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- PDB-1iqa: CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF MOUSE RANK LIGAND -

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Basic information

Entry
Database: PDB / ID: 1iqa
TitleCRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF MOUSE RANK LIGAND
ComponentsRECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA B LIGAND
KeywordsCYTOKINE / HOMOTRIMER / BETA-STRAND JELLYROLL / RANKL / RANK LIGAND / RANK / TNF / BONE REMODELING / OSTEOCLAST DIFFERENTIATION FACTOR
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 / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsIto, S. / Wakabayashi, K. / Ubukata, O. / Hayashi, S. / Okada, F. / Hata, T.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of the extracellular domain of mouse RANK ligand at 2.2-A resolution.
Authors: Ito, S. / Wakabayashi, K. / Ubukata, O. / Hayashi, S. / Okada, F. / Hata, T.
History
DepositionJul 11, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA B LIGAND
B: RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA B LIGAND
C: RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA B LIGAND


Theoretical massNumber of molelcules
Total (without water)54,0023
Polymers54,0023
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-23 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.680, 78.980, 100.050
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 RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA B LIGAND / TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11 / RANKL / TRANCE / OPGL / ODF


Mass: 18000.688 Da / Num. of mol.: 3 / Fragment: EXTRACELLULAR DOMAIN (RESIDUES 157-316) / Mutation: M198(MSE), M238(MSE), M255(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX-3X / Production host: Escherichia coli (E. coli) / References: UniProt: O35235
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8K, SODIUM CHLORIDE, ETHYLENE GLYCOL, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris-HCl1droppH7.4
230 mg/mlprotein1drop
314 %(w/v)PEG80001reservoir
430 %(v/v)ethylene glycol1reservoir
5300 mM1reservoirNaCl
60.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.98 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 16, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 26984 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 32
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 6.3 / % possible all: 97.4
Reflection
*PLUS
Num. measured all: 257901
Reflection shell
*PLUS
% possible obs: 97.4 %

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Processing

Software
NameClassification
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1986 7.9 %RANDOM
Rwork0.226 ---
obs-25282 93.7 %-
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.26 Å2--
2--14.35 Å2-
3----11.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 0 69 3768
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d28.8
X-RAY DIFFRACTIONx_improper_angle_d1.04
X-RAY DIFFRACTIONx_mcbond_it2.731.5
X-RAY DIFFRACTIONx_mcangle_it4.342
X-RAY DIFFRACTIONx_scbond_it3.882
X-RAY DIFFRACTIONx_scangle_it4.772.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 307 8.3 %
Rwork0.248 3390 -
obs-3697 83.8 %
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.04
LS refinement shell
*PLUS
Rfactor Rwork: 0.248 / Rfactor obs: 0.248

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