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- PDB-5bnq: Crystal structure of hRANKL-mRANK complex -

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Basic information

Entry
Database: PDB / ID: 5bnq
TitleCrystal structure of hRANKL-mRANK complex
Components(Tumor necrosis factor ...) x 2
KeywordsCYTOKINE / RANK / RANKL / RANKL-RANK complex / TNFSF11 / TNFRSF11a / TNF superfamily
Function / homology
Function and homology information


multinuclear osteoclast differentiation / positive regulation of fever generation by positive regulation of prostaglandin secretion / positive regulation of corticotropin-releasing hormone secretion / tooth eruption / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / osteoclast proliferation / circadian temperature homeostasis / cellular response to zinc ion starvation / positive regulation of osteoclast development / tumor necrosis factor receptor superfamily binding ...multinuclear osteoclast differentiation / positive regulation of fever generation by positive regulation of prostaglandin secretion / positive regulation of corticotropin-releasing hormone secretion / tooth eruption / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / osteoclast proliferation / circadian temperature homeostasis / cellular response to zinc ion starvation / positive regulation of osteoclast development / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor activity / TNFR2 non-canonical NF-kB pathway / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of homotypic cell-cell adhesion / paracrine signaling / osteoclast development / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / mammary gland epithelial cell proliferation / cytokine binding / monocyte chemotaxis / response to tumor necrosis factor / positive regulation of intracellular signal transduction / positive regulation of bone resorption / mammary gland alveolus development / response to mechanical stimulus / lymph node development / positive regulation of MAP kinase activity / bone resorption / calcium ion homeostasis / positive regulation of DNA-binding transcription factor activity / tumor necrosis factor-mediated signaling pathway / JNK cascade / ERK1 and ERK2 cascade / Transcriptional and post-translational regulation of MITF-M expression and activity / response to interleukin-1 / ossification / TNFR2 non-canonical NF-kB pathway / osteoclast differentiation / cellular response to leukemia inhibitory factor / cytokine activity / positive regulation of JNK cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / calcium-mediated signaling / positive regulation of NF-kappaB transcription factor activity / response to insulin / positive regulation of T cell activation / cytokine-mediated signaling pathway / response to ethanol / response to lipopolysaccharide / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / 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 / cell surface / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / metal ion binding / identical protein 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. ...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. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tumor necrosis factor ligand superfamily member 11 / Tumor necrosis factor receptor superfamily member 11A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRen, J.
CitationJournal: Sci Rep / Year: 2015
Title: A RANKL mutant used as an inter-species vaccine for efficient immunotherapy of osteoporosis.
Authors: Liu, C. / Zhao, Y. / He, W. / Wang, W. / Chen, Y. / Zhang, S. / Ma, Y. / Gohda, J. / Ishida, T. / Walter, T.S. / Owens, R.J. / Stuart, D.I. / Ren, J. / Gao, B.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
R: Tumor necrosis factor receptor superfamily member 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,75915
Polymers42,0722
Non-polymers68613
Water1,42379
1
A: Tumor necrosis factor ligand superfamily member 11
R: Tumor necrosis factor receptor superfamily member 11A
hetero molecules

A: Tumor necrosis factor ligand superfamily member 11
R: Tumor necrosis factor receptor superfamily member 11A
hetero molecules

A: Tumor necrosis factor ligand superfamily member 11
R: Tumor necrosis factor receptor superfamily member 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,27645
Polymers126,2176
Non-polymers2,05939
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
Buried area19810 Å2
ΔGint-356 kcal/mol
Surface area43450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.188, 122.188, 94.473
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-402-

CL

21A-525-

HOH

31A-542-

HOH

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Components

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Tumor necrosis factor ... , 2 types, 2 molecules AR

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


Mass: 18054.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF11, OPGL, RANKL, TRANCE / Plasmid: PLASMID / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: O14788
#2: Protein Tumor necrosis factor receptor superfamily member 11A / Osteoclast differentiation factor receptor / ODFR / Receptor activator of NF-KB / RANK


Mass: 24018.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfrsf11a, Rank / Plasmid: PLASMID / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: O35305

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Non-polymers , 4 types, 92 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.84 Å3/Da / Density % sol: 74.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium di-hydrogen phosphate, 2 M sodium chloride, 0.1 M potassium di-hydrogen phosphate and 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 19916 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ME2

3me2


Resolution: 2.8→29.37 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 15.775 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20292 1018 5.1 %RANDOM
Rwork0.17085 ---
obs0.17246 18885 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.656 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.35 Å20 Å2
2--0.35 Å20 Å2
3----1.15 Å2
Refinement stepCycle: 1 / Resolution: 2.8→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 29 79 2613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192598
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9423533
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21824.052116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76515410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4031511
X-RAY DIFFRACTIONr_chiral_restr0.0650.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211973
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0818.5261286
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.85914.3541604
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7489.2961312
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.87432.0673744
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.794→2.866 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 77 -
Rwork0.317 1311 -
obs--94.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4887-0.2952-0.02541.0898-0.26680.93210.0998-0.06320.24940.081-0.006-0.0397-0.29-0.0344-0.09380.2108-0.00110.03680.1845-0.01320.051359.51348.0546.867
22.89610.88680.86111.20672.5879.93590.1008-0.54890.6764-0.02660.1396-0.0495-0.3956-0.0108-0.24040.2613-0.14560.00150.4419-0.21410.244283.78655.13457.586
31.79621.145-2.28761.2947-2.32435.21530.1980.28620.28290.12290.05780.1961-0.3224-0.3871-0.25570.2476-0.09180.04950.360.04480.082181.0959.67510.619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A162 - 316
2X-RAY DIFFRACTION2R34 - 114
3X-RAY DIFFRACTION3R115 - 199

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