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- PDB-3eg1: Crystal structure of the N114Q mutant of ABL-SH3 domain complexed... -

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Basic information

Entry
Database: PDB / ID: 3eg1
TitleCrystal structure of the N114Q mutant of ABL-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions
Components
  • Proto-oncogene tyrosine-protein kinase ABL1
  • p41 peptide
KeywordsTransferase/Signaling protein / beta / SH3 domain / ATP-binding / Cell adhesion / Cytoskeleton / Kinase / Lipoprotein / Magnesium / Manganese / Metal-binding / Myristate / Nucleotide-binding / Nucleus / Phosphoprotein / Proto-oncogene / SH2 domain / Transferase / Tyrosine-protein kinase / SIGNALING PROTEIN / Transferase-Signaling protein COMPLEX
Function / homology
Function and homology information


negative regulation of phospholipase C activity / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine ...negative regulation of phospholipase C activity / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of extracellular matrix organization / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / regulation of Cdc42 protein signal transduction / activated T cell proliferation / cellular response to dopamine / regulation of cell motility / regulation of axon extension / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / regulation of hematopoietic stem cell differentiation / syntaxin binding / cardiac muscle cell proliferation / HDR through Single Strand Annealing (SSA) / regulation of T cell differentiation / negative regulation of double-strand break repair via homologous recombination / positive regulation of cell migration involved in sprouting angiogenesis / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of cell-cell adhesion / Myogenesis / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / negative regulation of cellular senescence / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of long-term synaptic potentiation / Bergmann glial cell differentiation / associative learning / neuromuscular process controlling balance / regulation of endocytosis / actin monomer binding / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / mismatch repair / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / BMP signaling pathway / canonical NF-kappaB signal transduction / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / signal transduction in response to DNA damage / peptidyl-tyrosine autophosphorylation / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / ruffle / ERK1 and ERK2 cascade / cellular response to transforming growth factor beta stimulus / positive regulation of establishment of T cell polarity / positive regulation of interleukin-2 production / actin filament polymerization / SH2 domain binding / response to endoplasmic reticulum stress / phosphotyrosine residue binding / ephrin receptor binding / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / post-embryonic development / protein kinase C binding / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of endothelial cell migration / thymus development / regulation of autophagy / neural tube closure / integrin-mediated signaling pathway / establishment of localization in cell / regulation of actin cytoskeleton organization
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsCamara-Artigas, A.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.
Authors: Palencia, A. / Camara-Artigas, A. / Pisabarro, M.T. / Martinez, J.C. / Luque, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand
Authors: Camara-Artigas, A. / Palencia, A. / Martinez, J.C. / Luque, I. / Gavira, J.A. / Garcia-Ruiz, J.M.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_entity_src_syn / 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 / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase ABL1
B: Proto-oncogene tyrosine-protein kinase ABL1
C: p41 peptide
D: p41 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3106
Polymers16,1184
Non-polymers1922
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Proto-oncogene tyrosine-protein kinase ABL1
C: p41 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1553
Polymers8,0592
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-9 kcal/mol
Surface area4370 Å2
MethodPISA
3
B: Proto-oncogene tyrosine-protein kinase ABL1
D: p41 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1553
Polymers8,0592
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area3970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.996, 47.636, 55.662
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNTHRTHR5AA64 - 1046 - 46
211ASNASNTHRTHR5BB64 - 1046 - 46
121GLYGLYVALVAL5AA109 - 11951 - 61
221GLYGLYVALVAL5BB109 - 11951 - 61
112ACEACEPROPRO4CC0 - 101 - 11
212ACEACEPROPRO4DD0 - 101 - 11

NCS ensembles :
ID
1
2

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase ABL1 / p150 / c- ABL / Abelson murine leukemia viral oncogene homolog 1


Mass: 7023.720 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 60-121 / Mutation: N114Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: PBAT4 / Gene: ABL1, ABL, JTK7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P00519, non-specific protein-tyrosine kinase
#2: Protein/peptide p41 peptide


Mass: 1035.149 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The author states that the p41 peptide is a member of a group of peptide ligands designed to bind specifically the Abl-SH3 domain.
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 2M ammonium sulphate, 0.4 M NaCl, 0.1 M sodium citrate, 10% glycerol, pH 3.5, vapor diffusion, hanging drop, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 19, 2005 / Details: Montel Optics
RadiationMonochromator: BRUKER MICROSTAR MICRO-FOCUS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→47.636 Å / Num. all: 10944 / Num. obs: 10158 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 17.692 Å2 / Rmerge(I) obs: 0.0653 / Rsym value: 0.0653
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 1.26 % / Rmerge(I) obs: 0.2426 / Mean I/σ(I) obs: 3.49 / Num. unique all: 1123 / Rsym value: 0.2649 / % possible all: 72.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2o88

2o88


Resolution: 1.85→18 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 7.118 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 998 9.9 %RANDOM
Rwork0.185 ---
obs0.192 10098 92.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.1 Å2 / Biso mean: 16.612 Å2 / Biso min: 4.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.85→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 10 54 1109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221091
X-RAY DIFFRACTIONr_angle_refined_deg2.1061.9761500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55525.31947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55615147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.349152
X-RAY DIFFRACTIONr_chiral_restr0.1510.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02862
X-RAY DIFFRACTIONr_nbd_refined0.2280.2516
X-RAY DIFFRACTIONr_nbtor_refined0.3230.2746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.212
X-RAY DIFFRACTIONr_mcbond_it1.3121.5690
X-RAY DIFFRACTIONr_mcangle_it1.93421106
X-RAY DIFFRACTIONr_scbond_it2.8253466
X-RAY DIFFRACTIONr_scangle_it3.8494.5393
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A208MEDIUM POSITIONAL0.170.5
1A202LOOSE POSITIONAL0.615
1A208MEDIUM THERMAL0.882
1A202LOOSE THERMAL1.8510
2C72MEDIUM POSITIONAL0.170.5
2C72MEDIUM THERMAL0.842
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 58 -
Rwork0.202 474 -
all-532 -
obs--69.63 %
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)
18.7591-2.74810.89999.1644.20047.68770.3111-0.3111-0.29550.2099-0.0843-0.00080.39680.2691-0.2268-0.11430.0021-0.0304-0.06280.0067-0.1085-3.35168.5298-13.5566
223.4244-5.48050.77923.9011.1943.99620.0133-0.04570.49170.10980.0845-0.0456-0.02840.0051-0.0978-0.0977-0.00750.0329-0.0843-0.0016-0.0609-7.995612.5223-9.4656
319.9043-2.111210.13424.19536.555419.8202-0.2563-0.323-0.59230.25490.29650.28871.02820.3351-0.0402-0.05460.02340.0287-0.07630.05810.0755-11.15211.6543-13.4951
46.67994.62493.542619.19026.056320.56980.2340.4465-0.064-1.0319-0.38081.02440.3669-0.71310.1468-0.07570.0536-0.0696-0.04520.00480.0384-15.72289.7662-22.0531
524.2608-8.3338-7.38895.3694-4.33523.2022-0.7235-1.8988-0.14150.61720.7593-0.08140.58851.3116-0.0358-0.03250.0697-0.02090.05390.0028-0.0177-11.14736.0147-6.7159
68.2578-5.87391.70394.3163-1.65433.165-0.01570.0141-0.0074-0.1553-0.0385-0.18950.35790.37220.0542-0.0049-0.0060.0079-0.1157-0.0038-0.0757-5.02776.2936-16.9306
712.20382.4741-4.51117.805-1.5821.37560.18381.31170.4366-1.06040.2533-0.18320.2418-0.4253-0.437-0.02350.0305-0.06830.02820.0169-0.0304-31.88372.1533-9.3193
811.60074.80376.157713.17713.18617.08410.1534-0.260.5520.353-0.0034-0.12570.40040.5206-0.15-0.08830.03970.0233-0.0474-0.0765-0.0621-26.95513.76024.3758
932.93980.16016.11473.61960.32315.28940.1634-0.27830.3503-0.0492-0.25210.0674-0.25830.02340.0887-0.0768-0.00470.008-0.0857-0.0011-0.0404-26.72946.638-0.8088
1027.8752-24.3902-1.698230.3396-1.59578.2894-0.24140.1998-0.2677-0.21410.070.34640.4712-0.26010.1714-0.0434-0.0217-0.0207-0.0688-0.0022-0.0831-23.46611.8684-10.6803
116.4953-3.46930.9416.3868-2.02369.67650.43960.2826-0.2884-0.6262-0.4457-0.40780.88350.72050.0061-0.0630.0697-0.0161-0.0413-0.0013-0.0375-19.4207-4.2114-3.4429
127.09672.8609-1.22434.0949-2.31914.43360.18110.16050.3711-0.3058-0.23580.1538-0.0744-0.22440.0547-0.09710.0238-0.0087-0.0836-0.033-0.0742-26.25493.4366-4.8635
1312.98425.4948-5.42426.015-4.5267.280.15590.1025-0.0869-0.1054-0.2859-0.0994-0.510.22950.13-0.02430.0073-0.0301-0.0730.03890.0028-11.509516.6731-20.1805
142.14462.02862.68218.7831-3.86459.32450.2451-0.593-0.0448-0.0634-0.02770.33420.4587-0.3767-0.21740.00010.0694-0.021-0.04070.0296-0.0776-22.9282-4.11844.6118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A64 - 73
2X-RAY DIFFRACTION2A74 - 87
3X-RAY DIFFRACTION3A88 - 93
4X-RAY DIFFRACTION4A94 - 99
5X-RAY DIFFRACTION5A100 - 109
6X-RAY DIFFRACTION6A110 - 121
7X-RAY DIFFRACTION7B64 - 69
8X-RAY DIFFRACTION8B70 - 76
9X-RAY DIFFRACTION9B77 - 87
10X-RAY DIFFRACTION10B88 - 93
11X-RAY DIFFRACTION11B94 - 102
12X-RAY DIFFRACTION12B103 - 119
13X-RAY DIFFRACTION13C1 - 10
14X-RAY DIFFRACTION14D1 - 10

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