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- PDB-5to6: Structure of the TPR oligomerization domain -

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Basic information

Entry
Database: PDB / ID: 5to6
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 / negative regulation of RNA export from nucleus / 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 / RNA import into nucleus / mRNA export from nucleus in response to heat stress / negative regulation of RNA export from nucleus / 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 / positive regulation of intracellular protein transport / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / response to epidermal growth factor / regulation of mitotic spindle assembly / SUMOylation of SUMOylation proteins / cytoplasmic dynein complex / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from 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 / 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 / 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 / ISG15 antiviral mechanism / kinetochore / positive regulation of protein import into nucleus / HCMV Early Events / protein import into nucleus / regulation of protein localization / Signaling by ALK fusions and activated point mutants / nuclear envelope / cellular response to heat / 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: 2.7 Å
AuthorsPal, K. / Bandyopadhyay, A. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)67,1204
Polymers67,1204
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.790, 34.860, 113.470
Angle α, β, γ (deg.)90.000, 91.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain b
21chain c
12chain a
22chain d

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain bb0
211chain cc0
112chain aa0
212chain dd0

NCS ensembles :
ID
1
2

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Components

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


Mass: 16779.877 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 / Details (production host): pet-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12270
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 299 K / Method: vapor diffusion / pH: 8
Details: 0.1M Tris (8.0), 150mM Sodium malonate, 29% PEG1000

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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: May 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→46.327 Å / Num. obs: 20228 / % possible obs: 94.5 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Net I/σ(I): 10.3
Reflection shellResolution: 2.7→2.74 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.629 / % possible all: 73.1

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TO5

5to5


Resolution: 2.7→46.327 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2882 842 4.98 %
Rwork0.2367 --
obs0.2392 16902 99.05 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.87 Å2 / Biso mean: 61.551 Å2 / Biso min: 22.2 Å2
Refinement stepCycle: final / Resolution: 2.7→46.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 0 52 4738
Biso mean---52.97 -
Num. residues----560
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B1279X-RAY DIFFRACTION5.318TORSIONAL
12C1279X-RAY DIFFRACTION5.318TORSIONAL
21A1262X-RAY DIFFRACTION5.318TORSIONAL
22D1262X-RAY DIFFRACTION5.318TORSIONAL
LS refinement shellResolution: 2.7→2.7628 Å
RfactorNum. reflection% reflection
Rfree0.4319 53 -
Rwork0.3033 --
obs-1037 95 %
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)
10.0012-0.001-0.00260.00450.00440.0040.0427-0.0168-0.02020.04080.04480.0552-0.05850.033100.46630.02-0.08030.24530.04830.460342.081137.2269117.6651
2-0.0131-0.02480.05480.1154-0.0048-0.03580.0068-0.0838-0.0003-0.0110.02090.0334-0.0154-0.05540.02860.2747-0.00570.03060.34520.0120.2532-29.902534.641966.3071
30.0011-0.00040.00040.0005-0.0006-0.0004-0.00240.00830.0208-0.0457-0.0277-0.0675-0.05880.0128-00.4673-0.02430.04160.39280.0990.470646.010244.0359104.2205
40.0179-0.05780.03120.062-0.007-0.0181-0.04060.09950.0565-0.04150.02590.0634-0.00570.109-0.00120.34440.02-0.0080.3238-0.02060.32-28.461332.703165.7849
50.0013-0.00070.0020.0022-0.00090.00330.07020.03150.0368-0.03020.0460.0025-0.0159-0.0165-00.707-0.0856-0.09430.7209-0.04080.8825-89.614741.7685.222
60.055-0.0776-0.0389-0.01410.03830.0496-0.0357-0.07260.1318-0.0267-0.0142-0.00080.0384-0.061-0.00010.3323-0.0269-0.02760.33160.01520.3823-15.825332.375451.627
70.0002-0.00010.00010.00050.00080.0011-0.0429-0.00940.00250.0388-0.0316-0.0240.04470.03850.00010.82350.0576-0.08660.9943-0.04420.6896-81.422231.7196-3.7874
80.0676-0.0825-0.05850.2003-0.02880.0952-0.05050.0814-0.10810.05750.0553-0.0965-0.05260.0028-00.38230.00690.03860.5049-0.02610.4005-14.456933.532950.4258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 18 )A2 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 142 )A19 - 142
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 18 )B3 - 18
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 141 )B19 - 141
5X-RAY DIFFRACTION5chain 'C' and (resid 3 through 18 )C3 - 18
6X-RAY DIFFRACTION6chain 'C' and (resid 19 through 142 )C19 - 142
7X-RAY DIFFRACTION7chain 'D' and (resid 3 through 18 )D3 - 18
8X-RAY DIFFRACTION8chain 'D' and (resid 19 through 142 )D19 - 142

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