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- PDB-7z9a: Sam68 -

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Basic information

Entry
Database: PDB / ID: 7z9a
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
NITRATE ION / S-1,2-PROPANEDIOL / KH domain-containing, RNA-binding, signal transduction-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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 20, 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
Revision 1.3Nov 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

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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)14,13811
Polymers13,4901
Non-polymers64810
Water362
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


Theoretical massNumber of molelcules
Total (without water)28,27722
Polymers26,9802
Non-polymers1,29720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x,-y,-z-1/21
Buried area5580 Å2
ΔGint-19 kcal/mol
Surface area14650 Å2
Unit cell
Length a, b, c (Å)96.984, 96.984, 83.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#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: 13489.932 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
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.57→43.41 Å / Num. obs: 13222 / % possible obs: 99.7 % / Redundancy: 8.3 % / CC1/2: 0.999 / Net I/σ(I): 16
Reflection shellResolution: 2.57→2.68 Å / Num. unique obs: 1593 / CC1/2: 0.527

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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: 2.57→43.41 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.538 / SU ML: 0.147 / Cross valid method: FREE R-VALUE / ESU R: 0.178 / ESU R Free: 0.168 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2279 652 4.957 %
Rwork0.1999 12500 -
all0.201 --
obs-13152 99.163 %
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: 80.939 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å20 Å2
2---2.3 Å20 Å2
3---4.599 Å2
Refinement stepCycle: LAST / Resolution: 2.57→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 42 2 987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.012995
X-RAY DIFFRACTIONr_angle_refined_deg2.111.6481319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8435117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9923.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.4215192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.75154
X-RAY DIFFRACTIONr_chiral_restr0.1640.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02738
X-RAY DIFFRACTIONr_nbd_refined0.2320.2399
X-RAY DIFFRACTIONr_nbtor_refined0.3280.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.226
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.6640.24
X-RAY DIFFRACTIONr_mcbond_it8.1487.21471
X-RAY DIFFRACTIONr_mcangle_it10.4310.796587
X-RAY DIFFRACTIONr_scbond_it13.198.608524
X-RAY DIFFRACTIONr_scangle_it17.36712.18732
X-RAY DIFFRACTIONr_lrange_it18.768138.4373738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.6370.513420.445927X-RAY DIFFRACTION99.8969
2.637-2.7090.374590.41871X-RAY DIFFRACTION100
2.709-2.7870.343420.411864X-RAY DIFFRACTION99.7797
2.787-2.8730.351430.347827X-RAY DIFFRACTION99.7706
2.873-2.9670.24500.287811X-RAY DIFFRACTION99.884
2.967-3.0710.302430.247786X-RAY DIFFRACTION100
3.071-3.1870.243550.23753X-RAY DIFFRACTION99.8764
3.187-3.3170.378290.221731X-RAY DIFFRACTION100
3.317-3.4640.228330.227734X-RAY DIFFRACTION100
3.464-3.6330.25350.217650X-RAY DIFFRACTION97.1631
3.633-3.8290.299290.237600X-RAY DIFFRACTION92.5
3.829-4.0610.177330.169611X-RAY DIFFRACTION99.5363
4.061-4.3410.212300.145583X-RAY DIFFRACTION99.8371
4.341-4.6880.152280.136537X-RAY DIFFRACTION99.4718
4.688-5.1350.162290.121511X-RAY DIFFRACTION99.2647
5.135-5.7390.173200.153466X-RAY DIFFRACTION99.1837
5.739-6.6230.26120.199414X-RAY DIFFRACTION99.5327
6.623-8.1010.214170.188362X-RAY DIFFRACTION98.9556
8.101-11.4170.136130.153289X-RAY DIFFRACTION99.67
11.417-43.410.293100.246173X-RAY DIFFRACTION94.3299

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