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- PDB-6nby: T.elongatus NDH (composite model) -

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Entry
Database: PDB / ID: 6nby
TitleT.elongatus NDH (composite model)
Components
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 12
  • (Proton-translocating NADH-quinone dehydrogenase subunit ...) x 2
  • NAD(P)H-quinone oxidoreductase chain 4 1
  • NADH dehydrogenase subunit 5
  • NADH-quinone oxidoreductase subunit JNADH dehydrogenase (quinone)
  • Tlr0636 protein
KeywordsOXIDOREDUCTASE / photosynthesis / bioenergetics / membrane protein complex
Function / homologyNAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / [NiFe]-hydrogenase, large subunit / 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 ...NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / [NiFe]-hydrogenase, large subunit / 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 / NADH-quinone oxidoreductase chain 4 / NADH dehydrogenase transmembrane subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / 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-dehyrogenase subunit F, TMs, (complex I) C-terminus / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH-quinone oxidoreductase, chain M/4 / Cyanobacterial and plastid NDH-1 subunit M / NADH-ubiquinone oxidoreductase chain 4L/K / 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:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-quinone oxidoreductase, subunit D / NADH-quinone oxidoreductase, chain I / 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 / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, 20 Kd subunit / Translocases, Catalysing the translocation of hydrons, Linked to oxidoreductase reactions / 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 4L / NAD(P)H-quinone oxidoreductase subunit 2 / 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 H / 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 3 / 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 / 3.1 Å resolution
AuthorsLaughlin, T.G. / Bayne, A. / Trempe, J.-F. / Savage, D.F. / Davies, K.M.
Funding supportUnited States , 3 items
OrganizationGrant numberCountry
Department of Energy (United States)DE-AC02-O5CH11231United States
National Institutes of Health/National Institute of General Medical Sciences5T32GM007232-38United States
Department of Energy (United States)DE-SC00016240United States
CitationJournal: Nature / Year: 2019
Title: Structure of the complex I-like molecule NDH of oxygenic photosynthesis.
Authors: Thomas G Laughlin / Andrew N Bayne / Jean-François Trempe / David F Savage / Karen M Davies
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 10, 2018 / Release: Feb 27, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 27, 2019Structure modelrepositoryInitial release
1.1Mar 6, 2019Structure modelData collection / Database referencescitation / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc_citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-0415
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  • Superimposition on EM map
  • EMDB-0425
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Structure viewerMolecule:
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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 NdhP
Q: Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ
S: Tlr0636 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,12221
Polyers454,06718
Non-polymers1,0553
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: homology, gel filtration, native gel electrophoresis, mass spectrometry, microscopy
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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/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)
Strain: BP-1
References: UniProt: Q8DL32, Translocases, Catalysing the translocation of hydrons, Linked to oxidoreductase reactions
#2: 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)
Strain: BP-1
References: UniProt: Q8DMR6, Translocases, Catalysing the translocation of hydrons, Linked to oxidoreductase reactions
#3: 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)
Strain: BP-1
References: UniProt: Q8DJ02, Translocases, Catalysing the translocation of hydrons, Linked to oxidoreductase reactions
#5: 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)
Strain: BP-1
References: UniProt: Q8DL29, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#8: 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)
Strain: BP-1
References: UniProt: Q8DJD9, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#9: 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)
Strain: BP-1
References: UniProt: Q8DL31, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#10: 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)
Strain: BP-1
References: UniProt: Q8DJ01, 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)
Strain: BP-1
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)
Strain: BP-1
References: UniProt: Q8DKZ3, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#13: 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)
Strain: BP-1
References: UniProt: Q8DLN5, 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)
Strain: BP-1
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 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)
Strain: BP-1
References: UniProt: Q8DMU4, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor

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Protein/peptide , 4 types, 4 molecules DFGS

#4: 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)
Strain: BP-1
References: UniProt: Q8DKY0, Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor
#6: Protein/peptide NADH dehydrogenase subunit 5 /


Mass: 72025.352 Da / Num. of mol.: 1
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DKX9
#7: Protein/peptide NADH-quinone oxidoreductase subunit J / NADH dehydrogenase (quinone)


Mass: 21580.568 Da / Num. of mol.: 1
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DL30, NADH dehydrogenase (quinone)
#18: Protein/peptide Tlr0636 protein


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

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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 NdhP


Mass: 4878.649 Da / Num. of mol.: 1
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Strain: BP-1
#17: Protein/peptide Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ


Mass: 4844.698 Da / Num. of mol.: 1
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Strain: BP-1

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Non-polymers , 1 types, 3 molecules

#19: 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: NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L) from T.elongatus
Type: COMPLEX / Details: composite model / Entity ID: 1,2,3,4,5,6,7,8,10,11,12,13,14,15,16,17,18 / Source: NATURAL
Molecular weightValue: 0.42 MDa / Experimental value: YES
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Buffer solutionpH: 6
Buffer component
IDConc.NameBuffer ID
120 mMBis-Tris1
2100 mMNaCl1
30.03 %b-dodecyl-maltoside1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 kelvins

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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: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7PHENIX1.13model fitting
12RELION3.0.b23D reconstruction
13PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 81670 / Algorithm: BACK PROJECTION
Details: A bulk of the model is comprise of EMD-0415 which is at an estimated resolution of 3.1 A, while a portion (NdhF/NdhF1, NdhQ, and NdhC) are from EMD-0425 which is at an estimated resolution of 3.5 A.
Symmetry type: POINT
Atomic model buildingOverall b value: 30 / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient
Atomic model building
IDPDB-ID 3D fitting ID
16NBQ1
26NBX1
Least-squares processHighest resolution: 3.1 Å

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