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- PDB-7z9b: Sam68 -

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Basic information

Entry
Database: PDB / ID: 7z9b
TitleSam68
ComponentsKH domain-containing, RNA-binding, signal transduction-associated protein 1
KeywordsRNA BINDING PROTEIN / Spinal Muscular Atrophy (SMA)
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: 3.333 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 ...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

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


Theoretical massNumber of molelcules
Total (without water)40,57912
Polymers39,7673
Non-polymers8129
Water1629
1
AAA: KH domain-containing, RNA-binding, signal transduction-associated protein 1
BBB: KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1038
Polymers26,5112
Non-polymers5926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-19 kcal/mol
Surface area14270 Å2
2
CCC: KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)26,9528
Polymers26,5112
Non-polymers4406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_553-x,y,-z-3/21
Buried area3220 Å2
ΔGint-26 kcal/mol
Surface area14260 Å2
Unit cell
Length a, b, c (Å)136.726, 237.593, 82.317
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-1001-

IOD

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53BBB
63CCC

NCS domain segments:

Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 144 - 259 / Label seq-ID: 1 - 116

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AAAA
221BBBB
332AAAA
442CCCC
553BBBB
663CCCC

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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Protein , 1 types, 3 molecules AAABBBCCC

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


Mass: 13255.592 Da / Num. of mol.: 3
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, 18 molecules

#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.31→188.8 Å / Num. obs: 19923 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC1/2: 0.996 / Net I/σ(I): 7.1
Reflection shellResolution: 3.33→3.35 Å / Num. unique obs: 2867 / CC1/2: 0.6

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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: 3.333→118.797 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.931 / SU B: 25.676 / SU ML: 0.332 / Cross valid method: FREE R-VALUE / ESU R: 0.452 / ESU R Free: 0.33 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2503 1054 5.293 %
Rwork0.2167 18860 -
all0.218 --
obs-19914 99.371 %
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: 117.854 Å2
Baniso -1Baniso -2Baniso -3
1--8.496 Å2-0 Å2-0 Å2
2--15.213 Å2-0 Å2
3----6.717 Å2
Refinement stepCycle: LAST / Resolution: 3.333→118.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 37 9 2832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122874
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.6443838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2385345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54723.333135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.59615564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.5481512
X-RAY DIFFRACTIONr_chiral_restr0.1840.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022110
X-RAY DIFFRACTIONr_nbd_refined0.2530.21228
X-RAY DIFFRACTIONr_nbtor_refined0.3310.21866
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.263
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.25
X-RAY DIFFRACTIONr_mcbond_it10.89211.1961389
X-RAY DIFFRACTIONr_mcangle_it16.40416.7941731
X-RAY DIFFRACTIONr_scbond_it14.16112.1431485
X-RAY DIFFRACTIONr_scangle_it19.50317.8642107
X-RAY DIFFRACTIONr_lrange_it23.716212.63211173
X-RAY DIFFRACTIONr_ncsr_local_group_10.0730.053625
X-RAY DIFFRACTIONr_ncsr_local_group_20.0730.053589
X-RAY DIFFRACTIONr_ncsr_local_group_30.0770.053580
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.073190.05011
12BBBX-RAY DIFFRACTIONLocal ncs0.073190.05011
23AAAX-RAY DIFFRACTIONLocal ncs0.073050.05011
24CCCX-RAY DIFFRACTIONLocal ncs0.073050.05011
35BBBX-RAY DIFFRACTIONLocal ncs0.077290.05011
36CCCX-RAY DIFFRACTIONLocal ncs0.077290.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.333-3.4190.54810.46413650.46914520.0040.00499.58680.445
3.419-3.5130.525600.44713560.4514180.1420.17399.8590.416
3.513-3.6140.409770.38313170.38413980.4180.41299.71390.349
3.614-3.7260.306800.33112420.3313310.6310.58899.32380.294
3.726-3.8480.409820.30812070.31412910.6160.68799.84510.265
3.848-3.9830.295760.28312010.28412880.7820.77999.1460.249
3.983-4.1330.267670.23511410.23712130.8280.86599.58780.202
4.133-4.3010.211620.2111080.2111760.8980.89499.48980.183
4.301-4.4920.175760.19110420.1911190.9330.91699.91060.168
4.492-4.7110.256660.18610280.1911020.8990.92599.2740.163
4.711-4.9660.276530.1629620.16710210.8720.94699.41230.144
4.966-5.2660.264350.1519430.1549850.9230.95899.28930.136
5.266-5.6290.157350.1798780.1789190.9520.94899.34710.152
5.629-6.0790.177340.1798220.1798590.9530.95399.65080.155
6.079-6.6570.186430.1697620.178110.9590.95599.26020.151
6.657-7.440.261320.1476910.1517300.9370.9799.04110.141
7.44-8.5860.15470.1166010.1186510.9710.98199.53920.118
8.586-10.5020.113260.1155210.1155580.9830.98598.02870.125
10.502-14.7940.203140.1564200.1584430.9550.97897.96840.182
14.794-118.7970.39180.3562530.3562750.8390.8794.90910.466

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