Protein/peptide NADH dehydrogenase subunit 6 /


Mass: 21580.568 Da / Num. of mol.: 1
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DL30
#13: Protein/peptide NADH dehydrogenase subunit 5 /


Mass: 72025.352 Da / Num. of mol.: 1
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DKX9

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

#8: Protein/peptide Proton-translocating NADH-quinone dehydrogenase subunit P NdhP


Mass: 4630.392 Da / Num. of mol.: 1
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
#18: Protein/peptide Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ


Mass: 4206.993 Da / Num. of mol.: 1
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Non-polymers , 3 types, 5 molecules

#19: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 1 / Formula: C40H56 / Beta-Carotene
#20: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Formula: C45H86O10
#21: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Formula: Fe4S4 / Iron–sulfur cluster

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: photosynthetic complex I / Type: COMPLEX / Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18 / Source: NATURAL
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 49.93 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 133485 / Symmetry type: POINT

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