8T8R | pdb_00008t8r

Sortilin-PGRN peptide complex

• PDB DOI: https://doi.org/10.2210/pdb8T8R/pdb

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


• Deposited: 2023-06-23 Released: 2024-06-26 
• Deposition Author(s): Srivastava, D.B., Srivastava, A., Cherf, G.M., Low, L.Y., Kannan, G.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 
  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Literature

Structural studies of Sortilin-PGRN peptide complex

Srivastava, D.B., Cherf, G.M., Low, L.Y., Kannan, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 79.33 kDa 
• Atom Count: 5,316 
• Modeled Residue Count: 662 
• Deposited Residue Count: 694 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sortilin	A	678	Homo sapiens	Mutation(s): 0  Gene Names: SORT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99523 (Homo sapiens) Explore Q99523  Go to UniProtKB:  Q99523
PHAROS:  Q99523 GTEx:  ENSG00000134243
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: Q99523-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Paragranulin peptide	B	16	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P28799 (Homo sapiens) Explore P28799  Go to UniProtKB:  P28799
PHAROS:  P28799 GTEx:  ENSG00000030582

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.945	α = 90
b = 78.618	β = 126.8
c = 111.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Srivastava, D.B., Srivastava, A., Cherf, G.M., Low, L.Y., Kannan, G.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary