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- PDB-4giq: Crystal Structure of mouse RANK bound to RANKL -

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Basic information

Entry
Database: PDB / ID: 4giq
TitleCrystal Structure of mouse RANK bound to RANKL
Components(Tumor necrosis factor ...) x 2
KeywordsPROTEIN BINDING/PROTEIN BINDING / RANK / ODFR / Activation-Induced Cytokine-Receptor / TNFRSF11A / RANKL / OPGL / TNF-like Cytokine / Cysteine-Rich Domain / Jelly-Roll fold / PROTEIN BINDING-PROTEIN BINDING 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsNelson, C.A. / Wang, M.W.-H. / 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
DepositionAug 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Feb 13, 2013Group: Other
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
R: Tumor necrosis factor receptor superfamily member 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4056
Polymers38,0902
Non-polymers3154
Water1,45981
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)115,21518
Polymers114,2706
Non-polymers94512
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
Buried area16380 Å2
ΔGint-117 kcal/mol
Surface area43300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.636, 120.636, 94.297
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-502-

HOH

21A-507-

HOH

31A-529-

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 / Tumor necrosis factor ligand superfamily member 11 / membrane form / Tumor necrosis factor ligand superfamily member 11 / soluble form


Mass: 19056.359 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: 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 11A / Osteoclast differentiation factor receptor / ODFR / Receptor activator of NF-KB


Mass: 19033.477 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rank, Tnfrsf11a / Cell (production host): HIGH FIVE INSECT CELLS / Production host: unidentified baculovirus / References: UniProt: O35305

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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 84 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 5.2 Å3/Da / Density % sol: 76.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0 M sodium chloride, 100 mM EDTA, 100 mM sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 21055 / Num. obs: 21040 / % possible obs: 98.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.7-2.870.537192.6
2.87-3.090.316197.2
3.09-3.40.175199.2
3.4-3.890.094199.7
3.89-4.890.055199.8
4.89-200.042199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
AMoREphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JTZ

1jtz


Resolution: 2.7→19.74 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 1995 9.48 %
Rwork0.188 --
obs0.191 21040 97.9 %
all-21055 -
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.99 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 17 81 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022565
X-RAY DIFFRACTIONf_angle_d0.5973469
X-RAY DIFFRACTIONf_dihedral_angle_d9.459908
X-RAY DIFFRACTIONf_chiral_restr0.043374
X-RAY DIFFRACTIONf_plane_restr0.003450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76660.34251320.30871226X-RAY DIFFRACTION89
2.7666-2.84120.31551330.29961282X-RAY DIFFRACTION94
2.8412-2.92460.33291330.28931316X-RAY DIFFRACTION96
2.9246-3.01870.34651420.27041364X-RAY DIFFRACTION97
3.0187-3.12620.33981440.26051364X-RAY DIFFRACTION98
3.1262-3.25080.24891460.23791366X-RAY DIFFRACTION99
3.2508-3.3980.24991420.21271364X-RAY DIFFRACTION99
3.398-3.57620.21631410.18461388X-RAY DIFFRACTION100
3.5762-3.79880.19171500.16341379X-RAY DIFFRACTION100
3.7988-4.08970.18941470.14741379X-RAY DIFFRACTION100
4.0897-4.49680.13731470.1361410X-RAY DIFFRACTION100
4.4968-5.13750.16441410.13421383X-RAY DIFFRACTION100
5.1375-6.43530.19371490.18381398X-RAY DIFFRACTION100
6.4353-19.74420.19951480.1871426X-RAY DIFFRACTION99

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