1CX8

CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.243 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

Crystal structure of the ectodomain of human transferrin receptor.

Lawrence, C.M., Ray, S., Babyonyshev, M., Galluser, R., Borhani, D.W., Harrison, S.C.

(1999) Science 286: 779-782

  • DOI: 10.1126/science.286.5440.779
  • Primary Citation of Related Structures:  
    1CX8

  • PubMed Abstract: 

    • The transferrin receptor (TfR) undergoes multiple rounds of clathrin-mediated endocytosis and reemergence at the cell surface, importing iron-loaded transferrin (Tf) and recycling apotransferrin after discharge of iron in the endosome. The crystal structure of the dimeric ectodomain of the human TfR, determined here to 3 ...

    The transferrin receptor (TfR) undergoes multiple rounds of clathrin-mediated endocytosis and reemergence at the cell surface, importing iron-loaded transferrin (Tf) and recycling apotransferrin after discharge of iron in the endosome. The crystal structure of the dimeric ectodomain of the human TfR, determined here to 3.2 angstroms resolution, reveals a three-domain subunit. One domain closely resembles carboxy- and aminopeptidases, and features of membrane glutamate carboxypeptidase can be deduced from the TfR structure. A model is proposed for Tf binding to the receptor.

    Organizational Affiliation: 

    Howard Hughes Medical Institute and Children's Hospital Laboratory of Molecular Medicine, 320 Longwood Avenue, Boston, MA 02115, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSFERRIN RECEPTOR PROTEIN
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
639Homo sapiensMutation(s): 0 
Gene Names: TFRC
UniProt & NIH Common Fund Data Resources
Find proteins for P02786 (Homo sapiens)
Explore P02786 
Go to UniProtKB:  P02786
PHAROS:  P02786
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02786
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AA [auth D],
AB [auth H],
BA [auth D],
CA [auth D],
GA [auth E],
AA [auth D],
AB [auth H],
BA [auth D],
CA [auth D],
GA [auth E],
HA [auth E],
I [auth A],
IA [auth E],
J [auth A],
K [auth A],
MA [auth F],
NA [auth F],
O [auth B],
OA [auth F],
P [auth B],
Q [auth B],
SA [auth G],
TA [auth G],
U [auth C],
UA [auth G],
V [auth C],
W [auth C],
YA [auth H],
ZA [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
SM
Query on SM
Download Ideal Coordinates CCD File 
BB [auth H],
CB [auth H],
DA [auth D],
DB [auth H],
EA [auth D],
BB [auth H],
CB [auth H],
DA [auth D],
DB [auth H],
EA [auth D],
FA [auth D],
JA [auth E],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
N [auth A],
PA [auth F],
QA [auth F],
R [auth B],
RA [auth F],
S [auth B],
T [auth B],
VA [auth G],
WA [auth G],
X [auth C],
XA [auth G],
Y [auth C],
Z [auth C]
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.4α = 90
b = 216.9β = 90
c = 361.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
CNSrefinement
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-09-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2016-12-14
    Changes: Structure summary
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary