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- PDB-4e4d: Crystal structure of mouse RANKL-OPG complex -

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Basic information

Entry
Database: PDB / ID: 4e4d
TitleCrystal structure of mouse RANKL-OPG complex
Components
  • Tumor necrosis factor ligand superfamily member 11, soluble form
  • Tumor necrosis factor receptor superfamily member 11B
KeywordsCytokine/Signaling Protein / TNF-Related Activation-Induced Cytokine-Receptor / Cysteine-Rich Domain / Jelly-Roll Fold / Cytokine-Signaling Protein complex
Function / homology
Function and homology information


negative regulation of odontogenesis of dentin-containing tooth / 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 ...negative regulation of odontogenesis of dentin-containing tooth / 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 / response to xenobiotic stimulus => GO:0009410 / positive regulation of homotypic cell-cell adhesion / regulation of osteoclast differentiation / paracrine signaling / response to arsenic-containing substance / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / negative regulation of bone resorption / osteoclast development / positive regulation of intracellular signal transduction / mammary gland epithelial cell proliferation / monocyte chemotaxis / response to magnesium ion / mammary gland alveolus development / positive regulation of bone resorption / calcium ion homeostasis / lymph node development / JNK cascade / positive regulation of phosphorylation / bone resorption / ERK1 and ERK2 cascade / tumor necrosis factor-mediated signaling pathway / extracellular matrix / ossification / extracellular matrix organization / osteoclast differentiation / response to nutrient / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to leukemia inhibitory factor / canonical NF-kappaB signal transduction / cytokine activity / calcium-mediated signaling / positive regulation of JNK cascade / animal organ morphogenesis / bone development / cytokine-mediated signaling pathway / response to estrogen / 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 / immune response / apoptotic process / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 11B / 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. / Tyrosine-protein kinase ephrin type A/B receptor-like / TNF family profile. / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. ...Tumour necrosis factor receptor 11B / 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. / Tyrosine-protein kinase ephrin type A/B receptor-like / 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 / Putative ephrin-receptor like / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 11B / Tumor necrosis factor ligand superfamily member 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNelson, C.A. / Fremont, D.H.
CitationJournal: Structure / Year: 2012
Title: RANKL Employs Distinct Binding Modes to Engage RANK and the Osteoprotegerin Decoy Receptor.
Authors: Nelson, C.A. / Warren, J.T. / Wang, M.W. / Teitelbaum, S.L. / Fremont, D.H.
History
DepositionMar 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 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 / 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 / _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

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Assembly

Deposited unit
X: Tumor necrosis factor ligand superfamily member 11, soluble form
R: Tumor necrosis factor receptor superfamily member 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8204
Polymers37,7492
Non-polymers712
Water1,67593
1
X: Tumor necrosis factor ligand superfamily member 11, soluble form
hetero molecules

X: Tumor necrosis factor ligand superfamily member 11, soluble form
R: Tumor necrosis factor receptor superfamily member 11B
hetero molecules

X: Tumor necrosis factor ligand superfamily member 11, soluble form
R: Tumor necrosis factor receptor superfamily member 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,08611
Polymers92,8745
Non-polymers2136
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation3_665-x+y+1,-x+1,z1
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
2
X: Tumor necrosis factor ligand superfamily member 11, soluble form
R: Tumor necrosis factor receptor superfamily member 11B
hetero molecules

X: Tumor necrosis factor ligand superfamily member 11, soluble form
R: Tumor necrosis factor receptor superfamily member 11B
hetero molecules

X: Tumor necrosis factor ligand superfamily member 11, soluble form
R: Tumor necrosis factor receptor superfamily member 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,45912
Polymers113,2466
Non-polymers2136
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 area13600 Å2
ΔGint-111 kcal/mol
Surface area40040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.763, 109.763, 78.800
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, soluble form / 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: 17376.463 Da / Num. of mol.: 1 / Fragment: UNP residues 162-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CD254, ODF, Opgl, Rankl, Tnfsf11, Trance / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus(DE3)-RIL / References: UniProt: O35235
#2: Protein Tumor necrosis factor receptor superfamily member 11B / Osteoclastogenesis inhibitory factor / Osteoprotegerin


Mass: 20372.166 Da / Num. of mol.: 1 / Fragment: UNP residues 22-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 B / Gene: Ocif, Opg, Osteoprotegerin, Tnfrsf11b / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HIGH FIVE / References: UniProt: O08712
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.71 Å3/Da / Density % sol: 66.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 100 mM sodium phosphate/citrate buffer, 14% polyethylene glycol 8000 and 250 mM sodium chloride, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9951 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9951 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14915 / % possible obs: 99.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 48.42 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.7-2.82.80.5631100
2.8-2.912.80.3851100
2.91-3.042.90.2811100
3.04-3.22.90.191100
3.2-3.42.80.1411100
3.4-3.662.90.117199.8
3.66-4.032.90.089199.4
4.03-4.622.80.062199.7
4.62-5.812.90.048198.9
5.81-502.90.029195.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JTZ
Resolution: 2.7→40.7 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1476 10.15 %
Rwork0.194 --
obs0.202 14542 97.1 %
all-42626 -
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.12 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 2 93 2372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022348
X-RAY DIFFRACTIONf_angle_d0.5933171
X-RAY DIFFRACTIONf_dihedral_angle_d9.943852
X-RAY DIFFRACTIONf_chiral_restr0.04336
X-RAY DIFFRACTIONf_plane_restr0.003411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78710.28331270.23771111X-RAY DIFFRACTION92
2.7871-2.88670.2841140.23381164X-RAY DIFFRACTION95
2.8867-3.00230.28171350.22091172X-RAY DIFFRACTION96
3.0023-3.13890.25011330.20781178X-RAY DIFFRACTION97
3.1389-3.30430.26231300.20751209X-RAY DIFFRACTION99
3.3043-3.51120.21931170.20081212X-RAY DIFFRACTION99
3.5112-3.78210.2311480.1841202X-RAY DIFFRACTION100
3.7821-4.16240.23321300.17041203X-RAY DIFFRACTION98
4.1624-4.76390.1831570.16111209X-RAY DIFFRACTION99
4.7639-5.99890.2211230.19251228X-RAY DIFFRACTION99
5.9989-40.70340.2661620.23671178X-RAY DIFFRACTION95
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.57751.5397-2.23812.83550.75632.6150.6831-1.3538-0.44850.2598-0.4248-0.24711.13371.2059-0.32461.18390.0909-0.14250.80770.12740.635766.6807-1.080827.5509
20.55590.0931.39432.2446-0.34163.6470.07770.1495-0.22550.0877-0.22120.07571.49480.51570.13581.25710.08090.04590.5755-0.0340.706958.65392.41194.5034
34.5249-0.1382-4.00952.96530.07426.6838-0.06580.59580.2261-0.93420.5103-1.43530.94821.9733-0.31921.09080.10730.24991.1385-0.22320.820668.747310.847-18.4317
40.2621-1.43650.69968.1575-2.73936.08770.5490.55970.0664-1.4366-1.0267-0.41040.9980.56230.05011.7367-0.55120.54912.557-0.58891.146182.886911.2919-29.3658
56.4417-5.5088-4.3514.82154.17624.8081-0.0515-0.05990.2790.35160.4126-0.3805-0.59670.1375-0.50551.3552-0.13260.34531.4101-0.03661.350476.59627.6354-33.8245
64.03710.8075.31669.11081.47578.68480.12310.7271-0.5028-0.60510.1119-1.19430.52681.6495-0.22570.3580.0008-0.040.52040.06130.613472.15129.26344.8917
72.80130.2372-0.64583.778-0.04553.3380.0219-0.171-0.3190.2644-0.1318-0.57420.23751.20250.13550.30240.00970.01020.57350.0510.361969.500428.71577.936
827.6293-5.78926.061-5.56456.31180.909-0.85681.01341.33880.35760.2483-1.093-0.2267-1.12781.6324-0.45650.2912.12030.0750.947468.256631.4592-25.0154
95.66440.8088-0.20154.75260.66043.51150.03750.4758-0.5162-0.5537-0.1493-0.25630.75090.72740.20820.42920.00970.06550.2559-0.08310.340663.083720.9015-2.4835
102.58240.0776-0.03684.47160.6424.9911-0.0348-0.05230.00260.0052-0.0134-0.05070.2050.62250.0630.14890.006-0.0280.30460.0130.305864.269328.02754.7835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain R and resid 7:39)R7 - 39
2X-RAY DIFFRACTION2(chain R and resid 40:88)R40 - 88
3X-RAY DIFFRACTION3(chain R and resid 89:121)R89 - 121
4X-RAY DIFFRACTION4(chain R and resid 122:125)R122 - 125
5X-RAY DIFFRACTION5(chain R and resid 126:141)R126 - 141
6X-RAY DIFFRACTION6(chain X and resid 162:179)X162 - 179
7X-RAY DIFFRACTION7(chain X and resid 180:226)X180 - 226
8X-RAY DIFFRACTION8(chain X and resid 227:232)X227 - 232
9X-RAY DIFFRACTION9(chain X and resid 233:266)X233 - 266
10X-RAY DIFFRACTION10(chain X and resid 267:315)X267 - 315

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