7R2T

SYNJ2BP complex with a phosphorylated Vangl2 peptide at the P-1 position.

• PDB DOI: https://doi.org/10.2210/pdb7R2T/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-02-05 Released: 2023-05-17 
• Deposition Author(s): Carrasco, K., Cousido Siah, A., Gogl, G., Betzi, S., McEwen, A., Kostmann, C., Trave, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.239 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 

Literature

SYNJ2BP PDZ domain in complex with a synthetic Vangl2 peptide.

Carrasco, K., Cousido Siah, A., Gogl, G., Betzi, S., McEwen, A., Kostmann, C., Trave, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 49.29 kDa 
• Atom Count: 3,332 
• Modelled Residue Count: 421 
• Deposited Residue Count: 431 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptojanin-2-binding protein,Annexin	A	422	Homo sapiens	Mutation(s): 0  Gene Names: SYNJ2BP, OMP25, ANXA2
UniProt & NIH Common Fund Data Resources
Find proteins for P57105 (Homo sapiens) Explore P57105  Go to UniProtKB:  P57105
PHAROS:  P57105 GTEx:  ENSG00000213463

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vangle2 peptide binding motif with the P-1 phosphrylated	B	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULK5 (Homo sapiens) Explore Q9ULK5  Go to UniProtKB:  Q9ULK5
PHAROS:  Q9ULK5 GTEx:  ENSG00000162738

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.239 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.1	α = 90
b = 61.38	β = 90
c = 145.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Carrasco, K., Cousido Siah, A., Gogl, G., Betzi, S., McEwen, A., Kostmann, C., Trave, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description