4V46 | pdb_00004v46

Crystal structure of the BAFF-BAFF-R complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.226 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.204 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4V46

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 1,406.71 kDa 
  • Atom Count: 79,720 
  • Modeled Residue Count: 10,140 
  • Deposited Residue Count: 12,660 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
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:|  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 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.204 (DCC) 
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

View Full Validation Report



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
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary