3V83

The 2.1 angstrom crystal structure of diferric human transferrin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis for iron piracy by pathogenic Neisseria.

Noinaj, N., Easley, N.C., Oke, M., Mizuno, N., Gumbart, J., Boura, E., Steere, A.N., Zak, O., Aisen, P., Tajkhorshid, E., Evans, R.W., Gorringe, A.R., Mason, A.B., Steven, A.C., Buchanan, S.K.

(2012) Nature 483: 53-58

  • DOI: 10.1038/nature10823
  • Primary Citation of Related Structures:  
    3SKP, 3V83, 3V89, 3V8U, 3V8X

  • PubMed Abstract: 

    • Neisseria are obligate human pathogens causing bacterial meningitis, septicaemia and gonorrhoea. Neisseria require iron for survival and can extract it directly from human transferrin for transport across the outer membrane. The transport system consists of TbpA, an integral outer membrane protein, and TbpB, a co-receptor attached to the cell surface; both proteins are potentially important vaccine and therapeutic targets ...

    Neisseria are obligate human pathogens causing bacterial meningitis, septicaemia and gonorrhoea. Neisseria require iron for survival and can extract it directly from human transferrin for transport across the outer membrane. The transport system consists of TbpA, an integral outer membrane protein, and TbpB, a co-receptor attached to the cell surface; both proteins are potentially important vaccine and therapeutic targets. Two key questions driving Neisseria research are how human transferrin is specifically targeted, and how the bacteria liberate iron from transferrin at neutral pH. To address these questions, we solved crystal structures of the TbpA-transferrin complex and of the corresponding co-receptor TbpB. We characterized the TbpB-transferrin complex by small-angle X-ray scattering and the TbpA-TbpB-transferrin complex by electron microscopy. Our studies provide a rational basis for the specificity of TbpA for human transferrin, show how TbpA promotes iron release from transferrin, and elucidate how TbpB facilitates this process.

    Organizational Affiliation: 

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland 20892, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serotransferrin
A, B, C, D, E, F
A, B, C, D, E, F
698Homo sapiensMutation(s): 1 
Gene Names: TF, PRO1400
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P02787 (Homo sapiens)
Explore P02787 
Go to UniProtKB:  P02787
PHAROS:  P02787
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02787
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G
Download Ideal Coordinates CCD File 
FA [auth B],
GA [auth B],
IB [auth D],
IC [auth F],
JB [auth D],
FA [auth B],
GA [auth B],
IB [auth D],
IC [auth F],
JB [auth D],
JC [auth F],
P [auth A],
Q [auth A],
R [auth A],
SA [auth C],
TA [auth C],
UA [auth C],
XB [auth E],
YB [auth E]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
CA [auth B],
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
CA [auth B],
CB [auth D],
DA [auth B],
DB [auth D],
DC [auth F],
EA [auth B],
EB [auth D],
EC [auth F],
FB [auth D],
FC [auth F],
GB [auth D],
GC [auth F],
HB [auth D],
HC [auth F],
K [auth A],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
OB [auth E],
PA [auth C],
PB [auth E],
QA [auth C],
QB [auth E],
RA [auth C],
RB [auth E],
SB [auth E],
TB [auth E],
UB [auth E],
VB [auth E],
W [auth B],
WB [auth E],
X [auth B],
Y [auth B],
Z [auth B],
ZA [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
BCT
Query on BCT
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AC [auth F],
G [auth A],
H [auth A],
HA [auth C],
IA [auth C],
AC [auth F],
G [auth A],
H [auth A],
HA [auth C],
IA [auth C],
KB [auth E],
LB [auth E],
S [auth B],
T [auth B],
VA [auth D],
WA [auth D],
ZB [auth F]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M		 Ligand Interaction
FE
Query on FE
Download Ideal Coordinates CCD File 
BC [auth F],
CC [auth F],
I [auth A],
J [auth A],
JA [auth C],
BC [auth F],
CC [auth F],
I [auth A],
J [auth A],
JA [auth C],
KA [auth C],
MB [auth E],
NB [auth E],
U [auth B],
V [auth B],
XA [auth D],
YA [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 254.531α = 90
b = 173.004β = 123.26
c = 150.151γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Database references
  • Version 1.2: 2012-04-18
    Changes: Database references