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- PDB-4v46: Crystal structure of the BAFF-BAFF-R complex -

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Basic information

Entry
Database: PDB / ID: 4v46
TitleCrystal structure of the BAFF-BAFF-R complex
Components
  • Tumor necrosis factor ligand superfamily member 13B
  • Tumor necrosis factor receptor superfamily member 13C
KeywordsCYTOKINE
Function / homology
Function and homology information


B cell costimulation / positive regulation of germinal center formation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / germinal center formation / tumor necrosis factor receptor binding / skin development / B cell proliferation / B cell homeostasis ...B cell costimulation / positive regulation of germinal center formation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / germinal center formation / tumor necrosis factor receptor binding / skin development / B cell proliferation / B cell homeostasis / T cell proliferation / positive regulation of T cell proliferation / positive regulation of B cell proliferation / tumor necrosis factor-mediated signaling pathway / T cell costimulation / cytokine activity / TNFR2 non-canonical NF-kB pathway / signaling receptor activity / adaptive immune response / receptor ligand activity / external side of plasma membrane / intracellular membrane-bounded organelle / focal adhesion / signaling receptor binding / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / Tumor necrosis factor receptor 13C/17 / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 13C / Tumor necrosis factor ligand superfamily member 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKim, 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.
CitationJournal: NAT.STRUCT.BIOL. / Year: 2003
Title: Crystal structure of the BAFF-BAFF-R complex and its implications for receptor activation
Authors: 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.
History
DepositionMar 23, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1OTZ, 1P0T
Revision 1.1Dec 10, 2014Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Tumor necrosis factor ligand superfamily member 13B
AB: Tumor necrosis factor ligand superfamily member 13B
AC: Tumor necrosis factor ligand superfamily member 13B
AD: Tumor necrosis factor ligand superfamily member 13B
AE: Tumor necrosis factor ligand superfamily member 13B
AF: Tumor necrosis factor ligand superfamily member 13B
AG: Tumor necrosis factor ligand superfamily member 13B
AH: Tumor necrosis factor ligand superfamily member 13B
AI: Tumor necrosis factor ligand superfamily member 13B
AJ: Tumor necrosis factor ligand superfamily member 13B
AK: Tumor necrosis factor ligand superfamily member 13B
AL: Tumor necrosis factor ligand superfamily member 13B
AM: Tumor necrosis factor ligand superfamily member 13B
AN: Tumor necrosis factor ligand superfamily member 13B
AO: Tumor necrosis factor ligand superfamily member 13B
AP: Tumor necrosis factor ligand superfamily member 13B
AQ: Tumor necrosis factor ligand superfamily member 13B
AR: Tumor necrosis factor ligand superfamily member 13B
AS: Tumor necrosis factor ligand superfamily member 13B
AT: Tumor necrosis factor ligand superfamily member 13B
AU: Tumor necrosis factor ligand superfamily member 13B
AV: Tumor necrosis factor ligand superfamily member 13B
AW: Tumor necrosis factor ligand superfamily member 13B
AX: Tumor necrosis factor ligand superfamily member 13B
AY: Tumor necrosis factor ligand superfamily member 13B
AZ: Tumor necrosis factor ligand superfamily member 13B
A0: Tumor necrosis factor ligand superfamily member 13B
A1: Tumor necrosis factor ligand superfamily member 13B
A2: Tumor necrosis factor ligand superfamily member 13B
A3: Tumor necrosis factor ligand superfamily member 13B
A4: Tumor necrosis factor ligand superfamily member 13B
A5: Tumor necrosis factor ligand superfamily member 13B
A6: Tumor necrosis factor ligand superfamily member 13B
A7: Tumor necrosis factor ligand superfamily member 13B
A8: Tumor necrosis factor ligand superfamily member 13B
A9: Tumor necrosis factor ligand superfamily member 13B
Aa: Tumor necrosis factor ligand superfamily member 13B
Ab: Tumor necrosis factor ligand superfamily member 13B
Ac: Tumor necrosis factor ligand superfamily member 13B
Ad: Tumor necrosis factor ligand superfamily member 13B
Ae: Tumor necrosis factor ligand superfamily member 13B
Af: Tumor necrosis factor ligand superfamily member 13B
Ag: Tumor necrosis factor ligand superfamily member 13B
Ah: Tumor necrosis factor ligand superfamily member 13B
Ai: Tumor necrosis factor ligand superfamily member 13B
Aj: Tumor necrosis factor ligand superfamily member 13B
Ak: Tumor necrosis factor ligand superfamily member 13B
Al: Tumor necrosis factor ligand superfamily member 13B
Am: Tumor necrosis factor ligand superfamily member 13B
An: Tumor necrosis factor ligand superfamily member 13B
Ao: Tumor necrosis factor ligand superfamily member 13B
Ap: Tumor necrosis factor ligand superfamily member 13B
Aq: Tumor necrosis factor ligand superfamily member 13B
Ar: Tumor necrosis factor ligand superfamily member 13B
As: Tumor necrosis factor ligand superfamily member 13B
At: Tumor necrosis factor ligand superfamily member 13B
Au: Tumor necrosis factor ligand superfamily member 13B
Av: Tumor necrosis factor ligand superfamily member 13B
Aw: Tumor necrosis factor ligand superfamily member 13B
Ax: Tumor necrosis factor ligand superfamily member 13B
BA: Tumor necrosis factor receptor superfamily member 13C
BB: Tumor necrosis factor receptor superfamily member 13C
BC: Tumor necrosis factor receptor superfamily member 13C
BD: Tumor necrosis factor receptor superfamily member 13C
BE: Tumor necrosis factor receptor superfamily member 13C
BF: Tumor necrosis factor receptor superfamily member 13C
BG: Tumor necrosis factor receptor superfamily member 13C
BH: Tumor necrosis factor receptor superfamily member 13C
BI: Tumor necrosis factor receptor superfamily member 13C
BJ: Tumor necrosis factor receptor superfamily member 13C
BK: Tumor necrosis factor receptor superfamily member 13C
BL: Tumor necrosis factor receptor superfamily member 13C
BM: Tumor necrosis factor receptor superfamily member 13C
BN: Tumor necrosis factor receptor superfamily member 13C
BO: Tumor necrosis factor receptor superfamily member 13C
BP: Tumor necrosis factor receptor superfamily member 13C
BQ: Tumor necrosis factor receptor superfamily member 13C
BR: Tumor necrosis factor receptor superfamily member 13C
BS: Tumor necrosis factor receptor superfamily member 13C
BT: Tumor necrosis factor receptor superfamily member 13C
BU: Tumor necrosis factor receptor superfamily member 13C
BV: Tumor necrosis factor receptor superfamily member 13C
BW: Tumor necrosis factor receptor superfamily member 13C
BX: Tumor necrosis factor receptor superfamily member 13C
BY: Tumor necrosis factor receptor superfamily member 13C
BZ: Tumor necrosis factor receptor superfamily member 13C
B0: Tumor necrosis factor receptor superfamily member 13C
B1: Tumor necrosis factor receptor superfamily member 13C
B2: Tumor necrosis factor receptor superfamily member 13C
B3: Tumor necrosis factor receptor superfamily member 13C
B4: Tumor necrosis factor receptor superfamily member 13C
B5: Tumor necrosis factor receptor superfamily member 13C
B6: Tumor necrosis factor receptor superfamily member 13C
B7: Tumor necrosis factor receptor superfamily member 13C
B8: Tumor necrosis factor receptor superfamily member 13C
B9: Tumor necrosis factor receptor superfamily member 13C
Ba: Tumor necrosis factor receptor superfamily member 13C
Bb: Tumor necrosis factor receptor superfamily member 13C
Bc: Tumor necrosis factor receptor superfamily member 13C
Bd: Tumor necrosis factor receptor superfamily member 13C
Be: Tumor necrosis factor receptor superfamily member 13C
Bf: Tumor necrosis factor receptor superfamily member 13C
Bg: Tumor necrosis factor receptor superfamily member 13C
Bh: Tumor necrosis factor receptor superfamily member 13C
Bi: Tumor necrosis factor receptor superfamily member 13C
Bj: Tumor necrosis factor receptor superfamily member 13C
Bk: Tumor necrosis factor receptor superfamily member 13C
Bl: Tumor necrosis factor receptor superfamily member 13C
Bm: Tumor necrosis factor receptor superfamily member 13C
Bn: Tumor necrosis factor receptor superfamily member 13C
Bo: Tumor necrosis factor receptor superfamily member 13C
Bp: Tumor necrosis factor receptor superfamily member 13C
Bq: Tumor necrosis factor receptor superfamily member 13C
Br: Tumor necrosis factor receptor superfamily member 13C
Bs: Tumor necrosis factor receptor superfamily member 13C
Bt: Tumor necrosis factor receptor superfamily member 13C
Bu: Tumor necrosis factor receptor superfamily member 13C
Bv: Tumor necrosis factor receptor superfamily member 13C
Bw: Tumor necrosis factor receptor superfamily member 13C
Bx: Tumor necrosis factor receptor superfamily member 13C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,406,707160
Polymers1,405,735120
Non-polymers97240
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.5, 194.8, 274.4
Angle α, β, γ (deg.)90, 93.3, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
Tumor necrosis factor ligand superfamily member 13B / B cell activation factor


Mass: 16701.051 Da / Num. of mol.: 60 / Fragment: residues 138-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y275
#2: Protein ...
Tumor necrosis factor receptor superfamily member 13C / BAFF-R / B cell-activating factor receptor


Mass: 6727.870 Da / Num. of mol.: 60 / Fragment: residues 1-63
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96RJ3
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.87 Å3/Da / Density % sol: 74.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: sodium formate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2003
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. all: 1550665 / Num. obs: 1448322 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.3→3.4 Å / % possible all: 87.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→19.95 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 165101.27 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 12736 4.9 %random
Rwork0.218 ---
all-276280 --
obs-258046 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.7187 Å2 / ksol: 0.285583 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1--11.83 Å20 Å2-2.74 Å2
2--14.62 Å20 Å2
3----2.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms68580 0 40 0 68620
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it3.022.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 2020 5 %
Rwork0.291 --
obs-38262 87.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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