4RQM | pdb_00004rqm

Crystal structure of the SeMET BICC1 SAM Domain R924E mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.267 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4RQM

This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6.

Rothe, B.Leettola, C.N.Leal-Esteban, L.Cascio, D.Fortier, S.Isenschmid, M.Bowie, J.U.Constam, D.B.

(2018) Structure 26: 209-224.e6

  • DOI: https://doi.org/10.1016/j.str.2017.12.002
  • Primary Citation Related Structures: 
    4RQM, 4RQN

  • PubMed Abstract: 

    Head-to-tail polymers of sterile alpha motifs (SAM) can scaffold large macromolecular complexes. Several SAM-domain proteins that bind each other are mutated in patients with cystic kidneys or laterality defects, including the Ankyrin (ANK) and SAM domain-containing proteins ANKS6 and ANKS3, and the RNA-binding protein Bicc1. To address how their interactions are regulated, we first determined a high-resolution crystal structure of a Bicc1-SAM polymer, revealing a canonical SAM polymer with a high degree of flexibility in the subunit interface orientations. We further mapped interactions between full-length and distinct domains of Bicc1, ANKS3, and ANKS6. Neither ANKS3 nor ANKS6 alone formed macroscopic homopolymers in vivo. However, ANKS3 recruited ANKS6 to Bicc1, and the three proteins together cooperatively generated giant macromolecular complexes. Thus, the giant assemblies are shaped by SAM domains, their flanking sequences, and SAM-independent protein-protein and protein-mRNA interactions.


  • Organizational Affiliation
    • Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, SV ISREC, Station 19, 1015 Lausanne, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 24.44 kDa 
  • Atom Count: 1,481 
  • Modeled Residue Count: 184 
  • Deposited Residue Count: 213 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein bicaudal C homolog 1
A, B, C
71Homo sapiensMutation(s): 1 
Gene Names: BICC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H694 (Homo sapiens)
Explore Q9H694 
Go to UniProtKB:  Q9H694
PHAROS:  Q9H694
GTEx:  ENSG00000122870 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H694
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on ZN



Download:Ideal Coordinates CCD File
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.267 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.81α = 90
b = 64.43β = 90
c = 70.64γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXCDphasing
SHELXEmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary