Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 108.99 kDa 
• Atom Count: 8498 
• Modelled Residue Count: 908 
• Deposited Residue Count: 914 
• Unique protein chains: 2

4OU3

Crystal structure of porcine aminopeptidase N complexed with CNGRCG tumor-homing peptide

• DOI: 10.2210/pdb4OU3/pdb

• Classification: HYDROLASE/PROTEIN BINDING
• Organism(s): Sus scrofa
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-02-14 Released: 2014-11-05 
• Deposition Author(s): Liu, C., Yang, Y., Chen, L., Lin, Y.-L., Li, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.190 
• R-Value Work: 0.140 
• R-Value Observed: 0.143 

Literature

A Unified Mechanism for Aminopeptidase N-based Tumor Cell Motility and Tumor-homing Therapy.

Liu, C., Yang, Y., Chen, L., Lin, Y.L., Li, F.

(2014) J Biol Chem 289: 34520-34529

• PubMed: 25359769 
• DOI: 10.1074/jbc.M114.566802
• Primary Citation of Related Structures:  
  4OU3


• PubMed Abstract: 
  

Tumor cell surface aminopeptidase N (APN or CD13) has two puzzling functions unrelated to its enzymatic activity: mediating tumor cell motility and serving as a receptor for tumor-homing peptides (peptides that bring anti-cancer drugs to tumor cells). To investigate APN-based tumor-homing therapy, we determined the crystal structure of APN complexed with a tumor-homing peptide containing a representative Asn-Gly-Arg (NGR) motif. The tumor-homing peptide binds to the APN enzymatic active site, but it resists APN degradation due to a distorted scissile peptide bond. To explore APN-based tumor cell motility, we examined the interactions between APN and extracellular matrix (ECM) proteins. APN binds to, but does not degrade, NGR motifs in ECM proteins that share similar conformations with the NGR motif in the APN-bound tumor-homing peptide. Therefore, APN-based tumor cell motility and tumor-homing therapy rely on a unified mechanism in which both functions are driven by the specific and stable interactions between APN and the NGR motifs in ECM proteins and tumor-homing peptides. This study further implicates APN as an integrin-like molecule that functions broadly in cell motility and adhesion by interacting with its signature NGR motifs in the extracellular environment.

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Organizational Affiliation: 

From the Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455 [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N	A	908	Sus scrofa	Mutation(s): 0  Gene Names: ANPEP EC: 3.4.11.2
Find proteins for P15145 (Sus scrofa) Explore P15145  Go to UniProtKB:  P15145

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
tumor-homing peptide	B	6	N/A	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F, G, H, I, J	2		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.190 
• R-Value Work: 0.140 
• R-Value Observed: 0.143 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 260.323	α = 90
b = 62.879	β = 100.59
c = 82.023	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-02-14 
• Released Date: 2014-11-05 
Deposition Author(s): Liu, C., Yang, Y., Chen, L., Lin, Y.-L., Li, F.

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Database references
• Version 1.2: 2015-01-14
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary