6FZR

Crystal structure of scFv-SM3 in complex with compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Water Sculpts the Distinctive Shapes and Dynamics of the Tumor-Associated Carbohydrate Tn Antigens: Implications for Their Molecular Recognition.

Bermejo, I.A.Usabiaga, I.Companon, I.Castro-Lopez, J.Insausti, A.Fernandez, J.A.Avenoza, A.Busto, J.H.Jimenez-Barbero, J.Asensio, J.L.Peregrina, J.M.Jimenez-Oses, G.Hurtado-Guerrero, R.Cocinero, E.J.Corzana, F.

(2018) J.Am.Chem.Soc. 140: 9952-9960

  • DOI: 10.1021/jacs.8b04801
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The tumor-associated carbohydrate Tn antigens include two variants, αGalNAc- O-Thr and αGalNAc- O-Ser. In solution, they exhibit dissimilar shapes and dynamics and bind differently to the same protein receptor. Here, we demonstrate experimentally and ...

    The tumor-associated carbohydrate Tn antigens include two variants, αGalNAc- O-Thr and αGalNAc- O-Ser. In solution, they exhibit dissimilar shapes and dynamics and bind differently to the same protein receptor. Here, we demonstrate experimentally and theoretically that their conformational preferences in the gas phase are highly similar, revealing the essential role of water. We propose that water molecules prompt the rotation around the glycosidic linkage in the threonine derivative, shielding its hydrophobic methyl group and allowing an optimal solvation of the polar region of the antigen. The unusual arrangement of αGalNAc- O-Thr features a water molecule bound into a "pocket" between the sugar and the threonine. This mechanism is supported by trapping, for the first time, such localized water in the crystal structures of an antibody bound to two glycopeptides that comprise fluorinated Tn antigens in their structure. According to several reported X-ray structures, installing oxygenated amino acids in specific regions of the receptor capable of displacing the bridging water molecule to the bulk-solvent may facilitate the molecular recognition of the Tn antigen with threonine. Overall, our data also explain how water fine-tunes the 3D structure features of similar molecules, which in turn are behind their distinct biological activities.


    Organizational Affiliation

    CIC bioGUNE , Bizkaia Technology Park, Building 801A , 48170 Derio , Spain.,Department of Organic Chemistry II, Faculty of Science & Technology , University of the Basque Country , 48940 Leioa , Spain.,Instituto de Química Orgánica General , IQOG-CSIC. 28006 Madrid , Spain.,Departamento de Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV-EHU), 48080 Bilbao , Spain.,Fundación ARAID , 50018 Zaragoza , Spain.,Departamento de Química, Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain.,Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), 48940 Leioa , Spain.,Ikerbasque , Basque Foundation for Science , Maria Diaz de Haro 13 , 48009 Bilbao , Spain.,Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza , BIFI-IQFR (CSIC), 50018 Zaragoza , Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
scFv-SM3
H
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mucin-1
P
6Homo sapiensMutation(s): 0 
Gene Names: MUC1 (PUM)
Find proteins for P15941 (Homo sapiens)
Go to Gene View: MUC1
Go to UniProtKB:  P15941
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EEQ
Query on EEQ

Download SDF File 
Download CCD File 
P
2-fluoranyl-~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]ethanamide
C8 H14 F N O6
LMPCEKTVFVQIPT-VDUCJHRSSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
H
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.274α = 90.00
b = 69.431β = 90.00
c = 90.778γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MICINNSpain, CTQ2013-44367-C2-2-P
MICINNSpainBFU2016-75633-P

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Advisory, Data collection, Derived calculations
  • Version 1.2: 2019-09-04
    Type: Data collection, Database references