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- PDB-7zaf: Sam68 -

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Basic information

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


poly(A) binding / regulation of alternative mRNA splicing, via spliceosome / SH3 domain binding / mRNA processing / mRNA binding / nucleus / membrane / cytoplasm
Similarity search - Function
Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / 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: 2.71 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,19615
Polymers13,2561
Non-polymers94114
Water27015
1
AAA: KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)28,39230
Polymers26,5112
Non-polymers1,88128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_654-x+y+1,y,-z-1/21
Buried area5680 Å2
ΔGint-8 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.340, 135.340, 81.659
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11AAA-1001-

IOD

21AAA-1002-

CL

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein KH domain-containing, RNA-binding, signal transduction-associated protein 1


Mass: 13255.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: N338_08991 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A094KT80

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Non-polymers , 5 types, 29 molecules

#2: Chemical ChemComp-IOD / IODIDE ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.71→47.657 Å / Num. obs: 12475 / % possible obs: 100 % / Redundancy: 20.9 % / CC1/2: 0.999 / Net I/σ(I): 16.4
Reflection shellResolution: 2.71→2.84 Å / Num. unique obs: 1606 / CC1/2: 0.545

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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: 2.71→47.657 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.787 / SU ML: 0.164 / Cross valid method: FREE R-VALUE / ESU R: 0.192 / ESU R Free: 0.199 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2561 235 1.888 %
Rwork0.2026 12214 -
all0.204 --
obs-12449 99.944 %
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: 76.455 Å2
Baniso -1Baniso -2Baniso -3
1--0.372 Å2-0.186 Å2-0 Å2
2---0.372 Å20 Å2
3---1.207 Å2
Refinement stepCycle: LAST / Resolution: 2.71→47.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms929 0 51 15 995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.012986
X-RAY DIFFRACTIONr_angle_refined_deg2.4091.6621299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6845115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13123.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.07515188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.287154
X-RAY DIFFRACTIONr_chiral_restr0.2080.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02706
X-RAY DIFFRACTIONr_nbd_refined0.2480.2430
X-RAY DIFFRACTIONr_nbtor_refined0.3380.2624
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.233
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.24
X-RAY DIFFRACTIONr_mcbond_it7.6486.969463
X-RAY DIFFRACTIONr_mcangle_it10.29310.423577
X-RAY DIFFRACTIONr_scbond_it11.7758.018523
X-RAY DIFFRACTIONr_scangle_it15.93111.454722
X-RAY DIFFRACTIONr_lrange_it17.604132.9733731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.780.398160.382876X-RAY DIFFRACTION99.888
2.78-2.8570.406150.367865X-RAY DIFFRACTION100
2.857-2.9390.446140.338839X-RAY DIFFRACTION100
2.939-3.030.251160.322814X-RAY DIFFRACTION99.8797
3.03-3.1290.336190.288774X-RAY DIFFRACTION100
3.129-3.2390.292190.27764X-RAY DIFFRACTION100
3.239-3.3610.257140.245740X-RAY DIFFRACTION100
3.361-3.4980.259110.229723X-RAY DIFFRACTION100
3.498-3.6530.315120.2682X-RAY DIFFRACTION100
3.653-3.8320.236120.184661X-RAY DIFFRACTION100
3.832-4.0390.262100.186633X-RAY DIFFRACTION100
4.039-4.2830.141110.164601X-RAY DIFFRACTION100
4.283-4.5790.244140.157561X-RAY DIFFRACTION100
4.579-4.9450.26750.152534X-RAY DIFFRACTION100
4.945-5.4160.368140.157488X-RAY DIFFRACTION100
5.416-6.0530.237110.192449X-RAY DIFFRACTION100
6.053-6.9870.12750.187399X-RAY DIFFRACTION100
6.987-8.5490.148110.161350X-RAY DIFFRACTION100
8.549-12.0590.27330.148285X-RAY DIFFRACTION100
12.059-47.6570.53630.284176X-RAY DIFFRACTION97.2826

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