3PEG

Crystal structure of Neurofibromins Sec14-PH module containing a patient derived duplication (TD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural and biochemical consequences of NF1 associated nontruncating mutations in the Sec14-PH module of neurofibromin.

Welti, S.Kuhn, S.D'Angelo, I.Brugger, B.Kaufmann, D.Scheffzek, K.

(2011) Hum Mutat 32: 191-197

  • DOI: https://doi.org/10.1002/humu.21405
  • Primary Citation of Related Structures:  
    3P7Z, 3PEG, 3PG7

  • PubMed Abstract: 

    Neurofibromatosis type 1 (NF1) is a common genetic disorder caused by alterations in the tumor suppressor gene NF1. Clinical manifestations include various neural crest derived tumors, pigmentation anomalies, bone deformations, and learning disabilities. NF1 encodes the Ras specific GTPase activating protein (RasGAP) neurofibromin, of which the central RasGAP related domain as well as a Sec14-like (residues 1560-1699) and a tightly interacting pleckstrin homology (PH)-like (1713-1818) domain are currently well defined. However, patient-derived nontruncating mutations have been reported along the whole NF1 gene, suggesting further essential protein functions. Focusing on the Sec14-PH module, we have engineered such nontruncating mutations and analyzed their implications on protein function and structure using lipid binding assays, CD spectroscopy and X-ray crystallography. Although lipid binding appears to be preserved among most nontruncating mutants, we see major structural changes for two of the alterations. Judging from these changes and our biochemical data, we suggest the presence of an intermolecular contact surface in the lid-lock region of the protein.


  • Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany. welti@embl.de


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neurofibromin290Homo sapiensMutation(s): 0 
Gene Names: NF1
UniProt & NIH Common Fund Data Resources
Find proteins for P21359 (Homo sapiens)
Explore P21359 
Go to UniProtKB:  P21359
PHAROS:  P21359
GTEx:  ENSG00000196712 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21359
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEV
Query on PEV

Download Ideal Coordinates CCD File 
H [auth A](1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C39 H78 N O8 P
RPJZYOHZALDGKI-QNGWXLTQSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.6α = 90
b = 104.6β = 90
c = 116.3γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
ADSCdata collection
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary