4IIM | pdb_00004iim

Crystal structure of the Second SH3 Domain of ITSN1 bound with a synthetic peptide

• PDB DOI: https://doi.org/10.2210/pdb4IIM/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-12-20 Released: 2013-01-23 
• Deposition Author(s): Dong, A., Guan, X., Huang, H., Wernimont, A., Gu, J., Sidhu, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Second SH3 Domain of ITSN1 bound with a synthetic peptide

Guan, X., Dong, A., Huang, H., Wernimont, A., Gu, J., Sidhu, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.09 kDa 
• Atom Count: 1,333 
• Modeled Residue Count: 141 
• Deposited Residue Count: 176 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intersectin-1	A, C [auth B]	70	Homo sapiens	Mutation(s): 0  Gene Names: ITSN1, ITSN, SH3D1A
UniProt & NIH Common Fund Data Resources
Find proteins for Q15811 (Homo sapiens) Explore Q15811  Go to UniProtKB:  Q15811
PHAROS:  Q15811 GTEx:  ENSG00000205726

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide ligand	B [auth C], D, E	12	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	F [auth A], G [auth A], H [auth C], I [auth C], J [auth C], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth D]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.048	α = 90
b = 51.393	β = 90
c = 69.26	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Dong, A., Guan, X., Huang, H., Wernimont, A., Gu, J., Sidhu, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description