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- PDB-5to5: Structure of the TPR oligomerization domain -

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Basic information

Entry
Database: PDB / ID: 5to5
TitleStructure of the TPR oligomerization domain
ComponentsNucleoprotein TPR
KeywordsCELL CYCLE / TPR oligomerization domain / Receptor tyrosine kinase / MET / Oncogenic Fusion kinases
Function / homology
Function and homology information


regulation of mitotic sister chromatid separation / negative regulation of RNA export from nucleus / RNA import into nucleus / mRNA export from nucleus in response to heat stress / cellular response to interferon-alpha / positive regulation of mitotic cell cycle spindle assembly checkpoint / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket ...regulation of mitotic sister chromatid separation / negative regulation of RNA export from nucleus / RNA import into nucleus / mRNA export from nucleus in response to heat stress / cellular response to interferon-alpha / positive regulation of mitotic cell cycle spindle assembly checkpoint / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / positive regulation of intracellular protein transport / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / cytoplasmic dynein complex / SUMOylation of SUMOylation proteins / response to epidermal growth factor / regulation of mitotic spindle assembly / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / mitogen-activated protein kinase binding / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / dynein complex binding / mitotic spindle assembly checkpoint signaling / SUMOylation of ubiquitinylation proteins / positive regulation of heterochromatin formation / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Signaling by ALK fusions and activated point mutants / Regulation of HSF1-mediated heat shock response / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / negative regulation of translational initiation / heat shock protein binding / nuclear periphery / SUMOylation of chromatin organization proteins / tubulin binding / positive regulation of protein export from nucleus / HCMV Late Events / Transcriptional regulation by small RNAs / mitotic spindle / ISG15 antiviral mechanism / kinetochore / HCMV Early Events / positive regulation of protein import into nucleus / protein import into nucleus / regulation of protein localization / cellular response to heat / nuclear envelope / snRNP Assembly / nuclear membrane / cell division / mRNA binding / chromatin binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nucleoprotein TPR/MLP1 / TPR/MLP1/MLP2-like protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPal, K. / Xu, Q. / Zhou, X.E. / Melcher, K. / Xu, H.E.
CitationJournal: Structure / Year: 2017
Title: Structural Basis of TPR-Mediated Oligomerization and Activation of Oncogenic Fusion Kinases.
Authors: Pal, K. / Bandyopadhyay, A. / Zhou, X.E. / Xu, Q. / Marciano, D.P. / Brunzelle, J.S. / Yerrum, S. / Griffin, P.R. / Vande Woude, G. / Melcher, K. / Xu, H.E.
History
DepositionOct 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein TPR
B: Nucleoprotein TPR


Theoretical massNumber of molelcules
Total (without water)33,4962
Polymers33,4962
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-58 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.177, 51.551, 94.980
Angle α, β, γ (deg.)90.000, 107.830, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-263-

HOH

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Components

#1: Protein Nucleoprotein TPR / Megator / NPC-associated intranuclear protein / Translocated promoter region protein


Mass: 16747.922 Da / Num. of mol.: 2 / Fragment: UNP residues 2-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12270
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6.25 / Details: 16% PEG1.5K, 0.1M Bistris (6.25)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07812 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 2.18→21.85 Å / Num. obs: 17251 / % possible obs: 96 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→21.411 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 29.96
RfactorNum. reflection% reflection
Rfree0.282 544 4.74 %
Rwork0.2294 --
obs0.2318 11481 95.85 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 125.41 Å2 / Biso mean: 37.5525 Å2 / Biso min: 18.01 Å2
Refinement stepCycle: final / Resolution: 2.5→21.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 0 126 2463
Biso mean---42.24 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042349
X-RAY DIFFRACTIONf_angle_d0.7223135
X-RAY DIFFRACTIONf_chiral_restr0.026355
X-RAY DIFFRACTIONf_plane_restr0.003415
X-RAY DIFFRACTIONf_dihedral_angle_d17.522973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.75120.3451400.27222743288398
2.7512-3.14820.29811370.25432790292798
3.1482-3.96230.27311380.22732734287296
3.9623-21.41230.25721290.2022670279992

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