1BTG

CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nerve growth factor in different crystal forms displays structural flexibility and reveals zinc binding sites.

Holland, D.R.Cousens, L.S.Meng, W.Matthews, B.W.

(1994) J.Mol.Biol. 239: 385-400

  • DOI: 10.1006/jmbi.1994.1380

  • PubMed Abstract: 
  • Murine beta-nerve growth factor (beta NGF) is a 118 amino acid residue polypeptide which, as a functional dimer, plays an important role in the survival and development of certain neuronal populations. The structure of the bis-desocta1-8 form of muri ...

    Murine beta-nerve growth factor (beta NGF) is a 118 amino acid residue polypeptide which, as a functional dimer, plays an important role in the survival and development of certain neuronal populations. The structure of the bis-desocta1-8 form of murine beta NGF has been determined in two different crystal modifications using X-ray methods. The two crystal forms, with space groups P2(1)2(1)2(1) and C2, were grown from 18 to 20% polyethylene glycol 8000 and 100 mM Pipes (pH 6.1) with zinc acetate concentrations of 1 mM and 100 mM, respectively. The C2 structure was solved by multiple isomorphous replacement using four heavy-atom derivatives and was refined to a crystallographic residual of 17.9% and 2.5 A resolution. The crystals contain three beta NGF monomers per asymmetric unit. Two monomers form a dimer related by a non-crystallographic 2-fold axis of symmetry. The third monomer also forms a dimer that is very similar, but with a crystallography related monomer as a partner. The electron density clearly defines residues 12 through 115 for all three monomers but the extreme N and C-terminal residues (9 to 11, 116 to 118) are ill defined in some cases. The P2(1)2(1)2(1) structure was solved by molecular replacement using the C2 structure as a search model and was refined to a crystallographic residual of 19.7% at 2.8 A resolution. This crystal form contains two monomers per asymmetric unit, again arranged as a non-crystallographic 2-fold-related dimer. The N and c termini are also variably defined. The core of each of the five monomers, which forms a cysteine knot motif, is very similar in all structures. Also, the dimer structures are very similar to one another, whether the monomers are related by crystallographic or non-crystallographic symmetry. However, three of the four loop regions that extend from the core of each monomer display substantial variability in conformation, even between monomers of the same dimer. This structural variability in the putative receptor binding regions suggests that structural malleability might be important in allowing the ligands to bind to different receptors with different affinities.(ABSTRACT TRUNCATED AT 400 WORDS)


    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute, Eugene, OR.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA NERVE GROWTH FACTOR
A, B, C
110Mus musculusGene Names: Ngf (Ngfb)
Find proteins for P01139 (Mus musculus)
Go to UniProtKB:  P01139
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.800α = 90.00
b = 93.900β = 123.10
c = 58.900γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
HOWARDdata collection
XUONG)data reduction
XENGENdata reduction
NIELSENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance