4Z88

SH3-II of Drosophila Rim-binding protein with Aplip1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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, K, L
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
JNK-interacting protein 1
M, N, O, P, Q
M, N, O, P, Q, R, S, T, U, V, W, X
17Drosophila melanogasterMutation(s): 2 
UniProt
Find proteins for Q9W0K0 (Drosophila melanogaster)
Explore Q9W0K0 
Go to UniProtKB:  Q9W0K0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9W0K0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth E]
CA [auth F]
DA [auth G]
EA [auth H]
AA [auth C],
BA [auth E],
CA [auth F],
DA [auth G],
EA [auth H],
FA [auth I],
GA [auth J],
HA [auth K],
IA [auth L],
Y [auth A],
Z [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.28α = 90
b = 62.42β = 90.27
c = 163.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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, Refinement description