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- PDB-1jh5: Crystal Structure of sTALL-1 of TNF family ligand -

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Basic information

Entry
Database: PDB / ID: 1jh5
TitleCrystal Structure of sTALL-1 of TNF family ligand
ComponentsTUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
KeywordsIMMUNE SYSTEM / ANTITUMOR PROTEIN / TALL-1 / BLYS / THANK / BAFF
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 / receptor ligand activity / 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
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 ligand superfamily member 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsLiu, Y. / Xu, L. / Opalka, N. / Shu, H.-B. / Zhang, G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Crystal structure of sTALL-1 reveals a virus-like assembly of TNF family ligands.
Authors: Liu, Y. / Xu, L. / Opalka, N. / Kappler, J. / Shu, H.B. / Zhang, G.
History
DepositionJun 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 4, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_biol
Item: _pdbx_struct_assembly_prop.biol_id
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
C: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
D: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
E: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
F: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
G: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
H: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
I: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
J: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B


Theoretical massNumber of molelcules
Total (without water)162,44610
Polymers162,44610
Non-polymers00
Water00
1
A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
B: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
C: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
D: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
E: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
F: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
G: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
H: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
I: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
J: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
x 6


Theoretical massNumber of molelcules
Total (without water)974,67660
Polymers974,67660
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area171710 Å2
ΔGint-582 kcal/mol
Surface area291860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.242, 234.242, 212.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Cell settinghexagonal
Space group name H-MP6322

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Components

#1: Protein
TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B / TNF family ligand / TNF-AND APOL-RELATED LEUKOCYTE EXPRESSED LIGAND 1 / TALL-1 / B LYMPHOCYTE ...TNF family ligand / TNF-AND APOL-RELATED LEUKOCYTE EXPRESSED LIGAND 1 / TALL-1 / B LYMPHOCYTE STIMULATOR / BLYS / B CELL-ACTIVATING FACTOR / tumor necrosis factor (ligand) superfamily / member 13b


Mass: 16244.602 Da / Num. of mol.: 10 / Fragment: sTALL-1, soluble part of TALL-1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y275

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 5.18 Å3/Da / Density % sol: 76.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 35% dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Method: vapor diffusion
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: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 69018 / Num. obs: 66001 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 12
Reflection
*PLUS
Num. measured all: 334821

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
SCALEPACKdata scaling
RefinementResolution: 3→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 172269.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2771 5.1 %RANDOM
Rwork0.236 ---
obs0.236 54509 79.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.285 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å25.87 Å20 Å2
2--1.5 Å20 Å2
3----3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11430 0 0 0 11430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 275 5 %
Rwork0.331 5219 -
obs--48.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAM
X-RAY DIFFRACTION3WATER.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 51752 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
LS refinement shell
*PLUS
Rfactor Rfree: 0.344 / % reflection Rfree: 5 % / Rfactor Rwork: 0.331

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