Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Macromolecule Content

• Total Structure Weight: 87.45 kDa 
• Atom Count: 5680 
• Residue Count: 704 
• Unique protein chains: 2

6EJE

Human Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT

• DOI: 10.2210/pdb6EJE/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-09-20 Released: 2018-05-02 
• Deposition Author(s): Briggs, D.C., Hohenester, E.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.235 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Structural Basis for the Initiation of Glycosaminoglycan Biosynthesis by Human Xylosyltransferase 1.

Briggs, D.C., Hohenester, E.

(2018) Structure 26: 801-809.e3

• PubMed: 29681470 
• DOI: 10.1016/j.str.2018.03.014
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Proteoglycans (PGs) are essential components of the animal extracellular matrix and are required for cell adhesion, migration, signaling, and immune function. PGs are composed of a core protein and long glycosaminoglycan (GAG) chains, which often specify PG function. GAG biosynthesis is initiated by peptide O-xylosyltransferases, which transfer xylose onto selected serine residues in the core proteins. We have determined crystal structures of human xylosyltransferase 1 (XT1) in complex with the sugar donor, UDP-xylose, and various acceptor peptides. The structures reveal unique active-site features that, in conjunction with functional experiments, explain the substrate specificity of XT1. A constriction within the peptide binding cleft requires the acceptor serine to be followed by glycine or alanine. The remainder of the cleft can accommodate a wide variety of sequences, but with a general preference for acidic residues. These findings provide a framework for understanding the selectivity of GAG attachment.

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Organizational Affiliation: 

Department of Life Sciences, Imperial College London, London SW7 2AZ, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Xylosyltransferase 1	A	751	Homo sapiens	Mutation(s): 0  Gene Names: XYLT1, XT1 EC: 2.4.2.26
Find proteins for Q86Y38 (Homo sapiens) Go to UniProtKB:  Q86Y38
NIH Common Fund Data Resources
PHAROS  Q86Y38 GTEx  ENSG00000103489

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Syndecan-1	B	12	Homo sapiens	Mutation(s): 0  Gene Names: SDC1, SDC
Find proteins for P18827 (Homo sapiens) Go to UniProtKB:  P18827
NIH Common Fund Data Resources
PHAROS  P18827 GTEx  ENSG00000115884

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.235 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.28	α = 90
b = 86.72	β = 90
c = 153.47	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-09-20 
• Released Date: 2018-05-02 
Deposition Author(s): Briggs, D.C., Hohenester, E.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	101748/Z/13/Z

Revision History 

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Database references