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- PDB-3qbq: Crystal structure of extracellular domains of mouse RANK-RANKL complex -

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Basic information

Entry
Database: PDB / ID: 3qbq
TitleCrystal structure of extracellular domains of mouse RANK-RANKL complex
Components
  • Tumor necrosis factor ligand superfamily member 11
  • Tumor necrosis factor receptor superfamily member 11A
KeywordsCYTOKINE/CYTOKINE RECEPTOR / tumor necrosis factor (TNF) Ligand-receptor superfamily fold / cytokine-cytokine receptor complex
Function / homology
Function and homology information


multinuclear osteoclast differentiation / 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 ...multinuclear osteoclast differentiation / 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 / circadian temperature homeostasis / tumor necrosis factor receptor activity / tumor necrosis factor receptor superfamily binding / TNFR2 non-canonical NF-kB pathway / positive regulation of homotypic cell-cell adhesion / regulation of osteoclast differentiation / cellular response to zinc ion starvation / 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 / cytokine binding / monocyte chemotaxis / mammary gland alveolus development / positive regulation of bone resorption / calcium ion homeostasis / lymph node development / response to tumor necrosis factor / response to mechanical stimulus / 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 / response to interleukin-1 / osteoclast differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytokine activity / response to cytokine / calcium-mediated signaling / animal organ morphogenesis / positive regulation of JNK cascade / response to insulin / bone development / response to organic cyclic compound / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / positive regulation of T cell activation / transmembrane signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / response to lipopolysaccharide / adaptive immune response / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / immune response / membrane raft / external side of plasma membrane / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 11A / Tumor necrosis factor receptor 11A, N-terminal / Rank, cysteine-rich repeat domain 2 / Receptor activator of the NF-KB cysteine-rich repeat domain 2 / Tumour necrosis factor receptor 11 / Tumour necrosis factor ligand 10/11 / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor family. / TNF family profile. ...Tumour necrosis factor receptor 11A / Tumor necrosis factor receptor 11A, N-terminal / Rank, cysteine-rich repeat domain 2 / Receptor activator of the NF-KB cysteine-rich repeat domain 2 / Tumour necrosis factor receptor 11 / Tumour necrosis factor ligand 10/11 / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor family. / TNF family profile. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. / Tumour necrosis factor domain / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 11 / Tumor necrosis factor receptor superfamily member 11A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTa, H.M. / Nguyen, G.T.T. / Jin, H.M. / Choi, J.K. / Park, H. / Kim, N.S. / Hwang, H.Y. / Kim, K.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure-based development of a receptor activator of nuclear factor-kappaB ligand (RANKL) inhibitor peptide and molecular basis for osteopetrosis
Authors: Ta, H.M. / Nguyen, G.T.T. / Jin, H.M. / Choi, J.K. / Park, H. / Kim, N.S. / Hwang, H.Y. / Kim, K.K.
History
DepositionJan 13, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionMar 2, 2011ID: 3NZY
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 11
B: Tumor necrosis factor receptor superfamily member 11A
C: Tumor necrosis factor ligand superfamily member 11
D: Tumor necrosis factor receptor superfamily member 11A


Theoretical massNumber of molelcules
Total (without water)73,0584
Polymers73,0584
Non-polymers00
Water3,279182
1
A: Tumor necrosis factor ligand superfamily member 11
B: Tumor necrosis factor receptor superfamily member 11A

A: Tumor necrosis factor ligand superfamily member 11
B: Tumor necrosis factor receptor superfamily member 11A

A: Tumor necrosis factor ligand superfamily member 11
B: Tumor necrosis factor receptor superfamily member 11A


Theoretical massNumber of molelcules
Total (without water)109,5876
Polymers109,5876
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
C: Tumor necrosis factor ligand superfamily member 11
D: Tumor necrosis factor receptor superfamily member 11A

C: Tumor necrosis factor ligand superfamily member 11
D: Tumor necrosis factor receptor superfamily member 11A

C: Tumor necrosis factor ligand superfamily member 11
D: Tumor necrosis factor receptor superfamily member 11A


Theoretical massNumber of molelcules
Total (without water)109,5876
Polymers109,5876
Non-polymers00
Water1086
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
Unit cell
Length a, b, c (Å)120.860, 120.860, 93.425
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 11 / RANKL


Mass: 17860.000 Da / Num. of mol.: 2 / Fragment: residues 157-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rankl / Plasmid: pVFT3S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O35235
#2: Protein Tumor necrosis factor receptor superfamily member 11A / RANK


Mass: 18669.074 Da / Num. of mol.: 2 / Fragment: residues 32-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rank / Plasmid: pVFT3S / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: O35305
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 5.4 Å3/Da / Density % sol: 77.2 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.6
Details: 100mM trisodium citrate, 1.2M ammonium sulfate, pH 5.6, microbatch, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jun 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→45.66 Å / Num. obs: 52575 / Redundancy: 10.46 % / Biso Wilson estimate: 52.2 Å2 / Rsym value: 0.089 / Net I/σ(I): 31.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IQA

1iqa


Resolution: 2.5→45.66 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.33 / Data cutoff high absF: 1976536 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2626 5 %RANDOM
Rwork0.227 ---
obs-52575 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5049 Å2 / ksol: 0.3327 e/Å3
Displacement parametersBiso max: 133.13 Å2 / Biso mean: 62.0759 Å2 / Biso min: 22.85 Å2
Baniso -1Baniso -2Baniso -3
1-11.73 Å211.27 Å20 Å2
2--11.73 Å20 Å2
3----23.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 0 182 5114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 429 5 %
Rwork0.387 8170 -
all-8599 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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