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- PDB-3j32: An asymmetric unit map from electron cryo-microscopy of Haliotis ... -

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Basic information

Entry
Database: PDB / ID: 3j32
TitleAn asymmetric unit map from electron cryo-microscopy of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
ComponentsHemocyanin isoform 1
KeywordsOXYGEN TRANSPORT / allosteric
Function / homology
Function and homology information


oxygen carrier activity / oxidoreductase activity
Similarity search - Function
Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily
Similarity search - Domain/homology
Hemocyanin isoform 1
Similarity search - Component
Biological speciesHaliotis diversicolor (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsZhang, Q. / Dai, X. / Cong, Y. / Zhang, J. / Chen, D.-H. / Dougherty, M. / Wang, J. / Ludtke, S. / Schmid, M.F. / Chiu, W.
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
DepositionFeb 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete point assembly
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Hemocyanin isoform 1
B: Hemocyanin isoform 1


Theoretical massNumber of molelcules
Total (without water)757,3462
Polymers757,3462
Non-polymers00
Water0
1
A: Hemocyanin isoform 1
B: Hemocyanin isoform 1
x 10


Theoretical massNumber of molelcules
Total (without water)7,573,45620
Polymers7,573,45620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation9
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: D5 (2x5 fold dihedral))

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Components

#1: Protein Hemocyanin isoform 1 / Coordinate model: Cα atoms only


Mass: 378672.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Haliotis diversicolor (invertebrata) / Tissue: lymph / References: UniProt: C7FEG7

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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: An asymmetric unit of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
Type: COMPLEX / Details: one asymmetric unit contains two subunits
Molecular weightValue: 0.8 MDa / Experimental value: NO
Buffer solutionName: 0.2M NaCl, 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2, pH 7.5
pH: 7.5
Details: 0.2M NaCl, 50mM Tris-HCl, 5mM CaCl2, 5mM MgCl2, pH 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh copper 1.2/1.3 quantifoil grid with continuous carbon support, glow discharged.
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 2 seconds before plunging in to liquid ethane (FEI VITROBOT MARK III)
Method: blot for 2 seconds before plunging

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Jul 7, 2008 / Details: MDS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 500 nm / Cs: 4.1 mm
Astigmatism: Objective lens astigmatism was corrected at 400,000 nominal magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Specimen holder type: liquid N2 cooled / Temperature: 88 K / Temperature (max): 100 K / Temperature (min): 80 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansNum. digital images: 784
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: EMAN / Version: 1 / Category: 3D reconstruction
CTF correctionDetails: each micrograph
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionMethod: projection matching / Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 28641 / Actual pixel size: 1.02 Å
Details: (Single particle details: processed with EMAN1 followed by segmentation of asymmetric unit.) (Single particle--Applied symmetry: D5)
Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 0 0 6606

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