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- PDB-1oqe: Crystal structure of sTALL-1 with BAFF-R -

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Basic information

Entry
Database: PDB / ID: 1oqe
TitleCrystal structure of sTALL-1 with BAFF-R
Components
  • Tumor necrosis factor ligand superfamily member 13B, soluble form
  • Tumor necrosis factor receptor superfamily member 13C
KeywordsIMMUNE SYSTEM / ligand receptor complex
Function / homology
Function and homology information


positive regulation of germinal center formation / B cell costimulation / 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 ...positive regulation of germinal center formation / B cell costimulation / 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. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls ...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. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
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 / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsZhang, G.
CitationJournal: Nature / Year: 2003
Title: Ligand-receptor binding revealed by the TNF family member TALL-1.
Authors: Liu, Y. / Hong, X. / Kappler, J. / Jiang, L. / Zhang, R. / Xu, L. / Pan, C.H. / Martin, W.E. / Murphy, R.C. / Shu, H.B. / Dai, S. / Zhang, G.
History
DepositionMar 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 13B, soluble form
B: Tumor necrosis factor ligand superfamily member 13B, soluble form
C: Tumor necrosis factor ligand superfamily member 13B, soluble form
D: Tumor necrosis factor ligand superfamily member 13B, soluble form
E: Tumor necrosis factor ligand superfamily member 13B, soluble form
F: Tumor necrosis factor ligand superfamily member 13B, soluble form
G: Tumor necrosis factor ligand superfamily member 13B, soluble form
H: Tumor necrosis factor ligand superfamily member 13B, soluble form
I: Tumor necrosis factor ligand superfamily member 13B, soluble form
J: Tumor necrosis factor ligand superfamily member 13B, soluble form
K: Tumor necrosis factor receptor superfamily member 13C
L: Tumor necrosis factor receptor superfamily member 13C
M: Tumor necrosis factor receptor superfamily member 13C
N: Tumor necrosis factor receptor superfamily member 13C
O: Tumor necrosis factor receptor superfamily member 13C
P: Tumor necrosis factor receptor superfamily member 13C
Q: Tumor necrosis factor receptor superfamily member 13C
R: Tumor necrosis factor receptor superfamily member 13C


Theoretical massNumber of molelcules
Total (without water)189,37518
Polymers189,37518
Non-polymers00
Water00
1
A: Tumor necrosis factor ligand superfamily member 13B, soluble form
B: Tumor necrosis factor ligand superfamily member 13B, soluble form
C: Tumor necrosis factor ligand superfamily member 13B, soluble form
D: Tumor necrosis factor ligand superfamily member 13B, soluble form
E: Tumor necrosis factor ligand superfamily member 13B, soluble form
F: Tumor necrosis factor ligand superfamily member 13B, soluble form
G: Tumor necrosis factor ligand superfamily member 13B, soluble form
H: Tumor necrosis factor ligand superfamily member 13B, soluble form
I: Tumor necrosis factor ligand superfamily member 13B, soluble form
J: Tumor necrosis factor ligand superfamily member 13B, soluble form
K: Tumor necrosis factor receptor superfamily member 13C
L: Tumor necrosis factor receptor superfamily member 13C
M: Tumor necrosis factor receptor superfamily member 13C
N: Tumor necrosis factor receptor superfamily member 13C
O: Tumor necrosis factor receptor superfamily member 13C
P: Tumor necrosis factor receptor superfamily member 13C
Q: Tumor necrosis factor receptor superfamily member 13C
R: Tumor necrosis factor receptor superfamily member 13C
x 6


Theoretical massNumber of molelcules
Total (without water)1,136,248108
Polymers1,136,248108
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Unit cell
Length a, b, c (Å)233.261, 233.261, 211.286
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein
Tumor necrosis factor ligand superfamily member 13B, soluble form / TNF-and APOL- related leukocyte expressed ligand 1 / TALL-1 / B lymphocyte stimulator / BLyS / B ...TNF-and APOL- related leukocyte expressed ligand 1 / TALL-1 / B lymphocyte stimulator / BLyS / B cell-activating factor / BAFF / Dendritic cell- derived TNF-like molecule


Mass: 16244.602 Da / Num. of mol.: 10 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y275
#2: Protein/peptide
Tumor necrosis factor receptor superfamily member 13C / B cell-activating factor receptor / BAFF receptor / BAFF-R / BLyS receptor


Mass: 3366.074 Da / Num. of mol.: 8 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RJ3

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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: 4.38 Å3/Da / Density % sol: 71.91 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Liu, Y., (2002) Cell, 108, 383.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
25 mMbeta-mercaptoethanol1reservoir
350 mMBicine1reservoirpH9.0
4150 mM1reservoirNaCl
535-38 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 2, 2003 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 121940 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.13 / Net I/σ(I): 11
Reflection shellResolution: 2.45→2.54 Å / % possible all: 90
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Num. measured all: 1415809 / Rmerge(I) obs: 0.135
Reflection shell
*PLUS
Rmerge(I) obs: 0.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1947 2 %RANDOM
Rwork0.244 ---
all0.287 ---
obs0.264 98973 85.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.7371 Å2 / ksol: 0.339398 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å26.32 Å20 Å2
2--2.13 Å20 Å2
3----4.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13240 0 0 0 13240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 246 2.1 %
Rwork0.365 11706 -
obs--62.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAM
X-RAY DIFFRACTION3WATER.PARAM
Refinement
*PLUS
Highest resolution: 2.5 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Rfactor Rfree: 0.437 / Rfactor Rwork: 0.46

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