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- PDB-7zam: Sam68 -

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Basic information

Entry
Database: PDB / ID: 7zam
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 / molecular function inhibitor activity / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / positive regulation of translational initiation ...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 / molecular function inhibitor activity / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / positive regulation of translational initiation / signaling adaptor activity / SH2 domain binding / protein tyrosine kinase binding / G1/S transition of mitotic cell cycle / SH3 domain binding / G2/M transition of mitotic cell cycle / mRNA processing / T cell receptor signaling pathway / spermatogenesis / regulation of apoptotic process / regulation of cell cycle / protein domain specific binding / negative regulation of DNA-templated transcription / mRNA binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm / cytosol
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: 2.79 Å
AuthorsNadal, M. / Fuentes-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 1.1Feb 8, 2023Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.2Apr 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Feb 7, 2024Group: 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_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,44922
Polymers26,9802
Non-polymers1,46920
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-31 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.459, 138.701, 82.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 143 - 260 / Label seq-ID: 1 - 118

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AAABBB

#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.: 2
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 , 5 types, 49 molecules

#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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

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: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.79→97.99 Å / Num. obs: 20122 / % possible obs: 99.7 % / Redundancy: 4.9 % / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shellResolution: 2.79→2.94 Å / Num. unique obs: 14029 / CC1/2: 0.693

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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: 2.79→97.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.585 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.223 / ESU R Free: 0.197 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2145 1002 4.983 %
Rwork0.1859 19108 -
all0.187 --
obs-20110 99.574 %
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: 87.623 Å2
Baniso -1Baniso -2Baniso -3
1--5.68 Å2-0 Å2-0 Å2
2--4.332 Å2-0 Å2
3---1.348 Å2
Refinement stepCycle: LAST / Resolution: 2.79→97.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 78 29 1991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121984
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.6552625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15623.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.23115384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.251158
X-RAY DIFFRACTIONr_chiral_restr0.1590.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021412
X-RAY DIFFRACTIONr_nbd_refined0.2330.2814
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21269
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.247
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.235
X-RAY DIFFRACTIONr_mcbond_it8.4378.036942
X-RAY DIFFRACTIONr_mcangle_it10.72612.0311174
X-RAY DIFFRACTIONr_scbond_it13.1399.1931042
X-RAY DIFFRACTIONr_scangle_it17.36613.231451
X-RAY DIFFRACTIONr_lrange_it18.284152.6687444
X-RAY DIFFRACTIONr_ncsr_local_group_10.0420.053657
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.042160.05011
12BBBX-RAY DIFFRACTIONLocal ncs0.042160.05011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.8580.417720.4071377X-RAY DIFFRACTION99.8622
2.858-2.9360.372670.391346X-RAY DIFFRACTION99.5772
2.936-3.0220.402710.3951319X-RAY DIFFRACTION99.7846
3.022-3.1140.361830.3331290X-RAY DIFFRACTION99.8545
3.114-3.2160.351550.2821259X-RAY DIFFRACTION99.7722
3.216-3.3290.296690.2551192X-RAY DIFFRACTION99.7627
3.329-3.4550.258650.2111171X-RAY DIFFRACTION99.7579
3.455-3.5960.185470.1731145X-RAY DIFFRACTION99.4992
3.596-3.7550.197530.1591087X-RAY DIFFRACTION99.7375
3.755-3.9380.175590.1531023X-RAY DIFFRACTION99.9077
3.938-4.1510.169520.148989X-RAY DIFFRACTION99.7126
4.151-4.4020.149350.15944X-RAY DIFFRACTION99.5931
4.402-4.7060.176510.14882X-RAY DIFFRACTION99.1498
4.706-5.0820.144450.129818X-RAY DIFFRACTION99.3096
5.082-5.5650.227400.14774X-RAY DIFFRACTION99.3895
5.565-6.2190.206450.177667X-RAY DIFFRACTION99.3027
6.219-7.1770.231250.184629X-RAY DIFFRACTION99.3921
7.177-8.7780.206410.161516X-RAY DIFFRACTION99.1103
8.778-12.3640.155220.158419X-RAY DIFFRACTION98.6577
12.364-97.990.3350.268261X-RAY DIFFRACTION97.0803

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