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- PDB-1lb5: TRAF6-RANK Complex -

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Basic information

Entry
Database: PDB / ID: 1lb5
TitleTRAF6-RANK Complex
Components
  • TNF receptor-associated factor 6
  • receptor activator of nuclear factor-kappa B
KeywordsSIGNALING PROTEIN / TRAF6-RANK complex
Function / homology
Function and homology information


multinuclear osteoclast differentiation / positive regulation of fever generation by positive regulation of prostaglandin secretion / circadian temperature homeostasis / tumor necrosis factor receptor activity / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / cellular response to zinc ion starvation / positive regulation of osteoclast differentiation / cellulase / cellulase activity / monocyte chemotaxis ...multinuclear osteoclast differentiation / positive regulation of fever generation by positive regulation of prostaglandin secretion / circadian temperature homeostasis / tumor necrosis factor receptor activity / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / cellular response to zinc ion starvation / positive regulation of osteoclast differentiation / cellulase / cellulase activity / monocyte chemotaxis / cytokine binding / mammary gland alveolus development / positive regulation of bone resorption / lymph node development / response to tumor necrosis factor / cellulose catabolic process / response to mechanical stimulus / positive regulation of JUN kinase activity / tumor necrosis factor-mediated signaling pathway / response to interleukin-1 / ossification / osteoclast differentiation / TNFR2 non-canonical NF-kB pathway / positive regulation of DNA-binding transcription factor activity / response to insulin / response to organic cyclic compound / transmembrane signaling receptor activity / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / signaling receptor activity / response to ethanol / adaptive immune response / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / membrane raft / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / metal ion binding / plasma membrane / cytosol
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 / Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A ...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 / Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / TNFR/NGFR family cysteine-rich region domain profile. / 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 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Endoglucanase / Tumor necrosis factor receptor superfamily member 11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYe, H. / Arron, J.R. / Lamothe, B. / Cirilli, M. / Kobayashi, T. / Shevde, N.K. / Segal, D. / Dzivenu, O. / Vologodskaia, M. / Yim, M. ...Ye, H. / Arron, J.R. / Lamothe, B. / Cirilli, M. / Kobayashi, T. / Shevde, N.K. / Segal, D. / Dzivenu, O. / Vologodskaia, M. / Yim, M. / Du, K. / Singh, S. / Pike, J.W. / Darnay, B.G. / Choi, Y. / Wu, H.
CitationJournal: Nature / Year: 2002
Title: Distinct molecular mechanism for initiating TRAF6 signalling.
Authors: Ye, H. / Arron, J.R. / Lamothe, B. / Cirilli, M. / Kobayashi, T. / Shevde, N.K. / Segal, D. / Dzivenu, O.K. / Vologodskaia, M. / Yim, M. / Du, K. / Singh, S. / Pike, J.W. / Darnay, B.G. / Choi, Y. / Wu, H.
History
DepositionApr 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF receptor-associated factor 6
B: receptor activator of nuclear factor-kappa B


Theoretical massNumber of molelcules
Total (without water)19,6892
Polymers19,6892
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-2 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.990, 44.991, 106.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TNF receptor-associated factor 6


Mass: 18676.549 Da / Num. of mol.: 1 / Fragment: residues 347-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4K3
#2: Protein/peptide receptor activator of nuclear factor-kappa B


Mass: 1012.048 Da / Num. of mol.: 1 / Fragment: residues 342-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANK / Production host: Escherichia coli (E. coli) / References: GenBank: 2612918, UniProt: Q9Y6Q6*PLUS
#3: 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-25 %PEG800011
2100 mMTris-HCl11pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 12396 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 14.1 Å2 / Rsym value: 0.055
Reflection shellResolution: 2.4→2.55 Å / % possible all: 95.8
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 86.9 % / Rmerge(I) obs: 0.139

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRAF6 apo form

Resolution: 2.4→19.63 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 739 -RANDOM
Rwork0.213 ---
obs-7408 10 %-
Displacement parametersBiso mean: 22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 0 79 1409
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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