[English] 日本語
Yorodumi
- EMDB-4032: Structure of mammalian respiratory Complex I, class2 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 4032
TitleStructure of mammalian respiratory Complex I, class2
SampleBovine respiratory Complex I
SourceBos taurus / mammal / ウシ /
Map dataThis deposited map is one of the classes of bovine Complex I enzyme. We call it class2.
Methodsingle particle reconstruction, at 4.35 Å resolution
AuthorsVinothkumar KR / Zhu J
CitationNature, 2016, 536, 354-358

Nature, 2016, 536, 354-358 Yorodumi Papers
Structure of mammalian respiratory complex I.
Jiapeng Zhu / Kutti R Vinothkumar / Judy Hirst

Validation ReportPDB-ID: 5lc5

SummaryFull reportAbout validation report
DateDeposition: Aug 22, 2016 / Header (metadata) release: Sep 7, 2016 / Map release: Sep 7, 2016 / Last update: Aug 23, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.165
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.165
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5lc5
  • Surface level: 0.165
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_4032.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.33 Å/pix.
= 478.8 Å
360 pix
1.33 Å/pix.
= 478.8 Å
360 pix
1.33 Å/pix.
= 478.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.33 Å
Density
Contour Level:0.165 (by author), 0.165 (movie #1):
Minimum - Maximum-0.272693 - 1.1030328
Average (Standard dev.)5.8559624E-5 (0.026418459)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 478.80002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z478.800478.800478.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2731.1030.000

-
Supplemental data

-
Sample components

+
Entire Bovine respiratory Complex I

EntireName: Bovine respiratory Complex I
Details: Complex I is the first enzyme in the electron transport chain located in the inner membrane of mitochondria and in higher eukaryotes, it is a multi-subunit membrane protein complex, consisting of >40 subunits.
Number of components: 51
MassTheoretical: 1000 kDa

+
Component #1: protein, Bovine respiratory Complex I

ProteinName: Bovine respiratory Complex I
Details: Complex I is the first enzyme in the electron transport chain located in the inner membrane of mitochondria and in higher eukaryotes, it is a multi-subunit membrane protein complex, consisting of >40 subunits.
Recombinant expression: No
MassTheoretical: 1000 kDa
SourceSpecies: Bos taurus / mammal / ウシ /
Source (natural)Organelle: Mitochondria / Location in cell: Mitochondria

+
Component #2: protein, NADH-ubiquinone oxidoreductase chain 3

ProteinName: NADH-ubiquinone oxidoreductase chain 3 / Recombinant expression: No
MassTheoretical: 12.510898 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #3: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
Details: This chain coordinates Iron-sulphur cluster. / Recombinant expression: No
MassTheoretical: 16.625518 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #4: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
Recombinant expression: No
MassTheoretical: 24.202396 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #5: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
Recombinant expression: No
MassTheoretical: 48.693758 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #6: protein, NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Details: This chain coordinates one FES. / Recombinant expression: No
MassTheoretical: 27.341496 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #7: protein, NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Details: This chain coordinates two iron-sulfur clusters and also binds Flavin mono nucleotide.
Recombinant expression: No
MassTheoretical: 50.718777 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #8: protein, NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochond...

ProteinName: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, NDUFS1
Details: This chain coordinates one binuclear FES and two SF4.
Recombinant expression: No
MassTheoretical: 66.442281 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #9: protein, NADH-ubiquinone oxidoreductase chain 1

ProteinName: NADH-ubiquinone oxidoreductase chain 1 / Recombinant expression: No
MassTheoretical: 35.084062 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #10: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
Details: This chain coordinates two SF4. / Recombinant expression: No
MassTheoretical: 20.219947 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #11: protein, NADH-ubiquinone oxidoreductase chain 6

ProteinName: NADH-ubiquinone oxidoreductase chain 6 / Recombinant expression: No
MassTheoretical: 18.622936 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #12: protein, NADH-ubiquinone oxidoreductase chain 4L

ProteinName: NADH-ubiquinone oxidoreductase chain 4L / Recombinant expression: No
MassTheoretical: 10.437718 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #13: protein, NADH-ubiquinone oxidoreductase chain 5

ProteinName: NADH-ubiquinone oxidoreductase chain 5 / Recombinant expression: No
MassTheoretical: 68.067609 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #14: protein, NADH-ubiquinone oxidoreductase chain 4

ProteinName: NADH-ubiquinone oxidoreductase chain 4 / Recombinant expression: No
MassTheoretical: 51.886402 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #15: protein, NADH-ubiquinone oxidoreductase chain 2

ProteinName: NADH-ubiquinone oxidoreductase chain 2 / Recombinant expression: No
MassTheoretical: 38.901461 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #16: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Recombinant expression: No
MassTheoretical: 34.014227 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #17: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Recombinant expression: No
MassTheoretical: 28.528021 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #18: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Recombinant expression: No
MassTheoretical: 9.634868 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #19: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Details: This chain coordinates a Zinc ion. / Recombinant expression: No
MassTheoretical: 8.316853 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #20: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Recombinant expression: No
MassTheoretical: 9.270575 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #21: protein, Acyl carrier protein, mitochondrial

ProteinName: Acyl carrier protein, mitochondrial / Recombinant expression: No
MassTheoretical: 8.672939 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #22: protein, Acyl carrier protein, mitochondrial

ProteinName: Acyl carrier protein, mitochondrial / Recombinant expression: No
MassTheoretical: 9.846298 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #23: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
Recombinant expression: No
MassTheoretical: 13.334608 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #24: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Recombinant expression: No
MassTheoretical: 15.083544 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #25: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Recombinant expression: No
MassTheoretical: 18.115223 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #26: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Recombinant expression: No
MassTheoretical: 14.412514 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #27: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Recombinant expression: No
MassTheoretical: 14.1359 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #28: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Recombinant expression: No
MassTheoretical: 8.117445 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #29: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
Recombinant expression: No
MassTheoretical: 7.860488 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #30: protein, NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Recombinant expression: No
MassTheoretical: 8.796211 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #31: protein, NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydr...

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2
Recombinant expression: No
MassTheoretical: 11.9883 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #32: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Recombinant expression: No
MassTheoretical: 12.694671 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #33: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
Recombinant expression: No
MassTheoretical: 6.978148 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #34: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
Recombinant expression: No
MassTheoretical: 17.594945 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #35: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Recombinant expression: No
MassTheoretical: 18.069865 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #36: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Recombinant expression: No
MassTheoretical: 11.636995 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2
Recombinant expression: No
MassTheoretical: 4.443468 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #38: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3
Recombinant expression: No
MassTheoretical: 6.315777 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #39: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8
Recombinant expression: No
MassTheoretical: 10.060393 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #40: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
Recombinant expression: No
MassTheoretical: 13.415493 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #41: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Recombinant expression: No
MassTheoretical: 19.246094 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #42: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
Recombinant expression: No
MassTheoretical: 7.5839 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #43: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10
Recombinant expression: No
MassTheoretical: 16.906949 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #44: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Recombinant expression: No
MassTheoretical: 16.309545 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #45: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7
Recombinant expression: No
MassTheoretical: 7.42214 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #46: protein, NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3
Recombinant expression: No
MassTheoretical: 2.996685 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

+
Component #47: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTER / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.35164 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, FLAVIN MONONUCLEOTIDE

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

+
Component #50: ligand, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

LigandName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.743405 kDa

+
Component #51: ligand, ZINC ION

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

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 3.5 mg/ml / pH: 8
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %
Details: The specimen was vitrified in an environmental plunge-freeze apparatus, blot for 12-15 seconds after the diameter of the blotted meniscus ceases to spread and plunged.

-
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: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 105263 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 85 - 85 K)
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionSampling size: 14 microns
Details: Images were collected in movie mode at 17 frames per second. Thus each frame has ~1.0 e/A2s

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 33301
Details: Each image was exposed for 2 seconds resulting in a total dose of ~35 e/A2s. The frames were captures with a in-house protocol at 17 frames/second.
3D reconstructionSoftware: RELION
CTF correction: Ctf was estimated from the whole micrograph. Ctf was corrected per particle.
Resolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more