[English] 日本語
Yorodumi
- EMDB-1648: Assembly and Allosteric Mechanism of Molluscan Hemocyanin Reveale... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1648
TitleAssembly and Allosteric Mechanism of Molluscan Hemocyanin Revealed by Cryo-EM Structure and Pseudo-atomic Model
Map dataThe whole structure of Haliotis diversicolor Hemocyanin isoform 1 (HdH1) is a hollow cylindrical dodecamer. Each of its 20 subunits is composed of 8 functional units (FUs).
Sample
  • Sample: Haliotis diversicolor (Gastropod, Mollusca) Hemocyanin isoform 1 (HdH1)
  • Protein or peptide: Hemocyanin
KeywordsOxygen binding / allosteric mechanism
Function / homologyDi-copper centre-containing domain superfamily / metabolic process
Function and homology information
Biological speciesHaliotis diversicolor (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsXinghong D / Junjie Z / Jiangyong W / Kunpeng L / Donghua C / Qinfen Z / Wah C
CitationJournal: Structure / Year: 2013
Title: Cryo-EM structure of a molluscan hemocyanin suggests its allosteric mechanism.
Authors: Qinfen Zhang / Xinghong Dai / Yao Cong / Junjie Zhang / Dong-Hua Chen / Matthew T Dougherty / Jiangyong Wang / Steven J Ludtke / Michael F Schmid / Wah Chiu /
Abstract: Hemocyanins are responsible for transporting O2 in the arthropod and molluscan hemolymph. Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) is an 8 MDa oligomer. Each subunit is made up of ...Hemocyanins are responsible for transporting O2 in the arthropod and molluscan hemolymph. Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1) is an 8 MDa oligomer. Each subunit is made up of eight functional units (FUs). Each FU contains two Cu ions, which can reversibly bind an oxygen molecule. Here, we report a 4.5 A° cryo-EM structure of HdH1. The structure clearly shows ten asymmetric units arranged with D5 symmetry. Each asymmetric unit contains two structurally distinct but chemically identical subunits. The map is sufficiently resolved to trace the entire subunit Ca backbone and to visualize densities corresponding to some large side chains, Cu ion pairs, and interaction networks of adjacent subunits. A FU topology path intertwining between the two subunits of the asymmetric unit is unambiguously determined. Our observations suggest a structural mechanism for the stability of the entire hemocyanin didecamer and 20 ‘‘communication clusters’’ across asymmetric units responsible for its allosteric property upon oxygen binding.
History
DepositionSep 10, 2009-
Header (metadata) releaseSep 24, 2009-
Map releaseNov 12, 2010-
UpdateMay 25, 2016-
Current statusMay 25, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_1648.map.gz / Format: CCP4 / Size: 300.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe whole structure of Haliotis diversicolor Hemocyanin isoform 1 (HdH1) is a hollow cylindrical dodecamer. Each of its 20 subunits is composed of 8 functional units (FUs).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 432 pix.
= 457.92 Å
1.06 Å/pix.
x 432 pix.
= 457.92 Å
1.06 Å/pix.
x 432 pix.
= 457.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy EMDB: 1.37 / Movie #1: 1.2
Minimum - Maximum-0.824038 - 3.20481
Average (Standard dev.)0.140338 (±0.509272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-216-216-216
Dimensions432432432
Spacing432432432
CellA=B=C: 457.92 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z457.920457.920457.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-216-216-216
NC/NR/NS432432432
D min/max/mean-0.8243.2050.140

-
Supplemental data

-
Sample components

-
Entire : Haliotis diversicolor (Gastropod, Mollusca) Hemocyanin isoform 1 ...

EntireName: Haliotis diversicolor (Gastropod, Mollusca) Hemocyanin isoform 1 (HdH1)
Components
  • Sample: Haliotis diversicolor (Gastropod, Mollusca) Hemocyanin isoform 1 (HdH1)
  • Protein or peptide: Hemocyanin

-
Supramolecule #1000: Haliotis diversicolor (Gastropod, Mollusca) Hemocyanin isoform 1 ...

SupramoleculeName: Haliotis diversicolor (Gastropod, Mollusca) Hemocyanin isoform 1 (HdH1)
type: sample / ID: 1000 / Oligomeric state: Dodecamer / Number unique components: 1
Molecular weightExperimental: 8 MDa / Theoretical: 8 MDa / Method: SDS-PAGE

-
Macromolecule #1: Hemocyanin

MacromoleculeName: Hemocyanin / type: protein_or_peptide / ID: 1 / Name.synonym: Hemocyanin / Number of copies: 20 / Oligomeric state: Dodecamer / Recombinant expression: No
Source (natural)Organism: Haliotis diversicolor (invertebrata) / Tissue: Blood
Molecular weightExperimental: 8 MDa / Theoretical: 8 MDa
SequenceGO: metabolic process / InterPro: Di-copper centre-containing domain superfamily

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Details: 0.2M NaCl , 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2, pH7.5
GridDetails: 1.2/1.3 copper Quantifoil grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 101 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 2 seconds before plunging

-
Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.1 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 60000
Specialist opticsEnergy filter - Name: JEOL in-column
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL 3200FSC CRYOHOLDER
TemperatureAverage: 101 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 times magnification
DetailsMDS
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 820 / Average electron dose: 18 e/Å2 / Bits/pixel: 16

-
Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 41650
DetailsParticles were automatically boxed out from micrographs by e2boxer.py from EMAN2 single particle analysis software package, and CTF correction was carried out with EMAN program CTFIT. All the 3D reconstruction was done with EMAN1.8.

+
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