[English] 日本語
Yorodumi
- EMDB-1434: Nautilus pompilius hemocyanin: 9 A cryo-EM structure and molecula... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1434
TitleNautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.
SampleNautilus pompilius hemocyanin
SourceNautilus pompilius / invertebrata / オウムガイ, オオムガイ, おおむがい
Map dataThis is a map of the hemocyanin from the mollusc Nautilus pompilius. Mass correlated threshold: 0.006
Methodsingle particle reconstruction, at 9.1 Å resolution
AuthorsGatsogiannis C / Moeller A / Depoix F / Meissner U / Markl J
CitationJ. Mol. Biol., 2007, 374, 465-486

J. Mol. Biol., 2007, 374, 465-486 StrPapers
Nautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.
Christos Gatsogiannis / Arne Moeller / Frank Depoix / Ulrich Meissner / Jürgen Markl

DateDeposition: Sep 26, 2007 / Header (metadata) release: Sep 26, 2007 / Map release: Sep 30, 2011 / Last update: Sep 26, 2007

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0055
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0055
  • 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_1434.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.85 Å/pix.
= 473.6 Å
256 pix
1.85 Å/pix.
= 473.6 Å
256 pix
1.85 Å/pix.
= 473.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.85 Å
Density
Contour Level:0.0055 (by emdb), 0.0055 (movie #1):
Minimum - Maximum-0.0368309 - 0.0538236
Average (Standard dev.)0.000232174 (0.00402936)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 473.6 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.851.851.85
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z473.600473.600473.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ10110173
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0370.0540.000

-
Supplemental data

-
Sample components

-
Entire Nautilus pompilius hemocyanin

EntireName: Nautilus pompilius hemocyanin
Oligomeric State: Nautilus pompilius hemocyanin is a decamer of a 350 kDa subunit. Each subunit is composed by 7 paralogous O2 binding functional units.
Number of components: 1
MassTheoretical: 3.5 MDa

-
Component #1: protein, Nautilus pompilius hemocyanin

ProteinName: Nautilus pompilius hemocyanin / a.k.a: Nautilus pompilius hemocyanin / Recombinant expression: No
MassExperimental: 3.5 MDa
SourceSpecies: Nautilus pompilius / invertebrata / オウムガイ, オオムガイ, おおむがい
Source (natural)Organ or tissue: hemolymph

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.4 mg/ml
Buffer solution: 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2, 150mM NaCl
pH: 7.4
Support film400 mesh copper
Stainingcryo-EM, no stain
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 86 K / Method: Single side blotting and rapid plunging
Details: Vitrification instrument: home made. Vitrification carried out in 100 percent nitrogen atmosphere

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
LensMagnification: 49000 X (nominal), 49000 X (calibrated) / Cs: 1.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 3300 nm
Specimen HolderHolder: Gatan single-tilt cryoholder / Model: GATAN LIQUID NITROGEN / Temperature: 86 K
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisition
63
Image acquisition
186
Image acquisition
8
Image acquisition
PRIMESCAN

-
Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 5200 / Number of projections: 16000
Details: The particles were selected using the automatic selection program boxer
Applied symmetry: C5 (5 fold cyclic)
3D reconstructionAlgorithm: Common Lines, projection matching / Software: IMAGIC-5 / CTF correction: CTFFIND3 and TRANSFER, IMAGIC 5 / Resolution: 9.1 Å / Resolution method: FSC 0.5

+
About Yorodumi

-
News

-
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)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

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