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- PDB-1jtz: CRYSTAL STRUCTURE OF TRANCE/RANKL CYTOKINE. -

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Basic information

Entry
Database: PDB / ID: 1jtz
TitleCRYSTAL STRUCTURE OF TRANCE/RANKL CYTOKINE.
ComponentsTUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11
KeywordsCYTOKINE / TUMOR NECROSIS FACTOR SUPERFAMILY MEMBER / JELLYROLL / BETA-SANDWICH
Function / homology
Function and homology information


positive regulation of corticotropin-releasing hormone secretion / positive regulation of fever generation by positive regulation of prostaglandin secretion / : / tooth eruption / positive regulation of osteoclast development / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / osteoclast proliferation / : / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding ...positive regulation of corticotropin-releasing hormone secretion / positive regulation of fever generation by positive regulation of prostaglandin secretion / : / tooth eruption / positive regulation of osteoclast development / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / osteoclast proliferation / : / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / TNFR2 non-canonical NF-kB pathway / positive regulation of homotypic cell-cell adhesion / regulation of osteoclast differentiation / paracrine signaling / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / osteoclast development / mammary gland epithelial cell proliferation / positive regulation of intracellular signal transduction / monocyte chemotaxis / mammary gland alveolus development / positive regulation of bone resorption / calcium ion homeostasis / lymph node development / positive regulation of phosphorylation / JNK cascade / bone resorption / ERK1 and ERK2 cascade / tumor necrosis factor-mediated signaling pathway / cellular response to leukemia inhibitory factor / ossification / osteoclast differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytokine activity / calcium-mediated signaling / animal organ morphogenesis / positive regulation of JNK cascade / bone development / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / positive regulation of T cell activation / positive regulation of canonical NF-kappaB signal transduction / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / immune response / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor ligand 10/11 / Tumour necrosis factor family. / TNF family profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNelson, C.A. / Fremont, D.H.
CitationJournal: J.Clin.Invest. / Year: 2001
Title: Crystal structure of the TRANCE/RANKL cytokine reveals determinants of receptor-ligand specificity
Authors: Lam, J. / Nelson, C.A. / Ross, F.P. / Teitelbaum, S.L. / Fremont, D.H.
History
DepositionAug 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11
Y: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11
Z: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11


Theoretical massNumber of molelcules
Total (without water)57,1693
Polymers57,1693
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-21 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.300, 82.000, 99.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
DetailsTHE BIOLOGICAL ASSEMBLY IS A TRIMER WHICH COMPRISES THE ASYMETRIC UNIT.

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Components

#1: Protein TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11 / TNF-RELATED ACTIVATION-INDUCED CYTOKINE / TRANCE / RECEPTOR ACTIVATOR OF NF-KAPPA-B LIGAND / RANKL ...TNF-RELATED ACTIVATION-INDUCED CYTOKINE / TRANCE / RECEPTOR ACTIVATOR OF NF-KAPPA-B LIGAND / RANKL / OSTEOCLAST DIFFERENTIATION FACTOR / ODF / OSTEOPROTEGERIN LIGAND / OPGL / TNFSF11


Mass: 19056.359 Da / Num. of mol.: 3
Fragment: C-TERMINAL RECEPTOR-BINDING ECTODOMAIN, Residues 156-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RANKL / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O35235
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 11-14% PEG 4000, 16 mM calcium chloride, 80 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mM1dropNaCl
320 mMTris-HCl1drop
480 mMHEPES1reservoir
516 mM1reservoirCaCl2
611-14 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 4, 2000 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 191355 / Num. obs: 16705 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 70.2 Å2 / Rsym value: 0.059 / Net I/σ(I): 32.3
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.449 / % possible all: 100
Reflection
*PLUS
Num. measured all: 191355 / Rmerge F obs: 0.059
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.449

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHIMERA OF PDB ENTRIES 1TNR (CHAIN A) AND 1D4V (CHAIN B)

1tnr

1d4v


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 53633.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: The following residues were included in 5 groups NCS GROUP 1:162-171,180-223,235-244,252-263,269-316 NCS GROUP 2:172-179 NCS GROUP 3:224-233 NCS GROUP 4:245-251 NCS GROUP 5:264-268 NOTES: ...Details: The following residues were included in 5 groups NCS GROUP 1:162-171,180-223,235-244,252-263,269-316 NCS GROUP 2:172-179 NCS GROUP 3:224-233 NCS GROUP 4:245-251 NCS GROUP 5:264-268 NOTES: Residues included in groups 1-5 (RMS for monomer X versus monomer Y) is identical to groups 6-10 (RMS for monomer X versus monomer Z)
RfactorNum. reflection% reflectionSelection details
Rfree0.286 781 4.9 %RANDOM
Rwork0.235 ---
obs0.235 16018 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.7347 Å2 / ksol: 0.260869 e/Å3
Displacement parametersBiso mean: 69 Å2
Baniso -1Baniso -2Baniso -3
1--6.16 Å20 Å20 Å2
2--19.96 Å20 Å2
3----13.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-6 Å
Luzzati sigma a0.62 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 0 147 3831
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_mcangle_it3.272
X-RAY DIFFRACTIONc_scbond_it1.562
X-RAY DIFFRACTIONc_scangle_it2.582.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11NCS CONSTRAINED USING FIVE GROUPSX-RAY DIFFRACTION0.3510
22GROUPS 1-5 RMS FOR X COMPARED TO YX-RAY DIFFRACTION0.84912
33GROUPS 6-10 RMS FOR X COMPARED TO ZX-RAY DIFFRACTION1.12522
44X-RAY DIFFRACTION1.11332
55X-RAY DIFFRACTION1.62532
66X-RAY DIFFRACTION0.326910
77X-RAY DIFFRACTION0.88172
88X-RAY DIFFRACTION0.78022
99X-RAY DIFFRACTION0.7382
1010X-RAY DIFFRACTION1.47712
LS refinement shellResolution: 2.6→2.72 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.44 93 5 %
Rwork0.39 1765 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 69 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_scbond_it1.562
X-RAY DIFFRACTIONc_mcangle_it3.272
X-RAY DIFFRACTIONc_scangle_it2.582.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.44 / % reflection Rfree: 5 % / Rfactor Rwork: 0.39

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