[English] 日本語
Yorodumi
- PDB-8qby: Respiratory complex I from Paracoccus denitrificans in MSP2N2 nan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qby
TitleRespiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs
Components
  • (NADH dehydrogenase subunit ...) x 3
  • (NADH-quinone ...) x 11
  • ETC complex I subunit conserved region
  • NADH:ubiquinone oxidoreductase 17.2 kD subunit
  • Protein-L-isoaspartate O-methyltransferase
  • Zinc finger CHCC-type domain-containing protein
KeywordsOXIDOREDUCTASE / Respiratory complex I / NADH:ubiquinone oxidoreductase / Nanodiscs
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / : / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity ...NADH:ubiquinone reductase (H+-translocating) / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / : / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / : / electron transport chain / protein modification process / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / methylation / oxidoreductase activity / iron ion binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial ...Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH-quinone oxidoreductase, chain G, C-terminal / : / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / SLBB domain / : / 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-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / 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 / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / 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 oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / 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. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 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 / Thioredoxin-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-P5S / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / UBIQUINONE-10 / NADH:ubiquinone oxidoreductase 17.2 kD subunit ...1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-P5S / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / UBIQUINONE-10 / NADH:ubiquinone oxidoreductase 17.2 kD subunit / ETC complex I subunit conserved region / Zinc finger CHCC-type domain-containing protein / NADH-quinone oxidoreductase subunit N / NADH dehydrogenase subunit M / NADH dehydrogenase subunit L / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit F / NADH dehydrogenase subunit E / NADH-quinone oxidoreductase subunit D / NADH-quinone oxidoreductase subunit C / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit A / Protein-L-isoaspartate O-methyltransferase / NADH-quinone oxidoreductase chain 10
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsIvanov, B.S. / Bridges, H.R. / Hirst, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00028/1 United Kingdom
CitationJournal: To Be Published
Title: Respiratory complex I from Paracoccus denitrificans
Authors: Ivanov, B.S. / Bridges, H.R. / Hirst, J. / Jarman, O.D.
History
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
K: NADH-quinone oxidoreductase subunit K
G: NADH-quinone oxidoreductase
t: Protein-L-isoaspartate O-methyltransferase
I: NADH-quinone oxidoreductase subunit I
E: NADH dehydrogenase subunit E
N: NADH-quinone oxidoreductase subunit N
H: NADH-quinone oxidoreductase subunit H
F: NADH-quinone oxidoreductase subunit F
D: NADH-quinone oxidoreductase subunit D
q: NADH:ubiquinone oxidoreductase 17.2 kD subunit
A: NADH-quinone oxidoreductase subunit A
J: NADH-quinone oxidoreductase chain 10
R: Zinc finger CHCC-type domain-containing protein
Q: ETC complex I subunit conserved region
C: NADH-quinone oxidoreductase subunit C
B: NADH-quinone oxidoreductase subunit B
L: NADH dehydrogenase subunit L
M: NADH dehydrogenase subunit M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)614,70967
Polymers585,12118
Non-polymers29,58849
Water19,4561080
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
NADH-quinone ... , 11 types, 11 molecules KGINHFDAJCB

#1: Protein NADH-quinone oxidoreductase subunit K / NADH dehydrogenase I subunit K / NADH dehydrogenase I / subunit 11 / NADH-quinone oxidoreductase ...NADH dehydrogenase I subunit K / NADH dehydrogenase I / subunit 11 / NADH-quinone oxidoreductase subunit 11 / NQO11 / NDH-1 subunit K / NDH-1


Mass: 10863.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B482, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NADH-quinone oxidoreductase


Mass: 73289.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B489, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#4: Protein NADH-quinone oxidoreductase subunit I


Mass: 18925.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B486
#6: Protein NADH-quinone oxidoreductase subunit N


Mass: 52564.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B479
#7: Protein NADH-quinone oxidoreductase subunit H


Mass: 38861.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B487
#8: Protein NADH-quinone oxidoreductase subunit F


Mass: 47281.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B491
#9: Protein NADH-quinone oxidoreductase subunit D


Mass: 46811.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B495
#11: Protein NADH-quinone oxidoreductase subunit A


Mass: 13686.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B498
#12: Protein NADH-quinone oxidoreductase chain 10


Mass: 21835.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: P29922
#15: Protein NADH-quinone oxidoreductase subunit C


Mass: 23920.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B496
#16: Protein NADH-quinone oxidoreductase subunit B


Mass: 19525.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B497

-
Protein , 4 types, 4 molecules tqRQ

#3: Protein Protein-L-isoaspartate O-methyltransferase


Mass: 23528.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B5L6
#10: Protein NADH:ubiquinone oxidoreductase 17.2 kD subunit


Mass: 14432.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B1H8
#13: Protein Zinc finger CHCC-type domain-containing protein


Mass: 7069.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B357
#14: Protein ETC complex I subunit conserved region


Mass: 12048.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B1M0

-
NADH dehydrogenase subunit ... , 3 types, 3 molecules ELM

#5: Protein NADH dehydrogenase subunit E


Mass: 26145.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B494
#17: Protein NADH dehydrogenase subunit L


Mass: 77811.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B481
#18: Protein NADH dehydrogenase subunit M


Mass: 56519.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B480

-
Non-polymers , 13 types, 1129 molecules

#19: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#20: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#21: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#22: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C39H77O8P
#23: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO10P
#24: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#25: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#26: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C81H156O17P2 / Comment: phospholipid*YM
#27: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#28: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#29: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#30: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#31: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1080 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Respiratory complex I / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Buffer solutionpH: 6.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grids were glow discharged at 20 mA for 90 s to clean and increase the hydrophilicity of the grid surface and then incubated in 5 mM 11-mercaptoundecyl hexaethyleneglycol in ethanol for ...Details: The grids were glow discharged at 20 mA for 90 s to clean and increase the hydrophilicity of the grid surface and then incubated in 5 mM 11-mercaptoundecyl hexaethyleneglycol in ethanol for two days under anaerobic conditions. The grids were then washed in 100% ethanol and dried three times prior to sample application.
Grid material: GOLD / Grid type: UltrAuFoil R0./1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.4 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 16814
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
2EPU2.7image acquisition
4CTFFIND4CTF correction
10RELION3.1.0final Euler assignment
11RELION3.1.0classification
12RELION3.1.03D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146603 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: Model Angelo / Source name: Other / Type: in silico model

+
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