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- PDB-7upm: Tribbles (TRIB2) pseudokinase bound to nanobody Nb4.103 -

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Basic information

Entry
Database: PDB / ID: 7upm
TitleTribbles (TRIB2) pseudokinase bound to nanobody Nb4.103
Components
  • Nb4.103 Nanobody
  • Tribbles homolog 2
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Tribbles / psuedokinase / TRB2 / TRIB2 / nanobody / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


ubiquitin-protein transferase regulator activity / regulation of MAP kinase activity / mitogen-activated protein kinase kinase binding / negative regulation of interleukin-10 production / negative regulation of fat cell differentiation / protein kinase inhibitor activity / negative regulation of protein kinase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / cytoskeleton ...ubiquitin-protein transferase regulator activity / regulation of MAP kinase activity / mitogen-activated protein kinase kinase binding / negative regulation of interleukin-10 production / negative regulation of fat cell differentiation / protein kinase inhibitor activity / negative regulation of protein kinase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / cytoskeleton / ubiquitin protein ligase binding / nucleus / cytoplasm
Similarity search - Function
Pseudokinase tribbles family/serine-threonine-protein kinase 40 / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJamieson, S.A. / Mace, P.D.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: Structure / Year: 2022
Title: Nanobodies identify an activated state of the TRIB2 pseudokinase.
Authors: Jamieson, S.A. / Pudjihartono, M. / Horne, C.R. / Viloria, J.S. / Dunlop, J.L. / McMillan, H.D. / Day, R.C. / Keeshan, K. / Murphy, J.M. / Mace, P.D.
History
DepositionApr 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tribbles homolog 2
B: Nb4.103 Nanobody


Theoretical massNumber of molelcules
Total (without water)42,9922
Polymers42,9922
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, Evidence for 2:1 complex at high concentration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.160, 75.160, 273.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Tribbles homolog 2 / TRB-2


Mass: 29987.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIB2, TRB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92519
#2: Antibody Nb4.103 Nanobody


Mass: 13004.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.2 M Magnesium nitrate hexahydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→45.67 Å / Num. obs: 13514 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.167 / Net I/σ(I): 10.2
Reflection shellResolution: 2.7→2.77 Å / Num. unique obs: 135 / CC1/2: 0.502

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cem

5cem


Resolution: 2.7→45.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.879 / SU B: 14.451 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25967 1021 8.4 %RANDOM
Rwork0.20187 ---
obs0.20676 11150 90.59 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.447 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.13 Å2-0 Å2
2---0.25 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 0 40 2954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0172977
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192758
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.8644018
X-RAY DIFFRACTIONr_angle_other_deg0.9022.6816352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8895365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47221.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16415506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4671522
X-RAY DIFFRACTIONr_chiral_restr0.0510.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02714
X-RAY DIFFRACTIONr_mcbond_it5.3755.811472
X-RAY DIFFRACTIONr_mcbond_other5.3545.8081471
X-RAY DIFFRACTIONr_mcangle_it8.3918.6911833
X-RAY DIFFRACTIONr_mcangle_other8.398.6951834
X-RAY DIFFRACTIONr_scbond_it5.6266.1921505
X-RAY DIFFRACTIONr_scbond_other5.6246.1921505
X-RAY DIFFRACTIONr_scangle_other8.8639.0982186
X-RAY DIFFRACTIONr_long_range_B_refined12.6965.6733200
X-RAY DIFFRACTIONr_long_range_B_other12.69765.7153195
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 9 -
Rwork0.265 135 -
obs--14.86 %

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