6H5T | pdb_00006h5t

Intersectin SH3A short isoform


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.191 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.176 (Depositor) 
  • R-Value Observed: 
    0.176 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6H5T

This is version 1.5 of the entry. See complete history

Literature

Exon Inclusion Modulates Conformational Plasticity and Autoinhibition of the Intersectin 1 SH3A Domain.

Gerth, F.Japel, M.Sticht, J.Kuropka, B.Schmitt, X.J.Driller, J.H.Loll, B.Wahl, M.C.Pagel, K.Haucke, V.Freund, C.

(2019) Structure 27: 977

  • DOI: https://doi.org/10.1016/j.str.2019.03.020
  • Primary Citation Related Structures: 
    6H5T

  • PubMed Abstract: 

    The scaffolding protein intersectin 1 plays important roles in clathrin-mediated endocytosis and in the replenishment of release-ready synaptic vesicles (SV). Two splice variants of intersectin's SH3A domain are expressed in the brain, and association of the neuron-specific variant with synapsin I has been shown to enable sustained neurotransmission and to be regulated by an adjacent C-terminal motif. Here, we demonstrate that the ubiquitously expressed short SH3A variant of intersectin 1 interacts with an N-terminal intramolecular sequence that operates synergistically with the C-terminal motif. NMR spectroscopic investigations show that the five-amino acid insertion into the β strand 2 of the neuronal SH3A variant introduces conformational plasticity incompatible with binding of the N-terminal sequence. The difference in the autoregulatory mechanism of the domain's variants differentially affects its synaptic binding partners, thereby establishing alternative splicing in conjunction with autoinhibitory motif variation as a mechanism to regulate protein interaction networks.


  • Organizational Affiliation
    • Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.

Macromolecule Content 

  • Total Structure Weight: 22.53 kDa 
  • Atom Count: 1,310 
  • Modeled Residue Count: 132 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Intersectin-1
A, B
99Homo sapiensMutation(s): 0 
Gene Names: ITSN1ITSNSH3D1A
UniProt & NIH Common Fund Data Resources
Find proteins for Q15811 (Homo sapiens)
Explore Q15811 
Go to UniProtKB:  Q15811
PHAROS:  Q15811
GTEx:  ENSG00000205726 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15811
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7PG

Query on 7PG



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL
C17 H36 O9
SZGNWRSFHADOMY-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
H [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.191 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.176 (Depositor) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.792α = 90
b = 86.792β = 90
c = 141.768γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB958

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-15
    Changes: Data collection
  • Version 1.3: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.4: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.5: 2024-05-15
    Changes: Data collection, Database references, Derived calculations