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- PDB-7z89: Sam68 -

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Basic information

Entry
Database: PDB / ID: 7z89
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: 2.76 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 16, 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 ...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 1.3Oct 9, 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)28,29821
Polymers26,9522
Non-polymers1,34619
Water37821
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)28,70726
Polymers26,9522
Non-polymers1,75524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6870 Å2
ΔGint-22 kcal/mol
Surface area15180 Å2
2
BBB: Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)27,88916
Polymers26,9522
Non-polymers93714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4300 Å2
ΔGint-29 kcal/mol
Surface area14810 Å2
Unit cell
Length a, b, c (Å)97.778, 97.500, 81.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 144 - 261 / 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

#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: 13475.904 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
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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

CrystalDensity Matthews: 4.57 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.8 M ammonium sulfate, 0.1 M sodium iodide

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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 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.76→48.937 Å / Num. obs: 19107 / % possible obs: 94 % / Redundancy: 3.8 % / CC1/2: 0.999 / Net I/σ(I): 14.5
Reflection shellResolution: 2.76→2.86 Å / Num. unique obs: 1894 / CC1/2: 0.483

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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: 2.76→48.937 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.838 / SU ML: 0.181 / Cross valid method: FREE R-VALUE / ESU R: 0.253 / ESU R Free: 0.225 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2358 942 4.93 %
Rwork0.1992 18165 -
all0.201 --
obs-19107 91.976 %
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: 92.094 Å2
Baniso -1Baniso -2Baniso -3
1-0.564 Å2-0 Å2-0 Å2
2---5.466 Å20 Å2
3---4.902 Å2
Refinement stepCycle: LAST / Resolution: 2.76→48.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 76 21 1981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121981
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.6572624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96323.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.4915382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.855158
X-RAY DIFFRACTIONr_chiral_restr0.1530.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021428
X-RAY DIFFRACTIONr_nbd_refined0.2440.2786
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21268
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.252
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.8140.26
X-RAY DIFFRACTIONr_mcbond_it8.7498.643942
X-RAY DIFFRACTIONr_mcangle_it10.80212.9221174
X-RAY DIFFRACTIONr_scbond_it12.4339.5181039
X-RAY DIFFRACTIONr_scangle_it16.25913.851450
X-RAY DIFFRACTIONr_lrange_it17.657163.2417390
X-RAY DIFFRACTIONr_ncsr_local_group_10.0530.053645
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.0530.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.0530.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.8320.402800.4721275X-RAY DIFFRACTION90.0931
2.832-2.9090.383630.4321338X-RAY DIFFRACTION94.9187
2.909-2.9930.454550.4261287X-RAY DIFFRACTION94.841
2.993-3.0850.404570.381260X-RAY DIFFRACTION94.8847
3.085-3.1870.364620.2941209X-RAY DIFFRACTION93.9394
3.187-3.2980.306590.2451164X-RAY DIFFRACTION93.2876
3.298-3.4230.249490.2211138X-RAY DIFFRACTION93.7599
3.423-3.5620.209440.2081082X-RAY DIFFRACTION92.5226
3.562-3.720.225840.1821003X-RAY DIFFRACTION92.5106
3.72-3.9020.204790.172959X-RAY DIFFRACTION91.6152
3.902-4.1120.195430.162948X-RAY DIFFRACTION92.5303
4.112-4.3610.149390.16874X-RAY DIFFRACTION91.9436
4.361-4.6620.204410.149836X-RAY DIFFRACTION90.8808
4.662-5.0340.21440.149768X-RAY DIFFRACTION91.0314
5.034-5.5130.211200.17733X-RAY DIFFRACTION89.5363
5.513-6.1620.329350.201638X-RAY DIFFRACTION88.5526
6.162-7.110.277210.209572X-RAY DIFFRACTION87.9822
7.11-8.6970.259320.168481X-RAY DIFFRACTION88.4483
8.697-12.2510.162190.156388X-RAY DIFFRACTION86.2288
12.251-48.9370.271160.248212X-RAY DIFFRACTION79.4425

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