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- PDB-3ma3: Crystal structure of human proto-oncogene serine threonine kinase... -

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Basic information

Entry
Database: PDB / ID: 3ma3
TitleCrystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a naphtho-difuran ligand
Components
  • Pimtide
  • Proto-oncogene serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / ONCOGENE / KINASE / SERINE-THREONINE / PIM1 / STRUCTURAL GENOMICS CONSORTIUM / SGC / ALTERNATIVE INITIATION / ATP-BINDING / MANGANESE / MEMBRANE / METAL-BINDING / NUCLEOTIDE-BINDING / NUCLEUS / PHOSPHOPROTEIN / PROTO-ONCOGENE / SERINE/THREONINE-PROTEIN KINASE / HOST-VIRUS INTERACTION / VIRAL IMMUNOEVASION / VIRION / VIRULENCE / Cell cycle / Cell membrane
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / 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 / cytoplasm / cytosol
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-01I / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsFilippakopoulos, P. / Bullock, A. / Fedorov, O. / Vollmar, M. / von Delft, F. / Cochet, C. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Faseb J. / Year: 2010
Title: New potent dual inhibitors of CK2 and Pim kinases: discovery and structural insights.
Authors: Lopez-Ramos, M. / Prudent, R. / Moucadel, V. / Sautel, C.F. / Barette, C. / Lafanechere, L. / Mouawad, L. / Grierson, D. / Schmidt, F. / Florent, J.C. / Filippakopoulos, P. / Bullock, A.N. / ...Authors: Lopez-Ramos, M. / Prudent, R. / Moucadel, V. / Sautel, C.F. / Barette, C. / Lafanechere, L. / Mouawad, L. / Grierson, D. / Schmidt, F. / Florent, J.C. / Filippakopoulos, P. / Bullock, A.N. / Knapp, S. / Reiser, J.B. / Cochet, C.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)36,9083
Polymers36,6122
Non-polymers2961
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint3 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.707, 97.707, 80.581
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 35670.477 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 / consensus PIM1 substrate peptide


Mass: 941.116 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-01I / naphtho[2,1-b:7,6-b']difuran-2,8-dicarboxylic acid


Mass: 296.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H8O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE EXPRESSED PROTEIN HAS THE SEQUENCE FROM GI 33304198 WHICH DIFFERS FROM GI ...AUTHORS STATE THAT THE EXPRESSED PROTEIN HAS THE SEQUENCE FROM GI 33304198 WHICH DIFFERS FROM GI 4505811 BY A SINGLE MUTATION R250G.

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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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% Isopropanol 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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 IV / Detector: IMAGE PLATE / Date: Mar 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 14.74 / Number: 72393 / Rmerge(I) obs: 0.079 / Χ2: 1.05 / D res high: 2.3 Å / D res low: 40 Å / Num. obs: 19082 / % possible obs: 97.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.954099.610.0371.0243.8
3.934.9599.810.0561.0583.8
3.443.9377.510.0871.0843.4
3.123.4410010.0741.0063.8
2.93.1210010.11.0683.8
2.732.910010.1421.0123.9
2.592.7310010.1991.0213.8
2.482.5910010.2661.0353.8
2.382.4810010.3511.0943.8
2.32.3810010.4461.0743.8
ReflectionResolution: 2.3→36.37 Å / Num. all: 19531 / Num. obs: 19082 / % possible obs: 97.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 / Rsym value: 0.076 / Χ2: 1.046 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1950 / Rsym value: 0.446 / Χ2: 1.074 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.46 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.79 Å
Translation2.5 Å41.79 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C3I

2c3i


Resolution: 2.3→36.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.845 / SU B: 10.71 / SU ML: 0.137 / SU R Cruickshank DPI: 0.214 / SU Rfree: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.233 942 4.9 %RANDOM
Rwork0.169 ---
all0.172 19492 --
obs0.172 19034 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.46 Å2 / Biso mean: 43.092 Å2 / Biso min: 11.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20.95 Å20 Å2
2--1.91 Å20 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 22 147 2385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212331
X-RAY DIFFRACTIONr_bond_other_d0.0010.021605
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9593168
X-RAY DIFFRACTIONr_angle_other_deg0.95733873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49623.025119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27315.039386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9081521
X-RAY DIFFRACTIONr_chiral_restr0.0880.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02505
X-RAY DIFFRACTIONr_mcbond_it3.95531367
X-RAY DIFFRACTIONr_mcbond_other1.2273551
X-RAY DIFFRACTIONr_mcangle_it5.88352217
X-RAY DIFFRACTIONr_scbond_it9.2648964
X-RAY DIFFRACTIONr_scangle_it11.26111951
LS refinement shellResolution: 2.3→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 62 -
Rwork0.252 1367 -
all-1429 -
obs--100 %
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)
11.48490.70831.14551.4378-0.53352.80680.2101-0.0875-0.00650.1898-0.00780.05540.2327-0.3694-0.20230.0662-0.0612-0.02010.11020.03920.0264-20.678231.45369.2838
20.57130.1018-0.06570.6216-0.11231.22950.00870.0556-0.0383-0.00070.05010.0419-0.04390.0948-0.05880.01830.0141-0.00170.0584-0.0050.01-2.674144.5461-1.8646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 123
2X-RAY DIFFRACTION2A124 - 305

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