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- PDB-3me2: Crystal structure of mouse RANKL-RANK complex -

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Basic information

Entry
Database: PDB / ID: 3me2
TitleCrystal structure of mouse RANKL-RANK complex
Components
  • Tumor necrosis factor ligand superfamily member 11
  • Tumor necrosis factor receptor superfamily member 11A
KeywordsCYTOKINE/CYTOKINE RECEPTOR / RANK / RANKL / RANKL-RANK complex / TNFSF11 / TNFRSF11a / TNF superfamily / 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: 2.8 Å
AuthorsWalter, S.W. / Liu, C.Z. / Zhu, X.K. / Wu, Y. / Owens, R.J. / Stuart, D.I. / Gao, B. / Ren, J.
CitationJournal: J.Immunol. / Year: 2010
Title: Structural and Functional Insights of RANKL-RANK Interaction and Signaling.
Authors: Liu, C. / Walter, T.S. / Huang, P. / Zhang, S. / Zhu, X. / Wu, Y. / Wedderburn, L.R. / Tang, P. / Owens, R.J. / Stuart, D.I. / Ren, J. / Gao, B.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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)43,2397
Polymers43,0742
Non-polymers1655
Water81145
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)129,71821
Polymers129,2236
Non-polymers49415
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 area14060 Å2
ΔGint-25 kcal/mol
Surface area44490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.225, 121.225, 94.995
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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


Mass: 19056.359 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 158-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: RAW264.7 / Gene: Opgl, Rankl, Tnfsf11, Trance / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: O35235
#2: Protein Tumor necrosis factor receptor superfamily member 11A / Receptor activator of NF-KB / Osteoclast differentiation factor receptor / ODFR / RANK


Mass: 24018.119 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: RAW264.7 / Gene: Rank, Tnfrsf11a / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: O35305
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.68 Å3/Da / Density % sol: 73.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium di-hydrogen phosphate, 2M sodium chloride, 0.1M potassium di-hydrogen phosphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9395
SYNCHROTRONESRF ID23-220.8726
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 14, 2007
MARMOSAIC 225 mm CCD2CCDJul 15, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.93951
20.87261
ReflectionResolution: 2.8→30 Å / Num. obs: 18587 / % possible obs: 100 % / Observed criterion σ(I): -1 / Redundancy: 16.3 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 18.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.995 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1970 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JTZ

1jtz


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.051 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20504 995 5.1 %RANDOM
Rwork0.17388 ---
obs0.17541 17956 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.14 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å21.1 Å20 Å2
2--2.21 Å20 Å2
3----3.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 5 45 2544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212570
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9343494
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7415320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82224.174115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79815407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3161511
X-RAY DIFFRACTIONr_chiral_restr0.0650.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211966
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_it1.20341602
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.27162582
X-RAY DIFFRACTIONr_scbond_it2.3536968
X-RAY DIFFRACTIONr_scangle_it3.69110912
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 75 -
Rwork0.28 1298 -
obs--96.49 %
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)
13.5185-0.29320.19571.9285-0.1162.62530.0021-0.17180.260.08470.0529-0.102-0.55480.0285-0.0550.1477-0.00190.03590.0372-0.03120.091259.13447.78647.345
24.28481.49253.11653.18585.464318.8774-0.1117-0.72430.8576-0.03590.12120.2722-1.428-0.8901-0.00960.3946-0.0299-0.00990.6031-0.18170.417382.58657.2464.516
31.30420.89751.84920.65831.688214.56570.0218-0.11680.1599-0.04950.02830.0343-0.70330.5584-0.05010.1756-0.13460.04890.4526-0.1110.264684.85150.07240.872
42.02451.9376-2.66922.9637-5.612.12680.21490.10550.11580.3829-0.01980.061-0.7594-0.0297-0.19510.2399-0.03810.10260.32920.04380.238478.27658.18718.358
514.3712-2.625-9.07883.0408-1.263612.32210.4751.68970.4456-0.4489-0.04120.3184-0.6313-1.6414-0.43380.30330.0163-0.05630.57730.04930.272885.37663.101-7.27
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A161 - 316
2X-RAY DIFFRACTION2R34 - 89
3X-RAY DIFFRACTION3R90 - 116
4X-RAY DIFFRACTION4R117 - 172
5X-RAY DIFFRACTION5R173 - 199

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