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- PDB-6r83: CryoEM structure and molecular model of squid hemocyanin (Todarod... -

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Entry
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 / homology
Function and homology information


oxidoreductase activity / metal ion binding
Tyrosinase 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 / Tyrosinase CuA-binding region signature. / Tyrosinase and hemocyanins CuB-binding region signature.
Hemocyanin subunit 1
Specimen sourceTodarodes 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 supportGermany , Japan , 3件
OrganizationGrant numberCountry
Max Planck SocietyGermany
German Research FoundationFOR1905Germany
Japan Society for the Promotion of Science26291008;24000011;15KK0248;16H00748;17K07942Japan
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
DateDeposition: Mar 31, 2019 / Release: May 8, 2019Array

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Structure visualization

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Structure viewerMolecule:
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Assembly

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
Polymers3,797,41210
Non-polymers00
Water0
1


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

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Components

#1: Protein/peptide
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

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Experimental details

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Experiment

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

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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

Buffer-ID: 1

IDConc.NameFormula
1100 mMHEPES
2200 mMcalcium chlorideCaCl2
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

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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
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
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 opticsSph aberration corrector: Microscope equipped with Cs corrector
Image scansMovie frames/image: 24 / Used frames/image: 1-24

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4SPHIRE1CTF correction
10SPHIRE1initial Euler assignment
11SPHIRE1final Euler assignment
12SPHIRE1classification
13SPHIRE3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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: Correlation Coefficient

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