2HAV | pdb_00002hav

Apo-Human Serum Transferrin (Glycosylated)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.293 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2HAV

This is version 1.4 of the entry. See complete history

Literature

The Crystal Structure of Iron-free Human Serum Transferrin Provides Insight into Inter-lobe Communication and Receptor Binding.

Wally, J.Halbrooks, P.J.Vonrhein, C.Rould, M.A.Everse, S.J.Mason, A.B.Buchanan, S.K.

(2006) J Biological Chem 281: 24934-24944

  • DOI: https://doi.org/10.1074/jbc.M604592200
  • Primary Citation Related Structures: 
    2HAU, 2HAV

  • PubMed Abstract: 

    Serum transferrin reversibly binds iron in each of two lobes and delivers it to cells by a receptor-mediated, pH-dependent process. The binding and release of iron result in a large conformational change in which two subdomains in each lobe close or open with a rigid twisting motion around a hinge. We report the structure of human serum transferrin (hTF) lacking iron (apo-hTF), which was independently determined by two methods: 1) the crystal structure of recombinant non-glycosylated apo-hTF was solved at 2.7-A resolution using a multiple wavelength anomalous dispersion phasing strategy, by substituting the nine methionines in hTF with selenomethionine and 2) the structure of glycosylated apo-hTF (isolated from serum) was determined to a resolution of 2.7A by molecular replacement using the human apo-N-lobe and the rabbit holo-C1-subdomain as search models. These two crystal structures are essentially identical. They represent the first published model for full-length human transferrin and reveal that, in contrast to family members (human lactoferrin and hen ovotransferrin), both lobes are almost equally open: 59.4 degrees and 49.5 degrees rotations are required to open the N- and C-lobes, respectively (compared with closed pig TF). Availability of this structure is critical to a complete understanding of the metal binding properties of each lobe of hTF; the apo-hTF structure suggests that differences in the hinge regions of the N- and C-lobes may influence the rates of iron binding and release. In addition, we evaluate potential interactions between apo-hTF and the human transferrin receptor.


  • Organizational Affiliation
    • NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 151.66 kDa 
  • Atom Count: 10,601 
  • Modeled Residue Count: 1,352 
  • Deposited Residue Count: 1,352 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serotransferrin
A, B
676Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02787 (Homo sapiens)
Explore P02787 
Go to UniProtKB:  P02787
PHAROS:  P02787
GTEx:  ENSG00000091513 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02787
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT

Query on CIT



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
I [auth B]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.293 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.324α = 90
b = 103.258β = 90
c = 200.362γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary