1CB6

STRUCTURE OF HUMAN APOLACTOFERRIN AT 2.0 A RESOLUTION.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.286 
  • R-Value Observed: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change.

Jameson, G.B.Anderson, B.F.Norris, G.E.Thomas, D.H.Baker, E.N.

(1998) Acta Crystallogr D Biol Crystallogr 54: 1319-1335

  • DOI: 10.1107/s0907444998004417
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The three-dimensional structure of a form of human apolactoferrin, in which one lobe (the N-lobe) has an open conformation and the other lobe (the C-lobe) is closed, has been refined at 2.0 A resolution. The refinement, by restrained least-squares me ...

    The three-dimensional structure of a form of human apolactoferrin, in which one lobe (the N-lobe) has an open conformation and the other lobe (the C-lobe) is closed, has been refined at 2.0 A resolution. The refinement, by restrained least-squares methods, used synchrotron radiation X-ray diffraction data combined with a lower resolution diffractometer data set. The final refined model (5346 protein atoms from residues 1-691, two Cl- ions and 363 water molecules) gives a crystallographic R factor of 0.201 (Rfree = 0. 286) for all 51305 reflections in the resolution range 10.0-2.0 A. The conformational change in the N-lobe, which opens up the binding cleft, involves a 54 degrees rotation of the N2 domain relative to the N1 domain. This also results in a small reorientation of the two lobes relative to one another with a further approximately 730 A2 of surface area being buried as the N2 domain contacts the C-lobe and the inter-lobe helix. These new contacts also involve the C-terminal helix and provide a mechanism through which the conformational and iron-binding status of the N-lobe can be signalled to the C-lobe. Surface-area calculations indicate a fine balance between open and closed forms of lactoferrin, which both have essentially the same solvent-accessible surface. Chloride ions are bound in the anion-binding sites of both lobes, emphasizing the functional significance of these sites. The closed configuration of the C-lobe, attributed in part to weak stabilization by crystal packing interactions, has important implications for lactoferrin dynamics. It shows that a stable closed structure, essentially identical to that of the iron-bound form, can be formed in the absence of iron binding.


    Related Citations: 
    • Apolactoferrin structure demonstrates ligand-induced conformational change in transferrins.
      Anderson, B.F., Baker, H.M., Norris, G.E., Rumball, S.V., Baker, E.N.
      (1990) Nature 344: 784
    • Structure of human lactoferrin: crystallographic structure analysis and refinement at 2.8 A resolution.
      Anderson, B.F., Baker, H.M., Norris, G.E., Rice, D.W., Baker, E.N.
      (1989) J Mol Biol 209: 711
    • Transferrins: Insights Into Structure and Function from Studies on Lactoferrin
      Baker, E.N., Rumball, S.V., Anderson, B.F.
      (1987) Trends Biochem Sci 12: 350
    • Structure of human lactoferrin at 3.2-A resolution.
      Anderson, B.F., Baker, H.M., Dodson, E.J., Norris, G.E., Rumball, S.V., Waters, J.M., Baker, E.N.
      (1987) Proc Natl Acad Sci U S A 84: 1769

    Organizational Affiliation

    Department of Chemistry, Massey University, Palmerston North, New Zealand.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lactotransferrin
A
691Homo sapiensMutation(s): 0 
Gene Names: LTFGIG12LF
EC: 3.4.21
Find proteins for P02788 (Homo sapiens)
Go to UniProtKB:  P02788
NIH Common Fund Data Resources
PHAROS  P02788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.286 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.09α = 90
b = 94.58β = 90
c = 55.79γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ALMNmodel building
SHELXL-97refinement
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-12
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-21
    Changes: Advisory, Database references, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2019-11-06
    Changes: Data collection, Database references