3THK

Structure of SH3 chimera with a type II ligand linked to the chain C-terminal

• PDB DOI: https://doi.org/10.2210/pdb3THK/pdb
• Entry: 3THK supersedes: 2PQH
• BMRB: 7033

• Classification: STRUCTURAL PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-19 Released: 2011-11-23 
• Deposition Author(s): Gabdulkhakov, A.G., Gushchina, L.V., Nikulin, A.D., Nikonov, S.V., Filimonov, V.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.201 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

High-Resolution Crystal Structure of Spectrin SH3 Domain Fused with a Proline-Rich Peptide.

Gushchina, L.V., Gabdulkhakov, A.G., Nikonov, S.V., Filimonov, V.V.

(2011) J Biomol Struct Dyn 29: 485-495

• PubMed: 22066535 
• DOI: https://doi.org/10.1080/07391102.2011.10507400
• Primary Citation of Related Structures:  
  3THK


• PubMed Abstract: 
  

  A new chimeric protein, named WT-CIIA, was designed by connecting the proline-rich decapeptide PPPVPPYSAG to the C-terminus of the alpha-spectrin SH3 domain through a natural twelve-residue linker to obtain a single-chain model that would imitate intramolecular SH3-ligand interaction. The crystal structure of this fusion protein was determined at 1.7 Å resolution. The asymmetric unit of the crystal contained two SH3 globules contacting with one PPPVPPY fragment located between them. The domains are related by the two-fold non-crystallographic axis and the ligand lies in two opposite orientations with respect to the conservative binding sites of SH3 domains.

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Organizational Affiliation: 

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.64 kDa 
• Atom Count: 1,152 
• Modelled Residue Count: 128 
• Deposited Residue Count: 166 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spectrin alpha chain, brain	A, B	73	Rattus norvegicus	Mutation(s): 0  Gene Names: Sptan1, Spna2, Spta2
UniProt
Find proteins for P16086 (Rattus norvegicus) Explore P16086  Go to UniProtKB:  P16086

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline-rich peptide	C, D	10	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	E [auth A], G [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.201 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.38	α = 90
b = 36.38	β = 90
c = 112.14	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-23 
Deposition Author(s): Gabdulkhakov, A.G., Gushchina, L.V., Nikulin, A.D., Nikonov, S.V., Filimonov, V.V.
• This entry supersedes: 2PQH

Revision History  

• Version 1.0: 2011-11-23
  Type: Initial release
  
• Version 1.1: 2011-11-30
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description