6LYN | pdb_00006lyn

CD146 D4-D5/AA98 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 
    0.262 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure basis for AA98 inhibition on the activation of endothelial cells mediated by CD146.

Chen, X.Yan, H.Liu, D.Xu, Q.Duan, H.Feng, J.Yan, X.Xie, C.

(2021) iScience 24: 102417-102417

  • DOI: https://doi.org/10.1016/j.isci.2021.102417
  • Primary Citation Related Structures: 
    6LYN

  • PubMed Abstract: 

    CD146 is an adhesion molecule that plays important roles in angiogenesis, cancer metastasis, and immune response. It exists as a monomer or dimer on the cell surface. AA98 is a monoclonal antibody that binds to CD146, which abrogates the activation of CD146-mediated signaling pathways and shows inhibitory effects on tumor growth. However, how AA98 inhibits the function of CD146 remains unclear. Here, we describe a crystal structure of the CD146/AA98 Fab complex at a resolution of 2.8 Å. Monomeric CD146 is stabilized by AA98 Fab binding to the junction region of CD146 domains 4 and 5. A higher-affinity AA98 variant (here named HA98) was thus rationally designed. Better binding to CD146 and prominent inhibition on cell migration were achieved with HA98. Further experiments on xenografted melanoma in mice with HA98 revealed superior inhibitory effects on tumor growth to those of AA98, which suggested future applications of this antibody in cancer therapy.


  • Organizational Affiliation
    • Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content 

  • Total Structure Weight: 137.61 kDa 
  • Atom Count: 9,727 
  • Modeled Residue Count: 1,224 
  • Deposited Residue Count: 1,238 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AA98 Fab heavy chainA,
F [auth H]
217Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AA98 Fab light chainB,
D [auth L]
218Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell surface glycoprotein MUC18C,
E [auth D]
184Homo sapiensMutation(s): 0 
Gene Names: MCAMMUC18
UniProt & NIH Common Fund Data Resources
Find proteins for P43121 (Homo sapiens)
Explore P43121 
Go to UniProtKB:  P43121
PHAROS:  P43121
GTEx:  ENSG00000076706 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43121
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P43121-1
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on EPE



Download:Ideal Coordinates CCD File
K [auth B],
P [auth L]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
L [auth C],
M [auth C],
Q [auth D],
R [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
G [auth A],
U [auth H]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
N [auth C],
O [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
S [auth D],
T [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.262 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.203α = 90
b = 88.387β = 89.93
c = 94.644γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770793
National Natural Science Foundation of China (NSFC)China31370740

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary