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- PDB-4esr: Molecular and Structural Characterization of the SH3 Domain of AH... -

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Basic information

Entry
Database: PDB / ID: 4esr
TitleMolecular and Structural Characterization of the SH3 Domain of AHI-1 in Regulation of Cellular Resistance of BCR-ABL+ Chronic Myeloid Leukemia Cells to Tyrosine Kinase Inhibitors
ComponentsJouberinAHI1
KeywordsPROTEIN BINDING / AHI-1 / AHI1 / AHI-1 SH3 domain / SH3 domain / Dynamin-2 / Chronic myeloid leukemia
Function / homology
Function and homology information


positive regulation of polarized epithelial cell differentiation / cloaca development / pronephric nephron tubule morphogenesis / pronephric duct morphogenesis / MKS complex / Kupffer's vesicle development / specification of axis polarity / ciliary basal body-plasma membrane docking / otic vesicle development / protein localization => GO:0008104 ...positive regulation of polarized epithelial cell differentiation / cloaca development / pronephric nephron tubule morphogenesis / pronephric duct morphogenesis / MKS complex / Kupffer's vesicle development / specification of axis polarity / ciliary basal body-plasma membrane docking / otic vesicle development / protein localization => GO:0008104 / photoreceptor cell outer segment organization / regulation of behavior / retina layer formation / left/right axis specification / morphogenesis of a polarized epithelium / hindbrain development / non-motile cilium / heart looping / positive regulation of receptor internalization / cilium assembly / vesicle-mediated transport / Anchoring of the basal body to the plasma membrane / centriole / ciliary basal body / central nervous system development / adherens junction / cilium / cell surface receptor protein tyrosine kinase signaling pathway / cell-cell junction / centrosome / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / identical protein binding / cytosol
Similarity search - Function
Jouberin, SH3 domain / : / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll ...Jouberin, SH3 domain / : / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Jouberin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.53 Å
AuthorsVan Petegem, X.F. / Liu, P.X. / Lobo, P. / Jiang, X.
CitationJournal: Proteomics / Year: 2012
Title: Molecular and structural characterization of the SH3 domain of AHI-1 in regulation of cellular resistance of BCR-ABL(+) chronic myeloid leukemia cells to tyrosine kinase inhibitors.
Authors: Liu, X. / Chen, M. / Lobo, P. / An, J. / Grace Cheng, S.W. / Moradian, A. / Morin, G.B. / Van Petegem, F. / Jiang, X.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Nov 15, 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Jouberin
B: Jouberin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2285
Polymers15,9092
Non-polymers3183
Water2,990166
1
A: Jouberin


Theoretical massNumber of molelcules
Total (without water)7,9551
Polymers7,9551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Jouberin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2734
Polymers7,9551
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.142, 68.142, 98.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1297-

HOH

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Components

#1: Protein Jouberin / AHI1 / Abelson helper integration site 1 protein homolog / AHI-1


Mass: 7954.657 Da / Num. of mol.: 2 / Fragment: Ahi-1 SH3 domain (unp residues 1048-1116)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AHI1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N157
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 0.2M ammonium sulphate, 10mM sodium bromide, 0.1M sodium acetate and 7% PEG200 MME, pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2010
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. all: 35758 / Num. obs: 34864 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 14.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 26.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.53-1.5613.30.208191.8
1.56-1.5814.90.187196.8
1.58-1.6214.90.163197
1.62-1.6514.90.142197.4
1.65-1.6814.90.124197.5
1.68-1.7214.90.104197.4
1.72-1.7714.90.093197.6
1.77-1.8114.90.085197.8
1.81-1.8714.80.075198
1.87-1.9314.80.071197.9
1.93-214.70.067198.3
2-2.0814.30.062198.5
2.08-2.1714.40.059198.5
2.17-2.2914.50.053198.5
2.29-2.4314.50.048198.9
2.43-2.6214.30.049199
2.62-2.8813.90.049199.3
2.88-3.313.80.045199
3.3-4.1513.30.045197.8
4.15-5011.90.045193.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementResolution: 1.53→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.023 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13907 1733 5 %RANDOM
Rwork0.12432 ---
obs0.12503 33024 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.679 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å2-0 Å2
2--0.84 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.53→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 21 166 1231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221182
X-RAY DIFFRACTIONr_bond_other_d0.0040.02777
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.9431619
X-RAY DIFFRACTIONr_angle_other_deg1.29531890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33224.60363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34615168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.94155
X-RAY DIFFRACTIONr_chiral_restr0.1490.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211363
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02254
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0831.5698
X-RAY DIFFRACTIONr_mcbond_other1.041.5278
X-RAY DIFFRACTIONr_mcangle_it4.39321133
X-RAY DIFFRACTIONr_scbond_it6.1673484
X-RAY DIFFRACTIONr_scangle_it8.7934.5482
X-RAY DIFFRACTIONr_rigid_bond_restr2.66231959
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.531→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.116 110 -
Rwork0.101 2295 -
obs--93.07 %

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