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- PDB-1s55: Mouse RANKL Structure at 1.9A Resolution -

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Basic information

Entry
Database: PDB / ID: 1s55
TitleMouse RANKL Structure at 1.9A Resolution
ComponentsTumor necrosis factor ligand superfamily member 11
KeywordsCYTOKINE
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 / TNFR2 non-canonical NF-kB pathway / positive regulation of homotypic cell-cell adhesion ...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 / 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 / tumor necrosis factor-mediated signaling pathway / ERK1 and ERK2 cascade / ossification / phosphatidylinositol 3-kinase/protein kinase B signal transduction / osteoclast differentiation / cellular response to leukemia inhibitory factor / cytokine activity / calcium-mediated signaling / animal organ morphogenesis / positive regulation of JNK cascade / bone development / positive regulation of DNA-binding transcription factor activity / positive regulation of T cell activation / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / 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(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 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTeale, M.J. / Feug, X. / Chen, L. / Bice, T. / Meehan, E.J.
CitationJournal: To be Published
Title: Murine RANKL Extra Cellular Domain Homotrimer Structure In Space Groups P212121 And H3 At 1.9 And 2.6 Respectively
Authors: Teale, M.J. / Schorman, N. / Feug, X. / Bice, T. / Meehan, E.J. / DeLucas, L.
History
DepositionJan 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 11
B: Tumor necrosis factor ligand superfamily member 11
C: Tumor necrosis factor ligand superfamily member 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4496
Polymers52,3433
Non-polymers1063
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-59 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.527, 81.322, 99.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 11 / Receptor activator of nuclear factor kappa B ligand / RANKL / TNF-related activation-induced ...Receptor activator of nuclear factor kappa B ligand / RANKL / TNF-related activation-induced cytokine / TRANCE / Osteoprotegerin ligand / OPGL / Osteoclast differentiation factor / ODF / Osteoclastogenesis-inhibitory factor / OCIF


Mass: 17447.539 Da / Num. of mol.: 3 / Fragment: residues 161-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: TNFSF11, RANKL, TRANCE, OPGL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O35235
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.57 Å3/Da / Density % sol: 51.68 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→45.4 Å / Num. all: 42727 / Num. obs: 39244 / % possible obs: 83.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 18.2 Å2
Reflection shellResolution: 1.9→2.02 Å

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.43 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1247693.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1781 5 %RANDOM
Rwork0.23 ---
obs0.23 35848 83.9 %-
all-42727 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.7446 Å2 / ksol: 0.353347 e/Å3
Displacement parametersBiso mean: 49.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.51 Å20 Å20 Å2
2--10.96 Å20 Å2
3----6.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 1.9→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 3 215 3917
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 171 4.8 %
Rwork0.42 3377 -
obs-1711 50.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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