7C94

Crystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide.

Ogasawara, S.Suzuki, K.Naruchi, K.Nakamura, S.Shimabukuro, J.Tsukahara, N.Kaneko, M.K.Kato, Y.Murata, T.

(2020) Biochem Biophys Res Commun 533: 57-63

  • DOI: https://doi.org/10.1016/j.bbrc.2020.08.103
  • Primary Citation of Related Structures:  
    7C94, 7C95

  • PubMed Abstract: 

    Podoplanin (PDPN) is a highly O-glycosylated glycoprotein that is utilized as a specific lymphatic endothelial marker under pathophysiological conditions. We previously developed an anti-human PDPN (hPDPN) monoclonal antibody (mAb), clone LpMab-3, which recognizes the epitope, including both the peptides and the attached disialy-core-l (NeuAcα2-3Galβl-3 [NeuAcα2-6]GalNAcαl-O-Thr) structure at the Thr76 residue in hPDPN. However, it is unclear if the mAb binds directly to both the peptides and glycans. In this study, we synthesized the binding epitope region of LpMab-3 that includes the peptide (- 67 LVATSVNSV-T-GIRIEDLP 84 -) possessing a disialyl-core-1 O-glycan at Thr76, and we determined the crystal structure of the LpMab-3 Fab fragment that was bound to the synthesized glycopeptide at a 2.8 Å resolution. The six amino acid residues and two sialic acid residues are directly associated with four complementarity-determining regions (CDRs; H1, H2, H3, and L3) and four CDRs (H2, H3, L1, and L3), respectively. These results suggest that IgG is advantageous for generating binders against spacious epitopes such as glycoconjugates.


  • Organizational Affiliation

    Graduate School of Science, Chiba University, Chiba, Japan; Molecular Chirality Research Center, Chiba University, Chiba, Japan. Electronic address: satoshi-ogasawara@chiba-u.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of Fab fragment
A, D
220Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of Fab fragment
B, E
225Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Podoplanin
C, F
18Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q86YL7 (Homo sapiens)
Explore Q86YL7 
Go to UniProtKB:  Q86YL7
PHAROS:  Q86YL7
GTEx:  ENSG00000162493 
Entity Groups  
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UniProt GroupQ86YL7
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q86YL7-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose
G, H
4O-Glycosylation
Glycosylation Resources
GlyTouCan:  G01614ZM
GlyCosmos:  G01614ZM
GlyGen:  G01614ZM
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth A],
N [auth D],
O [auth D],
S [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth B]
M [auth B]
P [auth D]
J [auth A],
K [auth A],
L [auth B],
M [auth B],
P [auth D],
Q [auth D],
R [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.1α = 90
b = 42.96β = 91.366
c = 221.08γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASESphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description