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- PDB-8trz: Cryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin -

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Basic information

Entry
Database: PDB / ID: 8trz
TitleCryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin
ComponentsHemocyanin
KeywordsOXYGEN TRANSPORT / Glycoprotein / Respiratory Pigment / Cooper Protein / Carbohydrates
Biological speciesPomacea canaliculata (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsBrola, T.R. / Chiumiento, I.R. / Gragera, M. / Carazo, J.M. / Heras, H. / Dreon, M.S. / Otero, L.H.
Funding support Argentina, 2items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT-2021-00158 Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT-2020- SERIEA-03047 Argentina
CitationJournal: To Be Published
Title: Cryo-EM structure of N-glycosylated Pomacea canaliculata hemocyanin
Authors: Brola, T.R. / Chiumiento, I.R. / Gragera, M. / Carazo, J.M. / Heras, H. / Dreon, M.S. / Otero, L.H.
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemocyanin
B: Hemocyanin
C: Hemocyanin
D: Hemocyanin
E: Hemocyanin
F: Hemocyanin
G: Hemocyanin
H: Hemocyanin
I: Hemocyanin
J: Hemocyanin
K: Hemocyanin
L: Hemocyanin
M: Hemocyanin
N: Hemocyanin
O: Hemocyanin
P: Hemocyanin
Q: Hemocyanin
R: Hemocyanin
S: Hemocyanin
T: Hemocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,831,135140
Polymers7,774,54320
Non-polymers56,593120
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Hemocyanin


Mass: 388727.125 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Pomacea canaliculata (invertebrata)
#2: Polysaccharide...
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 40
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide...
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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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: Didecameric complex of Pomacea canaliculata hemocyanin
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pomacea canaliculata (invertebrata)
Buffer solutionpH: 7.4
Buffer component
IDConc.FormulaBuffer-ID
120 mMTris-HCl1
220 mMCaCl21
320 mMMgCl21
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %

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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: OTHER / Nominal magnification: 59000 X / Nominal defocus max: 1900 nm / Nominal defocus min: 1100 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 36.75 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 4584

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Processing

EM software
IDNameCategory
1crYOLOparticle selection
4GctfCTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
14Scipion3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 64970
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29935 / Symmetry type: POINT
Atomic model buildingB value: 110 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 103.84 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034565232
ELECTRON MICROSCOPYf_angle_d0.6307768674
ELECTRON MICROSCOPYf_chiral_restr0.044682498
ELECTRON MICROSCOPYf_plane_restr0.0046100688
ELECTRON MICROSCOPYf_dihedral_angle_d6.032776126

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