4Z89 | pdb_00004z89

SH3-II of Drosophila Rim-binding protein bound to a Cacophony derived peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 
    0.312 (Depositor), 0.320 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 
    0.258 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4Z89

This is version 1.2 of the entry. See complete history

Literature

A high affinity RIM-binding protein/Aplip1 interaction prevents the formation of ectopic axonal active zones.

Siebert, M.Bohme, M.A.Driller, J.H.Babikir, H.Mampell, M.M.Rey, U.Ramesh, N.Matkovic, T.Holton, N.Reddy-Alla, S.Gottfert, F.Kamin, D.Quentin, C.Klinedinst, S.Andlauer, T.F.Hell, S.W.Collins, C.A.Wahl, M.C.Loll, B.Sigrist, S.J.

(2015) Elife 4

  • DOI: https://doi.org/10.7554/eLife.06935
  • Primary Citation Related Structures: 
    4Z88, 4Z89, 4Z8A

  • PubMed Abstract: 

    Synaptic vesicles (SVs) fuse at active zones (AZs) covered by a protein scaffold, at Drosophila synapses comprised of ELKS family member Bruchpilot (BRP) and RIM-binding protein (RBP). We here demonstrate axonal co-transport of BRP and RBP using intravital live imaging, with both proteins co-accumulating in axonal aggregates of several transport mutants. RBP, via its C-terminal Src-homology 3 (SH3) domains, binds Aplip1/JIP1, a transport adaptor involved in kinesin-dependent SV transport. We show in atomic detail that RBP C-terminal SH3 domains bind a proline-rich (PxxP) motif of Aplip1/JIP1 with submicromolar affinity. Pointmutating this PxxP motif provoked formation of ectopic AZ-like structures at axonal membranes. Direct interactions between AZ proteins and transport adaptors seem to provide complex avidity and shield synaptic interaction surfaces of pre-assembled scaffold protein transport complexes, thus, favouring physiological synaptic AZ assembly over premature assembly at axonal membranes.


  • Organizational Affiliation
    • Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany.

Macromolecule Content 

  • Total Structure Weight: 99.28 kDa 
  • Atom Count: 6,239 
  • Modeled Residue Count: 757 
  • Deposited Residue Count: 900 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RIM-binding protein, isoform F
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
73Drosophila melanogasterMutation(s): 0 
Gene Names: RbpDmel_CG43073
UniProt
Find proteins for A0A0B4JDC9 (Drosophila melanogaster)
Explore A0A0B4JDC9 
Go to UniProtKB:  A0A0B4JDC9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B4JDC9
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent calcium channel type A subunit alpha-117Drosophila melanogasterMutation(s): 2 
UniProt
Find proteins for P91645 (Drosophila melanogaster)
Explore P91645 
Go to UniProtKB:  P91645
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP91645
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
U [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free:  0.312 (Depositor), 0.320 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.3α = 90
b = 122.22β = 113.17
c = 68.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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: 2015-08-05
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary