[English] 日本語
Yorodumi
- PDB-3urf: Human RANKL/OPG complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3urf
TitleHuman RANKL/OPG complex
Components
  • Tumor necrosis factor ligand superfamily member 11, soluble form
  • Tumor necrosis factor receptor superfamily member 11B
KeywordsCYTOKINE / cystein-rich domain / beta-sandwich
Function / homology
Function and homology information


positive regulation of corticotropin-releasing hormone secretion / positive regulation of fever generation by positive regulation of prostaglandin secretion / negative regulation of odontogenesis of dentin-containing tooth / tooth eruption / osteoclast proliferation / tumor necrosis factor receptor superfamily binding / positive regulation of osteoclast development / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of homotypic cell-cell adhesion ...positive regulation of corticotropin-releasing hormone secretion / positive regulation of fever generation by positive regulation of prostaglandin secretion / negative regulation of odontogenesis of dentin-containing tooth / tooth eruption / osteoclast proliferation / tumor necrosis factor receptor superfamily binding / positive regulation of osteoclast development / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of homotypic cell-cell adhesion / osteoclast development / paracrine signaling / response to arsenic-containing substance / heparan sulfate binding / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of bone resorption / mammary gland epithelial cell proliferation / negative regulation of osteoclast differentiation / monocyte chemotaxis / response to magnesium ion / positive regulation of intracellular signal transduction / mammary gland alveolus development / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of bone resorption / bone resorption / calcium ion homeostasis / tumor necrosis factor-mediated signaling pathway / JNK cascade / extracellular matrix organization / response to nutrient / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / positive regulation of MAP kinase activity / extracellular matrix / osteoclast differentiation / ossification / cellular response to leukemia inhibitory factor / positive regulation of DNA-binding transcription factor activity / cytokine activity / skeletal system development / TNFR2 non-canonical NF-kB pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of JNK cascade / calcium-mediated signaling / cytokine-mediated signaling pathway / positive regulation of T cell activation / response to estrogen / positive regulation of NF-kappaB transcription factor activity / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / immune response / response to xenobiotic stimulus / 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 / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 11B / Tumor Necrosis Factor Receptor Superfamily Member 11B death domain / 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(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region domain profile. ...Tumour necrosis factor receptor 11B / Tumor Necrosis Factor Receptor Superfamily Member 11B death domain / 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(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 (TNF) homology domain (THD) profile. / 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, found in proteins involved in cell death (apoptosis). / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsWang, X.Q. / Luan, X.D. / Lu, Q.Y.
CitationJournal: J.Immunol. / Year: 2012
Title: Crystal Structure of Human RANKL Complexed with Its Decoy Receptor Osteoprotegerin
Authors: Luan, X.D. / Lu, Q.Y. / Jiang, Y.N. / Zhang, S.Y. / Wang, Q. / Yuan, H.H. / Zhao, W.M. / Wang, J.W. / Wang, X.Q.
History
DepositionNov 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,3833
Polymers38,1622
Non-polymers2211
Water64936
1
A: Tumor necrosis factor ligand superfamily member 11, soluble form
Z: Tumor necrosis factor receptor superfamily member 11B
hetero molecules

A: Tumor necrosis factor ligand superfamily member 11, soluble form
Z: Tumor necrosis factor receptor superfamily member 11B
hetero molecules

A: Tumor necrosis factor ligand superfamily member 11, soluble form
Z: Tumor necrosis factor receptor superfamily member 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1499
Polymers114,4866
Non-polymers6643
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6320 Å2
ΔGint-23 kcal/mol
Surface area18790 Å2
Unit cell
Length a, b, c (Å)144.800, 144.800, 144.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

-
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: 18424.529 Da / Num. of mol.: 1 / Fragment: UNP residues 162-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF11, OPGL, RANKL, TRANCE / Production host: Escherichia coli (E. coli) / References: UniProt: O14788
#2: Protein Tumor necrosis factor receptor superfamily member 11B / Osteoclastogenesis inhibitory factor / Osteoprotegerin


Mass: 19737.336 Da / Num. of mol.: 1 / Fragment: UNP residues 22-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF11B, OCIF, OPG / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O00300
#3: 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


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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M NaCl, 100mM MES pH 6.5, 100mM Sodium phosphate monobasic monohydrate, 100mM Potassium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2009
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40.16 Å / Num. all: 14808 / Num. obs: 14783 / % possible obs: 99.83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 63.9 Å2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.701→40.16 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8077 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 748 5.06 %
Rwork0.2023 --
obs0.2048 14783 99.83 %
all-14783 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.408 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 80.0395 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.701→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 14 36 2604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092654
X-RAY DIFFRACTIONf_angle_d1.2323585
X-RAY DIFFRACTIONf_dihedral_angle_d18.708955
X-RAY DIFFRACTIONf_chiral_restr0.085377
X-RAY DIFFRACTIONf_plane_restr0.005460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.701-2.90950.39841470.33582738100
2.9095-3.20220.32261570.24052743100
3.2022-3.66530.24881630.18792751100
3.6653-4.61680.19861510.15392808100
4.6168-40.16470.25221300.2127299599
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)
13.7691-0.23990.08922.72470.01243.235-0.0803-0.5201-0.28860.4776-0.0488-0.04010.2055-0.0806-0.00350.2779-0.0074-0.04510.35480.07060.28788.8381-0.607517.2613
20.8755-0.44910.11190.8659-0.37561.0451-0.3391-0.4917-0.48860.20770.27050.12410.0246-0.3981-0.00450.3243-0.02460.11910.51550.17340.3708-14.0164-6.427329.852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain Z

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more