[English] 日本語
Yorodumi
- EMDB-4093: Entire ovine respiratory complex I, Combined Map -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 4093
TitleEntire ovine respiratory complex I, Combined Map
Map data
SampleMitochondrial complex I
  • (Mitochondrial complex I, ...) x 42
  • Acyl carrier protein
  • NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
  • (ligand) x 10
Function / homologyNADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase, subunit C / NADH-quinone oxidoreductase, chain I / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, subunit G / CHCH / NADH dehydrogenase subunit 2, C-terminal / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, subunit NDUFB4 ...NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase, subunit C / NADH-quinone oxidoreductase, chain I / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, subunit G / CHCH / NADH dehydrogenase subunit 2, C-terminal / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH:ubiquinone oxidoreductase, MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH:ubiquinone oxidoreductase subunit B14.5a / NADH:ubiquinone oxidoreductase, subunit b14.5b / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH:ubiquinone oxidoreductase, chain 2 / NADH:ubiquinone oxidoreductase / NADH-plastoquinone oxidoreductase, chain 5 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-ubiquinone oxidoreductase, 20 Kd subunit / Phosphopantetheine attachment site / Molybdopterin oxidoreductase / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / GRIM-19 / Molybdopterin oxidoreductase, 4Fe-4S domain / Ribosomal protein/NADH dehydrogenase domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Complex 1 LYR protein / NADH:ubiquinone oxidoreductase, B18 subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / Phosphopantetheine binding ACP domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Proton-conducting membrane transporter / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Deoxynucleoside kinase domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / 2Fe-2S ferredoxin-like superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / P-loop containing nucleoside triphosphate hydrolase / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / [NiFe]-hydrogenase, large subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH-ubiquinone oxidoreductase flavoprotein 3 / Acyl carrier protein (ACP) / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 beta subcomplex subunit 2 / 4Fe-4S dicluster domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / SLBB domain / Zinc-finger domain / NADH-ubiquinone oxidoreductase subunit 10 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / Phosphopantetheine attachment site. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-ubiquinone oxidoreductase B12 subunit family / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature.
Function and homology information
SourceOvis aries (sheep) / Sheep (sheep)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsFiedorczuk K / Letts JA / Sazanov LA
CitationJournal: Nature / Year: 2016
Title: Atomic structure of the entire mammalian mitochondrial complex I.
Authors: Karol Fiedorczuk / James A Letts / Gianluca Degliesposti / Karol Kaszuba / Mark Skehel / Leonid A Sazanov
Validation ReportPDB-ID: 5lnk

SummaryFull reportAbout validation report
DateDeposition: Oct 28, 2016 / Header (metadata) release: Nov 23, 2016 / Map release: Nov 23, 2016 / Last update: Aug 30, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5lnk
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_4093.map.gz (map file in CCP4 format, 15207 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
129 pix
1.39 Å/pix.
= 179.31 Å
141 pix
1.39 Å/pix.
= 195.99 Å
209 pix
1.39 Å/pix.
= 290.51 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

(generated in cubic-lattice coordinate)

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:0.15 (by author), 0.15 (movie #1):
Minimum - Maximum-0.5494037 - 1.3139707
Average (Standard dev.)0.0089633055 (0.05093917)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZYX
Dimensions141209129
Origin0.00.00.0
Limit140.0208.0128.0
Spacing129141209
CellA: 179.31 Å / B: 195.99 Å / C: 290.51 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z129141209
origin x/y/z0.0000.0000.000
length x/y/z179.310195.990290.510
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ129141209
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS209141129
D min/max/mean-0.5491.3140.009

-
Supplemental data

-
Sample components

+
Entire Mitochondrial complex I

EntireName: Mitochondrial complex I / Number of components: 55

+
Component #1: protein, Mitochondrial complex I

ProteinName: Mitochondrial complex I / Recombinant expression: No
MassExperimental: 970 kDa
SourceSpecies: Ovis aries (sheep)

+
Component #2: protein, Mitochondrial complex I, 51 kDa subunit

ProteinName: Mitochondrial complex I, 51 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.678281 kDa
SourceSpecies: Sheep (sheep)

+
Component #3: protein, Mitochondrial complex I, 24 kDa subunit

ProteinName: Mitochondrial complex I, 24 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.840428 kDa
SourceSpecies: Sheep (sheep)

+
Component #4: protein, Mitochondrial complex I, 75 kDa subunit

ProteinName: Mitochondrial complex I, 75 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 77.031156 kDa
SourceSpecies: Sheep (sheep)

+
Component #5: protein, Mitochondrial complex I, 49 kDa subunit

ProteinName: Mitochondrial complex I, 49 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.120078 kDa
SourceSpecies: Sheep (sheep)

+
Component #6: protein, Mitochondrial complex I, 30 kDa subunit

ProteinName: Mitochondrial complex I, 30 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.441793 kDa
SourceSpecies: Sheep (sheep)

+
Component #7: protein, Mitochondrial complex I, PSST subunit

ProteinName: Mitochondrial complex I, PSST subunit / Details: NCBIProt XP_012033846.2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.104531 kDa
SourceSpecies: Sheep (sheep)

+
Component #8: protein, Mitochondrial complex I, TYKY subunit

ProteinName: Mitochondrial complex I, TYKY subunit / Details: NCBIprot XP_011972879.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.219947 kDa
SourceSpecies: Sheep (sheep)

+
Component #9: protein, Mitochondrial complex I, ND1 subunit

ProteinName: Mitochondrial complex I, ND1 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.884902 kDa
SourceSpecies: Sheep (sheep)

+
Component #10: protein, Mitochondrial complex I, ND2 subunit

ProteinName: Mitochondrial complex I, ND2 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.149805 kDa
SourceSpecies: Sheep (sheep)

+
Component #11: protein, Mitochondrial complex I, ND3 subunit

ProteinName: Mitochondrial complex I, ND3 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.10652 kDa
SourceSpecies: Sheep (sheep)

+
Component #12: protein, Mitochondrial complex I, ND4 subunit

ProteinName: Mitochondrial complex I, ND4 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.058734 kDa
SourceSpecies: Sheep (sheep)

+
Component #13: protein, Mitochondrial complex I, ND4L subunit

ProteinName: Mitochondrial complex I, ND4L subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.840228 kDa
SourceSpecies: Sheep (sheep)

+
Component #14: protein, Mitochondrial complex I, ND5 subunit

ProteinName: Mitochondrial complex I, ND5 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.554945 kDa
SourceSpecies: Sheep (sheep)

+
Component #15: protein, Mitochondrial complex I, ND6 subunit

ProteinName: Mitochondrial complex I, ND6 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.126619 kDa
SourceSpecies: Sheep (sheep)

+
Component #16: protein, Mitochondrial complex I, 10 kDa subunit

ProteinName: Mitochondrial complex I, 10 kDa subunit / Details: NCBIprot XP_011991231.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.423314 kDa
SourceSpecies: Sheep (sheep)

+
Component #17: protein, Mitochondrial complex I, 13 kDa subunit

ProteinName: Mitochondrial complex I, 13 kDa subunit / Details: NCBIprot XP_011980592.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.651796 kDa
SourceSpecies: Sheep (sheep)

+
Component #18: protein, Mitochondrial complex I, 18 kDa subunit

ProteinName: Mitochondrial complex I, 18 kDa subunit / Details: NCBIprot XP_004017046.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.3753 kDa
SourceSpecies: Sheep (sheep)

+
Component #19: protein, Mitochondrial complex I, 39 kDa subunit

ProteinName: Mitochondrial complex I, 39 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.660488 kDa
SourceSpecies: Sheep (sheep)

+
Component #20: protein, Mitochondrial complex I, B8 subunit

ProteinName: Mitochondrial complex I, B8 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.966627 kDa
SourceSpecies: Sheep (sheep)

+
Component #21: protein, Mitochondrial complex I, B13 subunit

ProteinName: Mitochondrial complex I, B13 subunit / Details: NCBIprot XP_004005022.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.156311 kDa
SourceSpecies: Sheep (sheep)

+
Component #22: protein, Mitochondrial complex I, B14 subunit

ProteinName: Mitochondrial complex I, B14 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.923245 kDa
SourceSpecies: Sheep (sheep)

+
Component #23: protein, Mitochondrial complex I, B14.5a subunit

ProteinName: Mitochondrial complex I, B14.5a subunit / Details: NCBIprot XP_004008614.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.399201 kDa
SourceSpecies: Sheep (sheep)

+
Component #24: protein, Mitochondrial complex I, B17.2 subunit

ProteinName: Mitochondrial complex I, B17.2 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.115508 kDa
SourceSpecies: Sheep (sheep)

+
Component #25: protein, Acyl carrier protein

ProteinName: Acyl carrier protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.119541 kDa
SourceSpecies: Sheep (sheep)

+
Component #26: protein, Mitochondrial complex I, 42 kDa subunit

ProteinName: Mitochondrial complex I, 42 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.803762 kDa
SourceSpecies: Sheep (sheep)

+
Component #27: protein, Mitochondrial complex I, 15 kDa subunit

ProteinName: Mitochondrial complex I, 15 kDa subunit / Details: NCBIprot XP_004001873.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.474397 kDa
SourceSpecies: Sheep (sheep)

+
Component #28: protein, Mitochondrial complex I, B9 subunit

ProteinName: Mitochondrial complex I, B9 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.194655 kDa
SourceSpecies: Sheep (sheep)

+
Component #29: protein, Mitochondrial complex I, B12 subunit

ProteinName: Mitochondrial complex I, B12 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.015482 kDa
SourceSpecies: Sheep (sheep)

+
Component #30: protein, Mitochondrial complex I, B14.5b subunit

ProteinName: Mitochondrial complex I, B14.5b subunit / Details: NCBIprot XP_004019479.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.23142 kDa
SourceSpecies: Sheep (sheep)

+
Component #31: protein, Mitochondrial complex I, B15 subunit

ProteinName: Mitochondrial complex I, B15 subunit / Details: NCBIprot XP_004003003.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.975999 kDa
SourceSpecies: Sheep (sheep)

+
Component #32: protein, Mitochondrial complex I, B16.6 subunit

ProteinName: Mitochondrial complex I, B16.6 subunit / Details: NCBIprot XP_004008450.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.635264 kDa
SourceSpecies: Sheep (sheep)

+
Component #33: protein, Mitochondrial complex I, B17 subunit

ProteinName: Mitochondrial complex I, B17 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.433929 kDa
SourceSpecies: Sheep (sheep)

+
Component #34: protein, Mitochondrial complex I, B18 subunit

ProteinName: Mitochondrial complex I, B18 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.28261 kDa
SourceSpecies: Sheep (sheep)

+
Component #35: protein, Mitochondrial complex I, B22 subunit

ProteinName: Mitochondrial complex I, B22 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.648715 kDa
SourceSpecies: Sheep (sheep)

+
Component #36: protein, Mitochondrial complex I, AGGG subunit

ProteinName: Mitochondrial complex I, AGGG subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.500289 kDa
SourceSpecies: Sheep (sheep)

+
Component #37: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.81807 kDa
SourceSpecies: Sheep (sheep)

+
Component #38: protein, Mitochondrial complex I, ESSS subunit

ProteinName: Mitochondrial complex I, ESSS subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.455033 kDa
SourceSpecies: Sheep (sheep)

+
Component #39: protein, Mitochondrial complex I, KFYI subunit

ProteinName: Mitochondrial complex I, KFYI subunit / Details: NCBIprot XP_004017292.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.808645 kDa
SourceSpecies: Sheep (sheep)

+
Component #40: protein, Mitochondrial complex I, MNLL subunit

ProteinName: Mitochondrial complex I, MNLL subunit / Details: NCBIprot XP_004018002.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.930083 kDa
SourceSpecies: Sheep (sheep)

+
Component #41: protein, Mitochondrial complex I, MWFE subunit

ProteinName: Mitochondrial complex I, MWFE subunit / Details: NCBIprot NP_001305903.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.211519 kDa
SourceSpecies: Sheep (sheep)

+
Component #42: protein, Mitochondrial complex I, PDSW subunit

ProteinName: Mitochondrial complex I, PDSW subunit / Details: NCBIprot XP_011999786.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.880752 kDa
SourceSpecies: Sheep (sheep)

+
Component #43: protein, Mitochondrial complex I, PGIV subunit

ProteinName: Mitochondrial complex I, PGIV subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.008014 kDa
SourceSpecies: Sheep (sheep)

+
Component #44: protein, Mitochondrial complex I, SGDH subunit

ProteinName: Mitochondrial complex I, SGDH subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.714369 kDa
SourceSpecies: Sheep (sheep)

+
Component #45: protein, Mitochondrial complex I, B14.7 subunit

ProteinName: Mitochondrial complex I, B14.7 subunit / Details: UniProt W5PAR2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.145497 kDa
SourceSpecies: Sheep (sheep)

+
Component #46: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

+
Component #47: ligand, FLAVIN MONONUCLEOTIDE

LigandName: FLAVIN MONONUCLEOTIDE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.456344 kDa

+
Component #48: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

+
Component #49: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.748065 kDa

+
Component #50: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.790145 kDa

+
Component #51: ligand, CARDIOLIPIN

LigandName: CARDIOLIPIN / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 1.464043 kDa

+
Component #52: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #53: ligand, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

LigandName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.745421 kDa

+
Component #54: ligand, S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)but...

LigandName: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.568704 kDa

+
Component #55: ligand, 4'-PHOSPHOPANTETHEINE

LigandName: 4'-PHOSPHOPANTETHEINEPhosphopantetheine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.358348 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 90 % / Details: 34s blotting.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 26 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal), 100720.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 2600 / Sampling size: 14 microns

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 82000
3D reconstructionSoftware: RELION / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 4HEA
Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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