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

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Basic information

Entry
Database: PDB / ID: 5tvb
TitleStructure of the TPR oligomerization domain
ComponentsNucleoprotein TPR
KeywordsTRANSFERASE / Receptor tyrosine kinase / 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 / regulation of mitotic spindle assembly / SUMOylation of SUMOylation proteins / response to epidermal growth factor / 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 / ISG15 antiviral mechanism / mitotic spindle / 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 / SAD / Resolution: 2.75 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
DepositionNov 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

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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)33,8132
Polymers33,8132
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-68 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.355, 50.669, 94.656
Angle α, β, γ (deg.)90.000, 108.010, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain aA0
211chain bB0
DetailsDimer as determined by size exclusion chromatography.

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Components

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


Mass: 16906.646 Da / Num. of mol.: 2 / Fragment: residues 2-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPR / Production host: Escherichia coli (E. coli) / References: UniProt: P12270
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 299 K / Method: evaporation / pH: 7.5 / Details: 0.1M HEPES 7.5, 30% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97622 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.75→41.187 Å / Num. obs: 9404 / % possible obs: 99.2 % / Redundancy: 15.1 % / Net I/σ(I): 39.36
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 15 % / Rmerge(I) obs: 0.256 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data scaling
SHELXphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.75→41.187 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.43
RfactorNum. reflection% reflection
Rfree0.3027 807 10.04 %
Rwork0.2415 --
obs0.2474 8040 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 74.87 Å2 / Biso mean: 28.8092 Å2 / Biso min: 4.73 Å2
Refinement stepCycle: final / Resolution: 2.75→41.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 0 51 2383
Biso mean---27.22 -
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032344
X-RAY DIFFRACTIONf_angle_d0.5723126
X-RAY DIFFRACTIONf_chiral_restr0.024352
X-RAY DIFFRACTIONf_plane_restr0.002414
X-RAY DIFFRACTIONf_dihedral_angle_d15.295974
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1145X-RAY DIFFRACTION5.138TORSIONAL
12B1145X-RAY DIFFRACTION5.138TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7501-2.8140.3509380.310833637461
2.814-2.88440.3621360.2833537167
2.8844-2.96240.387470.27541245977
2.9624-3.04950.3274490.291744649586
3.0495-3.14790.4053530.306247853191
3.1479-3.26040.3933590.288551357296
3.2604-3.39080.3374580.277952458298
3.3908-3.54510.3082550.277449555097
3.5451-3.73190.331550.230250155692
3.7319-3.96550.3248580.252850556397
3.9655-4.27140.2859580.222352658499
4.2714-4.70070.2144600.19254060099
4.7007-5.37960.2752580.212152057899
5.3796-6.77290.2827610.2558549610100
6.7729-41.19110.1934620.161155361598
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)
10.0003-0.00150.00030.007-0.0020.0012-0.00830.0021-0.00550.00860.0008-0.0318-0.00650.0033-0.00220.13540.07230.10910.009-0.09970.1379116.2761-17.536337.0588
2-0.0214-0.06320.1421-0.01490.0895-0.07370.021-0.04740.01920.0348-0.1136-0.0002-0.08430.0932-0.06210.11810.0690.0120.1573-0.05490.099138.9804-4.6865-3.8974
3-0.00050.0006-0.00020.00220.001-0.00080.00440.00870.02030.02370.0144-0.0011-0.00440.0002-00.37290.01970.03420.1648-0.04660.361112.9734-2.590439.9433
40.007-0.0960.37790.01190.04-0.22870.0795-0.07570.01010.0466-0.06960.0311-0.05510.2518-0.01150.05150.0982-0.02810.1787-0.00110.060739.4955-3.6997-5.7848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 18 )A3 - 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 142 )B19 - 142

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