4V46

Crystal structure of the BAFF-BAFF-R complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the BAFF-BAFF-R complex and its implications for receptor activation

Kim, H.M.Yu, K.S.Lee, M.E.Shin, D.R.Kim, Y.S.Paik, S.G.Yoo, O.J.Lee, H.Lee, J.-O.

(2003) Nat Struct Biol 10: 342-348

  • DOI: https://doi.org/10.1038/nsb925
  • Primary Citation of Related Structures:  
    4V46

  • PubMed Abstract: 

    B-cell activating factor (BAFF) is a key regulator of B-lymphocyte development. Its biological role is mediated by the specific receptors BCMA, TACI and BAFF-R. We have determined the crystal structure of the extracellular domain of BAFF-R bound to BAFF at a resolution of 3.3 A. The cysteine-rich domain (CRD) of the BAFF-R extracellular domain adopts a beta-hairpin structure and binds to the virus-like BAFF cage in a 1:1 molar ratio. The conserved DxL motif of BAFF-R is located on the tip of the beta-turn and is indispensable in the binding of BAFF. The crystal structure shows that a unique dimeric contact occurs between the BAFF-R monomers in the virus-like cage complex. The extracellular domain of TACI contains two CRDs, both of which contain the DxL motif. Modeling of TACI-BAFF complex suggests that both CDRs simultaneously interact with the BAFF dimer in the virus-like cage.


  • Organizational Affiliation

    Department of Biological Science, Korea Advanced Institute of Science and Technology, Daejeon, Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor ligand superfamily member 13B148Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y275 (Homo sapiens)
Explore Q9Y275 
Go to UniProtKB:  Q9Y275
PHAROS:  Q9Y275
GTEx:  ENSG00000102524 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y275
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 13C63Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RJ3 (Homo sapiens)
Explore Q96RJ3 
Go to UniProtKB:  Q96RJ3
PHAROS:  Q96RJ3
GTEx:  ENSG00000159958 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RJ3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth AQ]
AF [auth As]
BE [auth AR]
BF [auth Av]
CE [auth A1]
AE [auth AQ],
AF [auth As],
BE [auth AR],
BF [auth Av],
CE [auth A1],
CF [auth Aw],
DE [auth A4],
DF [auth Aw],
EE [auth A4],
FE [auth A5],
GE [auth A5],
HE [auth A6],
IE [auth A6],
JE [auth A7],
KE [auth A8],
LE [auth A8],
ME [auth A9],
NE [auth A9],
OE [auth Aa],
PE [auth Ac],
QD [auth AA],
QE [auth Ac],
RD [auth AA],
RE [auth Ad],
SD [auth AB],
SE [auth Af],
TD [auth AC],
TE [auth Ah],
UD [auth AD],
UE [auth Ak],
VD [auth AF],
VE [auth Am],
WD [auth AJ],
WE [auth An],
XD [auth AN],
XE [auth Ap],
YD [auth AO],
YE [auth Aq],
ZD [auth AQ],
ZE [auth Ar]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.5α = 90
b = 194.8β = 93.3
c = 274.4γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other