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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1434
TitleNautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.
Map dataThis is a map of the hemocyanin from the mollusc Nautilus pompilius. Mass correlated threshold: 0.006
Sample
  • Sample: Nautilus pompilius hemocyanin
  • Protein or peptide: Nautilus pompilius hemocyanin
Biological speciesNautilus pompilius (invertebrata)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 9.1 Å
AuthorsGatsogiannis C / Moeller A / Depoix F / Meissner U / Markl J
CitationJournal: J Mol Biol / Year: 2007
Title: Nautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.
Authors: Christos Gatsogiannis / Arne Moeller / Frank Depoix / Ulrich Meissner / Jürgen Markl /
Abstract: Hemocyanins are giant extracellular oxygen carriers in the hemolymph of many molluscs. Nautilus pompilius (Cephalopoda) hemocyanin is a cylindrical decamer of a 350 kDa polypeptide subunit that in ...Hemocyanins are giant extracellular oxygen carriers in the hemolymph of many molluscs. Nautilus pompilius (Cephalopoda) hemocyanin is a cylindrical decamer of a 350 kDa polypeptide subunit that in turn is a "pearl-chain" of seven different functional units (FU-a to FU-g). Each globular FU has a binuclear copper centre that reversibly binds one O(2) molecule, and the 70-FU decamer is a highly allosteric protein. Its primary structure and an 11 A cryo-electron microscopy (cryo-EM) structure have recently been determined, and the crystal structures of two related FU types are available in the databanks. However, in molluscan hemocyanin, the precise subunit pathway within the decamer, the inter-FU interfaces, and the allosteric unit are still obscure, but this knowledge is crucial to understand assembly and allosterism of these proteins. Here we present the cryo-EM structure of Nautilus hemocyanin at 9.1 A resolution (FSC(1/2-bit) criterion), and its molecular model obtained by rigid-body fitting of the individual FUs. In this model we identified the subunit dimer, the subunit pathway, and 15 types of inter-FU interface. Four interface types correspond to the association mode of the two protomers in the published Octopus FU-g crystal. Other interfaces explain previously described morphological structures such as the fenestrated wall (which shows D5 symmetry), the three horizontal wall tiers, the major and minor grooves, the anchor structure and the internal collar (which unexpectedly has C5 symmetry). Moreover, the potential calcium/magnesium and N-glycan binding sites have emerged. Many interfaces have amino acid constellations that might transfer allosteric interaction between FUs. From their topologies we propose that the prime allosteric unit is the oblique segment between major and minor groove, consisting of seven FUs from two different subunits. Thus, the 9 A structure of Nautilus hemocyanin provides fundamentally new insight into the architecture and function of molluscan hemocyanins.
History
DepositionSep 26, 2007-
Header (metadata) releaseSep 26, 2007-
Map releaseSep 30, 2011-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

-
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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

em-1434.png

Downloads & links

-
Map

FileDownload / File: emd_1434.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of the hemocyanin from the mollusc Nautilus pompilius. Mass correlated threshold: 0.006
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0055 / Movie #1: 0.0055
Minimum - Maximum-0.0368309 - 0.0538236
Average (Standard dev.)0.000232174 (±0.00402936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 473.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
Components
  • Sample: Nautilus pompilius hemocyanin
  • Protein or peptide: Nautilus pompilius hemocyanin

-
Supramolecule #1000: Nautilus pompilius hemocyanin

SupramoleculeName: Nautilus pompilius hemocyanin / type: sample / ID: 1000
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 unique components: 1
Molecular weightTheoretical: 3.5 MDa

-
Macromolecule #1: Nautilus pompilius hemocyanin

MacromoleculeName: Nautilus pompilius hemocyanin / type: protein_or_peptide / ID: 1 / Name.synonym: Nautilus pompilius hemocyanin / Recombinant expression: No
Source (natural)Organism: Nautilus pompilius (invertebrata) / Tissue: hemolymph
Molecular weightExperimental: 3.5 MDa

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4 / Details: 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2, 150mM NaCl
StainingType: NEGATIVE / Details: cryo-EM, no stain
GridDetails: 400 mesh copper
VitrificationCryogen name: ETHANE / Chamber temperature: 86 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: home made. Vitrification carried out in 100 percent nitrogen atmosphere
Method: Single side blotting and rapid plunging

-
Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureAverage: 86 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 1.86 µm / Number real images: 63 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 1.2 mm / Nominal defocus max: 3.3 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 49000
Sample stageSpecimen holder: Gatan single-tilt cryoholder / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

DetailsThe particles were selected using the automatic selection program boxer
CTF correctionDetails: CTFFIND3 and TRANSFER, IMAGIC 5
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC-5 / Number images used: 16000
Final two d classificationNumber classes: 5200

+
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