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- PDB-7zab: Sam68 -

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Basic information

Entry
Database: PDB / ID: 7zab
TitleSam68
ComponentsIsoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
KeywordsRNA BINDING PROTEIN / Spinal Muscular Atrophy
Function / homology
Function and homology information


regulation of RNA export from nucleus / Grb2-Sos complex / PTK6 Regulates Proteins Involved in RNA Processing / positive regulation of RNA export from nucleus / poly(A) binding / poly(U) RNA binding / regulation of alternative mRNA splicing, via spliceosome / positive regulation of translational initiation / signaling adaptor activity / protein tyrosine kinase binding ...regulation of RNA export from nucleus / Grb2-Sos complex / PTK6 Regulates Proteins Involved in RNA Processing / positive regulation of RNA export from nucleus / poly(A) binding / poly(U) RNA binding / regulation of alternative mRNA splicing, via spliceosome / positive regulation of translational initiation / signaling adaptor activity / protein tyrosine kinase binding / SH2 domain binding / G1/S transition of mitotic cell cycle / mRNA processing / SH3 domain binding / G2/M transition of mitotic cell cycle / T cell receptor signaling pathway / spermatogenesis / protein domain specific binding / mRNA binding / negative regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
IODIDE ION / : / KH domain-containing, RNA-binding, signal transduction-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsNadal, M. / Puestes-Prior, P.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Protein Sci. / Year: 2023
Title: Structure and function analysis of Sam68 and hnRNP A1 synergy in the exclusion of exon 7 from SMN2 transcripts.
Authors: Nadal, M. / Anton, R. / Dorca-Arevalo, J. / Estebanez-Perpina, E. / Tizzano, E.F. / Fuentes-Prior, P.
History
DepositionMar 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,39115
Polymers13,4901
Non-polymers90114
Water23413
1
AAA: Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules

AAA: Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 28.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)28,78230
Polymers26,9802
Non-polymers1,80228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_564x,-y+1,-z-1/21
Buried area7310 Å2
ΔGint-100 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.842, 97.842, 82.508
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11AAA-1001-

IOD

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1 / GAP-associated tyrosine phosphoprotein p62 / Src-associated in mitosis 68 kDa protein / Sam68 / p21 ...GAP-associated tyrosine phosphoprotein p62 / Src-associated in mitosis 68 kDa protein / Sam68 / p21 Ras GTPase-activating protein-associated p62 / p68


Mass: 13489.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHDRBS1, SAM68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07666

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Non-polymers , 8 types, 27 molecules

#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.46→48.92 Å / Num. obs: 15064 / % possible obs: 99.9 % / Redundancy: 8.5 % / CC1/2: 1 / Net I/σ(I): 26.5
Reflection shellResolution: 2.46→2.56 Å / Num. unique obs: 1673 / CC1/2: 0.531

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMO

5emo


Resolution: 2.46→43.795 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.962 / SU B: 7.011 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.149 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2232 776 5.156 %
Rwork0.2061 14275 -
all0.207 --
obs-15051 99.728 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 84.273 Å2
Baniso -1Baniso -2Baniso -3
1--1.953 Å20 Å20 Å2
2---1.953 Å20 Å2
3---3.905 Å2
Refinement stepCycle: LAST / Resolution: 2.46→43.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 47 13 1002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121001
X-RAY DIFFRACTIONr_angle_refined_deg2.1111.6561324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61723.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95915195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.07154
X-RAY DIFFRACTIONr_chiral_restr0.1440.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02706
X-RAY DIFFRACTIONr_nbd_refined0.2380.2385
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0760.227
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3330.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.7450.23
X-RAY DIFFRACTIONr_mcbond_it7.9897.711473
X-RAY DIFFRACTIONr_mcangle_it10.21511.517589
X-RAY DIFFRACTIONr_scbond_it13.8298.84528
X-RAY DIFFRACTIONr_scangle_it16.24112.648735
X-RAY DIFFRACTIONr_lrange_it16.711146.7153713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.5240.412580.4831018X-RAY DIFFRACTION99.722
2.524-2.5930.489490.4821016X-RAY DIFFRACTION99.7191
2.593-2.6680.477760.439970X-RAY DIFFRACTION100
2.668-2.750.425440.348943X-RAY DIFFRACTION100
2.75-2.8410.311500.324938X-RAY DIFFRACTION100
2.841-2.940.269480.261888X-RAY DIFFRACTION99.7868
2.94-3.0510.289520.252877X-RAY DIFFRACTION100
3.051-3.1750.351430.241835X-RAY DIFFRACTION100
3.175-3.3160.264420.215801X-RAY DIFFRACTION100
3.316-3.4780.253440.221777X-RAY DIFFRACTION100
3.478-3.6660.256330.205740X-RAY DIFFRACTION100
3.666-3.8880.224360.192705X-RAY DIFFRACTION99.7308
3.888-4.1560.174430.183651X-RAY DIFFRACTION99.4269
4.156-4.4880.167270.161622X-RAY DIFFRACTION99.3874
4.488-4.9160.158330.143571X-RAY DIFFRACTION99.3421
4.916-5.4940.228210.146532X-RAY DIFFRACTION100
5.494-6.3410.256300.205463X-RAY DIFFRACTION99.596
6.341-7.7580.179210.191398X-RAY DIFFRACTION98.8208
7.758-10.9370.129150.173331X-RAY DIFFRACTION99.1404
10.937-43.7950.226110.276199X-RAY DIFFRACTION95.8904

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