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- PDB-5to7: Structure of the TPR oligomerization domain -

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Basic information

Entry
Database: PDB / ID: 5to7
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 / RNA import into nucleus / mRNA export from nucleus in response to heat stress / cellular response to interferon-alpha / negative regulation of RNA export from nucleus / positive regulation of mitotic cell cycle spindle assembly checkpoint / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / positive regulation of intracellular protein transport ...regulation of mitotic sister chromatid separation / RNA import into nucleus / mRNA export from nucleus in response to heat stress / cellular response to interferon-alpha / negative regulation of RNA export from nucleus / positive regulation of mitotic cell cycle spindle assembly checkpoint / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / positive regulation of intracellular protein transport / 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) / regulation of mitotic spindle assembly / 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 / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / Regulation of HSF1-mediated heat shock response / mRNA export from nucleus / nuclear pore / SUMOylation of DNA damage response and repair proteins / heat shock protein binding / negative regulation of translational initiation / tubulin binding / SUMOylation of chromatin organization proteins / nuclear periphery / positive regulation of protein export from nucleus / HCMV Late Events / Transcriptional regulation by small RNAs / mitotic spindle / kinetochore / ISG15 antiviral mechanism / positive regulation of protein import into nucleus / HCMV Early Events / protein import into nucleus / Signaling by ALK fusions and activated point mutants / nuclear envelope / regulation of protein localization / snRNP Assembly / cellular response to heat / 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: 2.6 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 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein TPR
B: Nucleoprotein TPR
C: Nucleoprotein TPR
D: Nucleoprotein TPR


Theoretical massNumber of molelcules
Total (without water)67,0564
Polymers67,0564
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.490, 51.190, 113.800
Angle α, β, γ (deg.)90.000, 129.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 16763.898 Da / Num. of mol.: 4 / 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


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7.25 / Details: 28% PEG1K, 0.1M HEPES (7.25)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→47.49 Å / Num. obs: 28341 / % possible obs: 97.5 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.3 / % possible all: 98.8

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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
Starting model: 5TV5
Resolution: 2.6→44.019 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.45
RfactorNum. reflection% reflection
Rfree0.2809 1174 5.28 %
Rwork0.2362 --
obs0.2386 22233 97.02 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 113.83 Å2 / Biso mean: 55.3081 Å2 / Biso min: 19.47 Å2
Refinement stepCycle: final / Resolution: 2.6→44.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4696 0 0 128 4824
Biso mean---55.38 -
Num. residues----564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054726
X-RAY DIFFRACTIONf_angle_d0.7336308
X-RAY DIFFRACTIONf_chiral_restr0.025712
X-RAY DIFFRACTIONf_plane_restr0.002836
X-RAY DIFFRACTIONf_dihedral_angle_d13.4151944
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.65310.3835750.32821241131699
2.6531-2.71070.311720.32331248132099
2.7107-2.77380.3173620.30861268133099
2.7738-2.84310.3487640.285312561320100
2.8431-2.920.371770.27591222129998
2.92-3.00590.2935850.26751233131899
3.0059-3.10290.3497810.29371225130698
3.1029-3.21380.3296620.28161285134799
3.2138-3.34240.3112660.25771267133399
3.3424-3.49450.2434690.252412631332100
3.4945-3.67860.2619470.2483987103497
3.6786-3.9090.2886740.21481165123998
3.909-4.21060.2745540.21441265131999
4.2106-4.63390.2789620.193112921354100
4.6339-5.30340.2733730.20731251132497
5.3034-6.6780.2844620.27151308137099
6.678-44.02520.1898890.15731283137296

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