8TNV | pdb_00008tnv

Hemocyanin Functional Unit CCHB-g of Concholepas concholepas


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8TNV

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural insights into a functional unit from an immunogenic mollusk hemocyanin.

Munoz, S.M.Vallejos-Baccelliere, G.Manubens, A.Salazar, M.L.Nascimento, A.F.Z.Tapia-Reyes, P.Meneses, C.Ambrosio, A.L.B.Becker, M.I.Guixe, V.Castro-Fernandez, V.

(2024) Structure 32: 812-823.e4

  • DOI: https://doi.org/10.1016/j.str.2024.02.018
  • Primary Citation Related Structures: 
    8TNV

  • PubMed Abstract: 

    Mollusk hemocyanins, among the largest known proteins, are used as immunostimulants in biomedical and clinical applications. The hemocyanin of the Chilean gastropod Concholepas concholepas (CCH) exhibits unique properties, which makes it safe and effective for human immunotherapy, as observed in animal models of bladder cancer and melanoma, and dendritical cell vaccine trials. Despite its potential, the structure and amino acid sequence of CCH remain unknown. This study reports two sequence fragments of CCH, representing three complete functional units (FUs). We also determined the high-resolution (1.5 Å) X-ray crystal structure of an "FU-g type" from the CCHB subunit. This structure enables in-depth analysis of chemical interactions at the copper-binding center and unveils an unusual, truncated N-glycosylation pattern. These features are linked to eliciting more robust immunological responses in animals, offering insights into CCH's enhanced immunostimulatory properties and opening new avenues for its potential applications in biomedical research and therapies.


  • Organizational Affiliation
    • Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 780003, Chile.

Macromolecule Content 

  • Total Structure Weight: 93.62 kDa 
  • Atom Count: 7,593 
  • Modeled Residue Count: 786 
  • Deposited Residue Count: 786 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemocyanin Functional Unit CCHB-g
A, B
393Concholepas concholepasMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G39203UC
GlyCosmos: G39203UC
GlyGen: G39203UC

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG6

Query on PG6



Download:Ideal Coordinates CCD File
J [auth B],
K [auth B]
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B],
I [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
L [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
CUO

Query on CUO



Download:Ideal Coordinates CCD File
E [auth A],
M [auth B]
CU2-O2 CLUSTER
Cu2 O2
PCGDDKBKPXANNY-UHFFFAOYSA-N
BR

Query on BR



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
N [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.682α = 90
b = 103.368β = 90
c = 119.048γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Comision Nacional Cientifica y Technologica (CONICYT)ChileFAPESP 2019/13318-5
Comision Nacional Cientifica y Technologica (CONICYT)Chile1191321
Comision Nacional Cientifica y Technologica (CONICYT)Chile1201200
Comision Nacional Cientifica y Technologica (CONICYT)ChileEQM 120208

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Structure summary