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- PDB-6dc0: Tribbles (TRIB1) pseudokinase fused to CCAAT-enhancer binding pro... -

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Basic information

Entry
Database: PDB / ID: 6dc0
TitleTribbles (TRIB1) pseudokinase fused to CCAAT-enhancer binding protein (C/EBPalpha) degron
ComponentsTribbles homolog 1,CCAAT/enhancer-binding protein alpha
KeywordsSIGNALING PROTEIN / Tribbles / psuedokinase / CCAAT-enhancer binding protein / TRB1
Function / homology
Function and homology information


ubiquitin-protein transferase regulator activity / positive regulation of eosinophil differentiation / RNA polymerase I transcription regulatory region sequence-specific DNA binding / positive regulation of DNA-templated transcription initiation / negative regulation of smooth muscle cell migration / regulation of MAP kinase activity / granulocyte differentiation / negative regulation of neutrophil differentiation / positive regulation of macrophage differentiation / negative regulation of lipopolysaccharide-mediated signaling pathway ...ubiquitin-protein transferase regulator activity / positive regulation of eosinophil differentiation / RNA polymerase I transcription regulatory region sequence-specific DNA binding / positive regulation of DNA-templated transcription initiation / negative regulation of smooth muscle cell migration / regulation of MAP kinase activity / granulocyte differentiation / negative regulation of neutrophil differentiation / positive regulation of macrophage differentiation / negative regulation of lipopolysaccharide-mediated signaling pathway / urea cycle / negative regulation of cyclin-dependent protein serine/threonine kinase activity / myeloid cell differentiation / NGF-stimulated transcription / positive regulation of macrophage activation / positive regulation of transcription by RNA polymerase III / mitogen-activated protein kinase kinase binding / interleukin-6-mediated signaling pathway / cellular response to lithium ion / protein kinase inhibitor activity / fat cell differentiation / lipid homeostasis / transcription by RNA polymerase I / inner ear development / transcription factor binding / macrophage differentiation / cellular response to organic cyclic compound / white fat cell differentiation / embryonic placenta development / positive regulation of fat cell differentiation / positive regulation of osteoblast differentiation / brown fat cell differentiation / JNK cascade / cell maturation / Notch signaling pathway / viral process / cholesterol metabolic process / mitochondrion organization / liver development / generation of precursor metabolites and energy / negative regulation of smooth muscle cell proliferation / negative regulation of protein kinase activity / lung development / negative regulation of DNA-binding transcription factor activity / cytokine-mediated signaling pathway / kinase binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / cellular response to tumor necrosis factor / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / response to lipopolysaccharide / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Tribbles homologue 1 / Pseudokinase tribbles family/serine-threonine-protein kinase 40 / CCAAT/enhancer-binding protein, chordates / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. ...Tribbles homologue 1 / Pseudokinase tribbles family/serine-threonine-protein kinase 40 / CCAAT/enhancer-binding protein, chordates / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
CCAAT/enhancer-binding protein alpha / Tribbles homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJamieson, S.A. / Brewster, J.L. / Mace, P.D.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
Royal Society of New ZealandRutherford Discovery Fellowship New Zealand
CitationJournal: Sci Signal / Year: 2018
Title: Substrate binding allosterically relieves autoinhibition of the pseudokinase TRIB1.
Authors: Jamieson, S.A. / Ruan, Z. / Burgess, A.E. / Curry, J.R. / McMillan, H.D. / Brewster, J.L. / Dunbier, A.K. / Axtman, A.D. / Kannan, N. / Mace, P.D.
History
DepositionMay 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tribbles homolog 1,CCAAT/enhancer-binding protein alpha
B: Tribbles homolog 1,CCAAT/enhancer-binding protein alpha


Theoretical massNumber of molelcules
Total (without water)65,6192
Polymers65,6192
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-18 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.809, 98.809, 332.705
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 89 - 508 / Label seq-ID: 6 - 283

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Tribbles homolog 1,CCAAT/enhancer-binding protein alpha / TRB-1 / G-protein-coupled receptor-induced gene 2 protein / GIG-2 / SKIP1 / C/EBP alpha


Mass: 32809.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIB1, C8FW, GIG2, TRB1, CEBPA, CEBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RU8, UniProt: P49715
#2: 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: 3.57 Å3/Da / Density % sol: 65.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.8 M Na Acetate, 0.1 M BIS-TRIS prop 7 pH with 5% sodium citrate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→48.7 Å / Num. obs: 24777 / % possible obs: 99.4 % / Redundancy: 10.4 % / Net I/σ(I): 19.8
Reflection shellResolution: 2.8→2.95 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CEM

5cem


Resolution: 2.8→48.7 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 39.462 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R: 0.533 / ESU R Free: 0.34 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27679 1222 5 %RANDOM
Rwork0.2199 ---
obs0.22254 23461 99.73 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 113 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.21 Å2-0 Å2
2---0.41 Å20 Å2
3---1.34 Å2
Refinement stepCycle: 1 / Resolution: 2.8→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 0 40 4351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194416
X-RAY DIFFRACTIONr_bond_other_d0.0050.024263
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9675967
X-RAY DIFFRACTIONr_angle_other_deg1.33839816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8055531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52222.217203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.3315784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9161543
X-RAY DIFFRACTIONr_chiral_restr0.10.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214851
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021030
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7746.6282136
X-RAY DIFFRACTIONr_mcbond_other3.7696.6282135
X-RAY DIFFRACTIONr_mcangle_it5.8539.9462660
X-RAY DIFFRACTIONr_mcangle_other5.8539.9472661
X-RAY DIFFRACTIONr_scbond_it4.1157.092279
X-RAY DIFFRACTIONr_scbond_other4.1147.0912280
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.67610.4543307
X-RAY DIFFRACTIONr_long_range_B_refined11.39263.36518093
X-RAY DIFFRACTIONr_long_range_B_other11.39263.36218090
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 30588 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.799→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 77 -
Rwork0.366 1669 -
obs--98.15 %
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)
11.837-0.59910.13124.2619-1.34281.73310.12040.0460.06070.4067-0.28720.1490.08470.01890.16690.1725-0.0752-0.04570.25560.20630.33237.804130.9651184.7332
22.66761.561-0.24054.8588-0.46491.51330.24340.34070.3886-0.5356-0.5982-0.4171-0.0029-0.0080.35490.13890.16280.12740.44120.53740.81323.067661.2422159.372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 509
2X-RAY DIFFRACTION2B89 - 516

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