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- PDB-2o88: Crystal structure of the N114A mutant of ABL-SH3 domain complexed... -

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Basic information

Entry
Database: PDB / ID: 2o88
TitleCrystal structure of the N114A mutant of ABL-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions
Components
  • P41 peptide
  • Proto-oncogene tyrosine-protein kinase ABL1
KeywordsSIGNALING PROTEIN / SH3 domain High affinity peptide complex
Function / homology
Function and homology information


: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process ...: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / transitional one stage B cell differentiation / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / cerebellum morphogenesis / neuroepithelial cell differentiation / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / microspike assembly / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / mitochondrial depolarization / regulation of cell motility / bubble DNA binding / positive regulation of establishment of T cell polarity / cellular response to dopamine / activated T cell proliferation / positive regulation of blood vessel branching / proline-rich region binding / negative regulation of mitotic cell cycle / regulation of Cdc42 protein signal transduction / regulation of hematopoietic stem cell differentiation / mitogen-activated protein kinase binding / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of dendrite development / syntaxin binding / peptidyl-tyrosine autophosphorylation / positive regulation of peptidyl-tyrosine phosphorylation / regulation of T cell differentiation / regulation of axon extension / alpha-beta T cell differentiation / negative regulation of cell-cell adhesion / neuromuscular process controlling balance / HDR through Single Strand Annealing (SSA) / Myogenesis / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Bergmann glial cell differentiation / regulation of microtubule polymerization / negative regulation of long-term synaptic potentiation / myoblast proliferation / negative regulation of cellular senescence / positive regulation of vasoconstriction / actin monomer binding / associative learning / positive regulation of focal adhesion assembly / negative regulation of BMP signaling pathway / cardiac muscle cell proliferation / RHO GTPases Activate WASPs and WAVEs / canonical NF-kappaB signal transduction / ephrin receptor signaling pathway / BMP signaling pathway / cellular response to transforming growth factor beta stimulus / negative regulation of endothelial cell apoptotic process / positive regulation of T cell migration / endothelial cell migration / negative regulation of double-strand break repair via homologous recombination / regulation of cell adhesion / mismatch repair / spleen development / ephrin receptor binding / four-way junction DNA binding / positive regulation of stress fiber assembly / signal transduction in response to DNA damage / ruffle / ERK1 and ERK2 cascade / phosphotyrosine residue binding / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / positive regulation of mitotic cell cycle / positive regulation of interleukin-2 production / SH2 domain binding / peptidyl-tyrosine phosphorylation / thymus development / response to endoplasmic reticulum stress / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of release of sequestered calcium ion into cytosol / protein kinase C binding / integrin-mediated signaling pathway / B cell receptor signaling pathway
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 ...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 / SH3 type barrels. / SH2 domain / Src homology 3 domains / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / Resolution: 1.75 Å
AuthorsCamara-Artigas, A.
CitationJournal: 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
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / struct_biol / 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
Revision 1.5Aug 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.end_auth_comp_id
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)15,0236
Polymers14,8304
Non-polymers1922
Water1,20767
1
A: Proto-oncogene tyrosine-protein kinase ABL1
C: P41 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5113
Polymers7,4152
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-26 kcal/mol
Surface area4360 Å2
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase ABL1
D: P41 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5113
Polymers7,4152
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-26 kcal/mol
Surface area4050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.170, 50.093, 56.431
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:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUVALVALAA65 - 1192 - 56
21LEULEUVALVALBB65 - 1192 - 56
12ALAALAPROPROCC1 - 102 - 11
22ALAALAPROPRODD1 - 102 - 11

NCS ensembles :
ID
1
2
DetailsThe biological assembly is formed by the SH3 domain (chain A/B) complexed with the acetylated peptide p41 (chain C/D)

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Components

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


Mass: 6380.054 Da / Num. of mol.: 2 / Fragment: SH3 domain, residues 64-121 / Mutation: N114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: pBAT4 / Gene: ABL1, ABL, JTK7 / Species (production host): Escherichia coli / 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 / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 293 K / Method: capillary counter diffusion / pH: 7
Details: Ammoniun sulphate, pH 7, Capillary counter diffusion, temperature 293K

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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: Feb 2, 2006 / Details: Bruker Microstar micro-focus (Montel Optics)
RadiationMonochromator: Bruker Microstar micro-focus (Montel Optics) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 13236 / Num. obs: 13236 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 19.272 Å2 / Rmerge(I) obs: 0.0682 / Rsym value: 0.0415 / Net I/σ(I): 16.43
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 2.79 % / Rmerge(I) obs: 0.2453 / Mean I/σ(I) obs: 4.41 / Num. unique all: 1638 / Rsym value: 0.219 / % possible all: 75.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.96 Å36.64 Å
Translation1.96 Å36.64 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BBZ

1bbz


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.793 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 647 4.9 %RANDOM
Rwork0.169 ---
obs0.171 13178 92.18 %-
all-12531 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 10 67 1114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221087
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.9771497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5435134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41525.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98915144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.692152
X-RAY DIFFRACTIONr_chiral_restr0.1120.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02858
X-RAY DIFFRACTIONr_nbd_refined0.2060.2359
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2728
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.28
X-RAY DIFFRACTIONr_mcbond_it1.0671.5701
X-RAY DIFFRACTIONr_mcangle_it1.5821110
X-RAY DIFFRACTIONr_scbond_it2.3613458
X-RAY DIFFRACTIONr_scangle_it3.4434.5385
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A428MEDIUM POSITIONAL0.320.5
1A428MEDIUM THERMAL0.882
2C75MEDIUM POSITIONAL0.090.5
2C75MEDIUM THERMAL0.492
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 39 -
Rwork0.206 745 -
obs-784 74.6 %
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)
110.57775.43350.558215.0571.62935.19120.2108-0.05370.2719-0.10490.0164-0.1308-0.16480.0708-0.2273-0.09010.01170.0185-0.1067-0.0438-0.2088-4.4397-10.128713.5651
248.022410.9001-0.52036.93190.41242.2929-0.11790.0138-0.6152-0.20620.1651-0.11880.17540.0346-0.0472-0.05530.0045-0.0155-0.1371-0.0264-0.2044-9.2682-14.39119.9087
335.5955-1.1015-22.65577.08154.245422.0563-0.56770.14631.61640.01410.52351.0688-0.09250.37510.0441-0.0556-0.01140.0008-0.08890.10560.223-10.1293-2.681212.0597
425.3671-2.92966.012810.768110.18941.28180.4464-1.85030.90961.1413-0.39080.8194-0.1489-0.8227-0.0555-0.0118-0.04620.048-0.0573-0.0926-0.0345-16.5271-9.613521.3094
59.8854.01151.00484.0983-0.51443.8152-0.10350.75690.6059-0.16110.33810.0412-0.33940.252-0.2346-0.0709-0.00830.0111-0.10460.0095-0.1119-7.9996-7.167112.2045
612.0372-3.3993-1.44024.80291.74417.16840.18460.04030.03480.0249-0.222-0.06630.0141-0.01850.0374-0.0941-0.0421-0.0106-0.216-0.0162-0.1377-27.6095-3.53020.9099
726.87153.9249-5.32751.5272-1.405821.81630.0417-0.2506-0.58050.2184-0.32990.24370.5753-0.73750.2882-0.0532-0.0486-0.0053-0.0997-0.0324-0.0679-34.1139-6.8422.5733
817.859712.3674-3.737614.53821.82824.7684-0.6034-0.2560.08420.24840.28530.0928-0.2949-0.10540.31810.00430.0057-0.0413-0.0930.0142-0.1136-24.4538-2.268910.6468
915.5422-5.35863.75924.1529-0.228210.45640.1257-0.17821.2270.103-0.2405-0.0016-0.69170.64930.1148-0.0737-0.04630.0085-0.1112-0.0201-0.0602-19.75124.96523.5082
107.3843-3.69850.57296.3706-2.0853.60190.0359-0.2128-0.27450.3101-0.14010.26590.1505-0.07340.1042-0.0692-0.02270.0063-0.1536-0.0139-0.1833-27.0019-3.75594.888
116.5322-7.71126.973210.9356-8.682112.038-0.1506-0.010.19850.3946-0.3414-0.4638-0.02910.72840.492-0.0397-0.0396-0.0004-0.09890.068-0.0641-12.6057-17.435720.3005
1215.6762-4.28440.64048.6992-4.51797.09210.25990.23460.0810.2140.0660.4037-0.2438-0.2469-0.3259-0.011-0.00810.0222-0.07720.0568-0.1117-23.30614.5074-4.7948
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA64 - 741 - 11
22AA75 - 8612 - 23
33AA87 - 9324 - 30
44AA94 - 10031 - 37
55AA101 - 12138 - 58
66BB64 - 811 - 18
77BB82 - 8719 - 24
88BB88 - 9325 - 30
99BB94 - 10131 - 38
1010BB102 - 11939 - 56
1111CC1 - 102 - 11
1212DD1 - 102 - 11

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