[English] 日本語
Yorodumi
- PDB-6q9d: CI Peripheral Arm focused refinement from Ovine respiratory SC I+III2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q9d
TitleCI Peripheral Arm focused refinement from Ovine respiratory SC I+III2
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 5
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH:ubiquinone oxidoreductase core subunit ...) x 5
  • (NADH:ubiquinone oxidoreductase subunit ...) x 4
  • Acyl carrier protein
  • NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
KeywordsELECTRON TRANSPORT / complex I / peripheral arm / cellular respiration / mitochondria
Function / homology
Function and homology information


mitochondrial ATP synthesis coupled electron transport / blastocyst hatching / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / cellular respiration / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport ...mitochondrial ATP synthesis coupled electron transport / blastocyst hatching / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / cellular respiration / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / mitochondrial large ribosomal subunit / apoptotic mitochondrial changes / reactive oxygen species metabolic process / respiratory electron transport chain / respirasome / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / regulation of mitochondrial membrane potential / regulation of protein phosphorylation / 2 iron, 2 sulfur cluster binding / mitochondrial intermembrane space / positive regulation of fibroblast proliferation / fatty acid biosynthetic process / circadian rhythm / negative regulation of cell growth / NAD binding / brain development / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / response to oxidative stress / nuclear body / mitochondrial matrix / oxidoreductase activity / protein-containing complex binding / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
2Fe-2S iron-sulfur cluster binding domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / Thioredoxin-like [2Fe-2S] ferredoxin / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 ...2Fe-2S iron-sulfur cluster binding domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / Thioredoxin-like [2Fe-2S] ferredoxin / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH:ubiquinone oxidoreductase, subunit G / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NuoE domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH dehydrogenase, subunit C / NADH-quinone oxidoreductase subunit E, N-terminal / SLBB domain / NADH-quinone oxidoreductase subunit E-like / Soluble ligand binding domain / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / Complex 1 protein (LYR family) / Complex 1 LYR protein / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Acyl carrier protein (ACP) / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Complex I subunit B13 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-30kD / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Epimerase domain-containing protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / FE2/S2 (INORGANIC) CLUSTER / Complex I-B14.5a / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial ...Complex I subunit B13 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-30kD / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Epimerase domain-containing protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / FE2/S2 (INORGANIC) CLUSTER / Complex I-B14.5a / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / FLAVIN MONONUCLEOTIDE / Chem-ZMP / IRON/SULFUR CLUSTER / Chem-NDP / Complex I-B14
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLetts, J.A. / Sazanov, L.A.
Funding support Austria, 1items
OrganizationGrant numberCountry
European Research Council701309 Austria
CitationJournal: Mol Cell / Year: 2019
Title: Structures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk.
Authors: James A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov /
Abstract: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4480
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
V1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
V2: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
S1: NADH:ubiquinone oxidoreductase core subunit S1
S2: NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2
S3: NADH:ubiquinone oxidoreductase core subunit S3
S7: NADH:ubiquinone oxidoreductase core subunit S7
S8: NADH:ubiquinone oxidoreductase core subunit S8
V3: NADH:ubiquinone oxidoreductase subunit V3
S6: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
S4: NADH:ubiquinone oxidoreductase subunit S4
A9: NADH:ubiquinone oxidoreductase subunit A9
A2: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
A5: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
A6: NADH:ubiquinone oxidoreductase subunit A6
A7: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
AL: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
AA: Acyl carrier protein
AM: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)438,23330
Polymers433,93618
Non-polymers4,29712
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area94400 Å2
ΔGint-496 kcal/mol
Surface area125870 Å2
MethodPISA

-
Components

+
NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules V1V2

#1: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 48678.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart
References: UniProt: W5PUX0, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating)
#2: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


Mass: 23840.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: W5NRY1

+
NADH:ubiquinone oxidoreductase core subunit ... , 5 types, 5 molecules S1S2S3S7S8

#3: Protein NADH:ubiquinone oxidoreductase core subunit S1


Mass: 77031.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: W5QB34
#4: Protein NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2


Mass: 49193.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart
#5: Protein NADH:ubiquinone oxidoreductase core subunit S3


Mass: 26441.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: W5PB27
#6: Protein NADH:ubiquinone oxidoreductase core subunit S7


Mass: 20104.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart
#7: Protein NADH:ubiquinone oxidoreductase core subunit S8


Mass: 20219.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart

+
NADH:ubiquinone oxidoreductase subunit ... , 4 types, 4 molecules V3S4A9A6

#8: Protein NADH:ubiquinone oxidoreductase subunit V3 /


Mass: 8423.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart
#10: Protein NADH:ubiquinone oxidoreductase subunit S4 /


Mass: 15375.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: W5PE07
#11: Protein NADH:ubiquinone oxidoreductase subunit A9 /


Mass: 38660.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: W5PI58
#14: Protein NADH:ubiquinone oxidoreductase subunit A6 /


Mass: 14923.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: W5QC06

+
Protein , 2 types, 2 molecules S6AA

#9: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 10651.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart
#17: Protein Acyl carrier protein /


Mass: 10119.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: W5NQT7

+
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 5 types, 5 molecules A2A5A7ALAM

#12: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 10966.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: W5QAH8
#13: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5


Mass: 13156.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: W5PNX7
#15: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7


Mass: 12399.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: W5P0I2
#16: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart / References: UniProt: B9VGZ9
#18: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 16635.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: This is a focused refinement so only the N-terminal part of this subunit is present in the map.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: CardiacHeart

+
Non-polymers , 6 types, 12 molecules

#19: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#20: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#21: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#22: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#23: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#24: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49N2O8PS

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Ovine mitochondrial SC I+III2 / Type: COMPLEX
Details: Complex I membrane arm focused refinement from ovine respiratory SC I+III2
Entity ID: #1-#18 / Source: NATURAL
Molecular weightValue: 1.4 MDa / Experimental value: NO
Source (natural)Organism: Ovis aries (sheep) / Cellular location: Mitochondrial inner membrane / Organ: Heart / Organelle: Mitochondria / Tissue: Cardiac
Buffer solutionpH: 7.4 / Details: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35
Buffer component
IDConc.NameFormulaBuffer-ID
10.25 Msodium chlorideNaClSodium chloride1
20.02 MHEPES1
30.02 %Brij-351
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: PROPANE / Humidity: 95 % / Chamber temperature: 277 K
Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing

-
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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 51 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1854
Image scansMovie frames/image: 34

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9PHENIX1.13-2998model refinement
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 400000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178121 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 90 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 1LNK

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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