[English] 日本語
- PDB-6r83: CryoEM structure and molecular model of squid hemocyanin (Todarod... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 6r83
TitleCryoEM structure and molecular model of squid hemocyanin (Todarodes pacificus , TpH)
ComponentsHemocyanin subunit 1
KeywordsOXYGEN TRANSPORT / oxygen transporter / mollusc / hemocyanin / copper / symmetry mismatch
Function / homologyTyrosinase copper-binding domain / Uncharacterised domain, di-copper centre / Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Common central domain of tyrosinase / Haemocyanin beta-sandwich / oxidoreductase activity / metal ion binding / Hemocyanin subunit 1
Function and homology information
Biological speciesTodarodes pacificus (Japanese flying squid)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsTanaka, Y. / Kato, S. / Stabrin, M. / Raunser, S. / Matsui, T. / Gatsogiannis, C.
Funding support Germany, Japan, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research FoundationFOR1905 Germany
Japan Society for the Promotion of Science26291008;24000011;15KK0248;16H00748;17K07942 Japan
CitationJournal: IUCrJ / Year: 2019
Title: Cryo-EM reveals the asymmetric assembly of squid hemocyanin.
Authors: Yoshikazu Tanaka / Sanae Kato / Markus Stabrin / Stefan Raunser / Takashi Matsui / Christos Gatsogiannis /
Abstract: The oxygen transporter of molluscs, hemocyanin, consists of long pearl-necklace-like subunits of several globular domains. The subunits assemble in a complex manner to form cylindrical decamers. ...The oxygen transporter of molluscs, hemocyanin, consists of long pearl-necklace-like subunits of several globular domains. The subunits assemble in a complex manner to form cylindrical decamers. Typically, the first six domains of each subunit assemble together to form the cylinder wall, while the C-terminal domains form a collar that fills or caps the cylinder. During evolution, various molluscs have been able to fine-tune their oxygen binding by deleting or adding C-terminal domains and adjusting their inner-collar architecture. However, squids have duplicated one of the wall domains of their subunits instead. Here, using cryo-EM and an optimized refinement protocol implemented in , this work tackled the symmetry-mismatched structure of squid hemocyanin, revealing the precise effect of this duplication on its quaternary structure and providing a potential model for its structural evolution.
Validation Report
SummaryFull reportAbout validation report
DepositionMar 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Nov 6, 2019Group: Data collection / Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4750
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


Deposited unit
1a: Hemocyanin subunit 1
2a: Hemocyanin subunit 1
3a: Hemocyanin subunit 1
4a: Hemocyanin subunit 1
5a: Hemocyanin subunit 1
6a: Hemocyanin subunit 1
7a: Hemocyanin subunit 1
8a: Hemocyanin subunit 1
9a: Hemocyanin subunit 1
10a: Hemocyanin subunit 1

Theoretical massNumber of molelcules
Total (without water)3,797,41210

  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein
Hemocyanin subunit 1 /

Mass: 379741.188 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Source: (natural) Todarodes pacificus (Japanese flying squid)
References: UniProt: A0A0P0UX03

Experimental details


EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

Sample preparation

ComponentName: Squid Hemocyanin / Type: COMPLEX
Details: TpH is a decamer of a 400 kDa subunit. Each subunit is composed by 8 paralogous O2 binding functional units (A,B,C,D,D*,E,F,G). The ten subunits of TpH acquire 4 different overall conformations.
Entity ID: 1 / Source: NATURAL
Molecular weightValue: 3.8 MDa / Experimental value: NO
Source (natural)Organism: Todarodes pacificus (Japanese flying squid)
Buffer solutionpH: 7.5
Buffer component
1100 mMHEPES1
2200 mMcalcium chlorideCaCl21
SpecimenConc.: 2.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 0 mm
Image recordingAverage exposure time: 1 sec. / Electron dose: 56 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5092
EM imaging opticsSpherical aberration corrector: Microscope equipped with Cs corrector
Image scansMovie frames/image: 24 / Used frames/image: 1-24


EM software
2EPUimage acquisition
4SPHIRE1CTF correction
10SPHIRE1initial Euler assignment
11SPHIRE1final Euler assignment
13SPHIRE3D reconstruction
Particle selectionNum. of particles selected: 359250
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196315 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient

About Yorodumi


Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

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. (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 PDBe / 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

Read more


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