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- PDB-3cbl: Crystal structure of human feline sarcoma viral oncogene homologu... -

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Basic information

Entry
Database: PDB / ID: 3cbl
TitleCrystal structure of human feline sarcoma viral oncogene homologue (v-FES) in complex with staurosporine and a consensus peptide
Components
  • Proto-oncogene tyrosine-protein kinase Fes/Fps
  • Synthetic peptidePeptide synthesis
KeywordsTRANSFERASE / FES / v-fes / Fujinami / avian sarcoma / viral / oncogene / feline sarcoma virus / SGC / Structural Genomics Consortium / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Proto-oncogene / SH2 domain / Tyrosine-protein kinase
Function / homology
Function and homology information


positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cellular response to vitamin D / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle ...positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cellular response to vitamin D / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle / myoblast proliferation / cardiac muscle cell proliferation / immunoglobulin receptor binding / regulation of cell differentiation / Sema3A PAK dependent Axon repulsion / regulation of cell adhesion / positive regulation of microtubule polymerization / phosphatidylinositol binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / microtubule cytoskeleton / chemotaxis / regulation of cell population proliferation / regulation of cell shape / cytoplasmic vesicle / microtubule binding / protein tyrosine kinase activity / protein autophosphorylation / cell adhesion / focal adhesion / Golgi apparatus / ATP binding / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / SHC Adaptor Protein ...Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
STAUROSPORINE / Tyrosine-protein kinase Fes/Fps
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsFilippakopoulos, P. / Salah, E. / Cooper, C. / Picaud, S.S. / Elkins, J.M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. ...Filippakopoulos, P. / Salah, E. / Cooper, C. / Picaud, S.S. / Elkins, J.M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural Coupling of SH2-Kinase Domains Links Fes and Abl Substrate Recognition and Kinase Activation
Authors: Filippakopoulos, P. / Kofler, M. / Hantschel, O. / Gish, G.D. / Grebien, F. / Salah, E. / Neudecker, P. / Kay, L.E. / Turk, B.E. / Superti-Furga, G. / Pawson, T. / Knapp, S.
History
DepositionFeb 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 tyrosine-protein kinase Fes/Fps
B: Synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8075
Polymers43,4082
Non-polymers1,4003
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-2.2 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.679, 77.178, 149.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE BIOLOGICAL UNIT IS A MONOMERIC COMPLEX BETWEEN PROTEIN (CHAIN A) AND THE CONSENSUS PEPTIDE (CHAIN B).

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Fes/Fps / C-Fes


Mass: 42758.043 Da / Num. of mol.: 1 / Fragment: Residues 448-822
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FES, FPS / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-Yop-PPase
References: UniProt: P07332, non-specific protein-tyrosine kinase
#2: Protein/peptide Synthetic peptide / Peptide synthesis


Mass: 649.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.1M Na Malate, pH 7.5, 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: 1.54178 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 42677 / Num. obs: 42378 / % possible obs: 99.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 12.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2 / Num. unique all: 6133 / Rsym value: 0.541 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å37.31 Å
Translation3 Å37.31 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BKB

3bkb


Resolution: 1.75→38.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.401 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2141 5.1 %RANDOM
Rwork0.18 ---
all0.183 42304 --
obs0.183 42304 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.409 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 105 328 3255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223060
X-RAY DIFFRACTIONr_bond_other_d0.0010.022060
X-RAY DIFFRACTIONr_angle_refined_deg1.5912.0314185
X-RAY DIFFRACTIONr_angle_other_deg1.2913.0044973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46123.984128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79715503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7491518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
X-RAY DIFFRACTIONr_mcbond_it2.93431815
X-RAY DIFFRACTIONr_mcbond_other0.9483726
X-RAY DIFFRACTIONr_mcangle_it4.35252934
X-RAY DIFFRACTIONr_scbond_it6.89971245
X-RAY DIFFRACTIONr_scangle_it8.936111249
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 168 -
Rwork0.231 2943 -
all-3111 -
obs--99.97 %
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)
13.2562-1.58222.91074.2172-3.149512.03590.63180.1669-0.5638-0.1658-0.18570.15731.69630.4477-0.44610.37440.0674-0.1361-0.0159-0.07810.222812.868-2.647-1.155
22.78630.7144-0.03221.53640.08632.4488-0.02810.2684-0.4994-0.11440.0945-0.13820.3645-0.1003-0.0664-0.0972-0.01560.0071-0.0696-0.0521-0.04217.23511.2438.254
31.1486-0.0135-0.54891.26940.67071.99860.0236-0.1233-0.02260.1739-0.0340.03850.06260.03550.0104-0.1483-0.0088-0.0045-0.14430.0085-0.126210.50123.90931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA446 - 5331 - 88
2X-RAY DIFFRACTION2AA534 - 59489 - 149
3X-RAY DIFFRACTION3AA595 - 821150 - 376

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