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- PDB-3qf9: Crystal structure of human proto-oncogene serine threonine kinase... -

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Basic information

Entry
Database: PDB / ID: 3qf9
TitleCrystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a furan-thiazolidinedione ligand
Components
  • Proto-oncogene serine/threonine-protein kinase pim-1
  • pimtide
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE/PEPTIDE / COMPLEX TRANSFERASE-PEPTIDE / PIM1 / KINASE / CANCER / LEUKEMIA / ATP-BINDING / NUCLEAR PROTEIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION / PROTO-ONCOGENE / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / negative regulation of innate immune response / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Serine/threonine-protein kinase pim-1/2/3 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NM8 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsFilippakopoulos, P. / Bullock, A.N. / Fedorov, O. / Miduturu, C.V. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Grey, N. ...Filippakopoulos, P. / Bullock, A.N. / Fedorov, O. / Miduturu, C.V. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Grey, N. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a furan-thiazolidinedione ligand
Authors: Filippakopoulos, P. / Bullock, A.N. / Fedorov, O. / Miduturu, C.V. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Grey, N. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene serine/threonine-protein kinase pim-1
B: pimtide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8765
Polymers37,1832
Non-polymers6933
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-17 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.843, 97.843, 80.428
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Proto-oncogene serine/threonine-protein kinase pim-1


Mass: 35590.500 Da / Num. of mol.: 1 / Fragment: unp residues 92-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Protein/peptide pimtide


Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 134 molecules

#3: Chemical ChemComp-NM8 / 6-{5-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]furan-2-yl}-N-{3-[(4-ethylpiperazin-1-yl)methyl]-5-(trifluoromethyl)phenyl}naphthalene-1-carboxamide / (Z)-6-(5-((2,4-dioxothiazolidin-5-ylidene)methyl)furan-2-yl)-N-(3-((4-ethylpiperazin-1-yl)methyl)-5-(trifluoromethyl)phenyl)-1-naphthamide


Mass: 634.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H29F3N4O4S
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BTP, 20 % PEG 3350 10 % ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionRedundancy: 5.6 % / Av σ(I) over netI: 7.4 / Number: 124052 / Rsym value: 0.101 / D res high: 2.2 Å / D res low: 37.484 Å / Num. obs: 22340 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.9637.4899.410.0250.0255.4
4.926.9610010.0380.0385.6
4.024.9210010.0370.0375.6
3.484.0210010.0540.0545.6
3.113.4810010.10.15.6
2.843.1110010.1790.1795.6
2.632.8410010.2910.2915.6
2.462.6310010.4310.4315.5
2.322.4610010.610.615.5
2.22.3210010.8510.8515.5
ReflectionResolution: 2.2→37.484 Å / Num. all: 22340 / Num. obs: 22340 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.325.50.8510.91779132510.851100
2.32-2.465.50.611.31691430760.61100
2.46-2.635.50.4311.81587528690.431100
2.63-2.845.60.2912.71490226840.291100
2.84-3.115.60.1794.31393024920.179100
3.11-3.485.60.17.61261922470.1100
3.48-4.025.60.054141115619780.054100
4.02-4.925.60.03719.3954416950.037100
4.92-6.965.60.03819.2735313090.038100
6.96-37.4845.40.02524.739687390.02599.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.72 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.48 Å
Translation2.5 Å37.48 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2C3I

2c3i


Resolution: 2.2→37.48 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.1957 / WRfactor Rwork: 0.1639 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8819 / SU B: 9.776 / SU ML: 0.118 / SU R Cruickshank DPI: 0.1943 / SU Rfree: 0.1733 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1110 5 %RANDOM
Rwork0.1858 ---
all0.1878 22314 --
obs0.1878 22310 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 136.21 Å2 / Biso mean: 40.7836 Å2 / Biso min: 12.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20.46 Å20 Å2
2--0.92 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 28 131 2429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212403
X-RAY DIFFRACTIONr_bond_other_d0.0010.021666
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9613267
X-RAY DIFFRACTIONr_angle_other_deg0.9383.0024004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69922.903124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6215393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9741524
X-RAY DIFFRACTIONr_chiral_restr0.0970.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
X-RAY DIFFRACTIONr_mcbond_it3.58631417
X-RAY DIFFRACTIONr_mcbond_other1.1653571
X-RAY DIFFRACTIONr_mcangle_it5.24352296
X-RAY DIFFRACTIONr_scbond_it8.4898986
X-RAY DIFFRACTIONr_scangle_it9.96111970
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 85 -
Rwork0.303 1570 -
all-1655 -
obs--99.88 %
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)
12.3788-2.6432.914114.23591.94126.0090.34510.0898-0.24960.0014-0.26241.01020.6160.2636-0.08260.2153-0.1446-0.10270.9195-0.0570.5115-27.66830.943.807
27.3112.94642.80346.72560.54987.60080.3349-0.4768-0.36220.4901-0.2011-0.0130.6634-0.3975-0.13380.1528-0.11550.02650.26540.05750.0802-19.48530.92710.062
32.05480.09250.00792.8014-0.71773.43750.0414-0.0149-0.0617-0.09940.02660.00730.06140.0447-0.0680.0208-0.0055-0.00890.0551-0.01270.0097-2.79744.706-1.965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 50
2X-RAY DIFFRACTION2A51 - 122
3X-RAY DIFFRACTION3A123 - 305

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