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- PDB-4a90: Crystal structure of mouse SAP18 residues 1-143 -

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Basic information

Entry
Database: PDB / ID: 4a90
TitleCrystal structure of mouse SAP18 residues 1-143
ComponentsHISTONE DEACETYLASE COMPLEX SUBUNIT SAP18
KeywordsTRANSCRIPTION / SPLICING / RNA PROCESSING / NONSENSE MEDIATED DECAY / NMD
Function / homology
Function and homology information


ASAP complex / HDACs deacetylate histones / mRNA Splicing - Major Pathway / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / histone deacetylase complex / RNA splicing / mRNA processing / transcription corepressor activity / transcription regulator complex ...ASAP complex / HDACs deacetylate histones / mRNA Splicing - Major Pathway / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / histone deacetylase complex / RNA splicing / mRNA processing / transcription corepressor activity / transcription regulator complex / nuclear body / nuclear speck / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol
Similarity search - Function
ASAP complex, SAP18 subunit / Sin3 associated polypeptide p18 / Histone deacetylase complex subunit SAP18 / Sin3 associated polypeptide p18 superfamily / Sin3 associated polypeptide p18 (SAP18) / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Histone deacetylase complex subunit SAP18
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMurachelli, A.G. / Ebert, J. / Basquin, C. / Le Hir, H. / Conti, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The Structure of the Asap Core Complex Reveals the Existence of a Pinin-Containing Psap Complex
Authors: Murachelli, A.G. / Ebert, J. / Basquin, C. / Le Hir, H. / Conti, E.
History
DepositionNov 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18
B: HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1684
Polymers32,9842
Non-polymers1842
Water1,49583
1
A: HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6763
Polymers16,4921
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18


Theoretical massNumber of molelcules
Total (without water)16,4921
Polymers16,4921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.420, 65.140, 61.610
Angle α, β, γ (deg.)90.00, 119.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18 / / 18 KDA SIN3-ASSOCIATED POLYPEPTIDE / SIN3-ASSOCIATED POLYPEPTIDE P18 / SAP18 / HDAC


Mass: 16491.881 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O55128
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.34 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M SODIUM CACODYLATE PH 6.5, 5% POLYETHYLENEGLYCOL 8000, 5% GLYCEROL, 40% 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→32.57 Å / Num. obs: 25741 / % possible obs: 98.9 % / Observed criterion σ(I): 3.9 / Redundancy: 7.5 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A6Q

4a6q


Resolution: 1.9→23.688 Å / SU ML: 0.54 / σ(F): 0 / Phase error: 33.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 1294 5.1 %
Rwork0.2146 --
obs0.2164 25639 98.49 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.192 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso mean: 55.6 Å2
Baniso -1Baniso -2Baniso -3
1--12.1944 Å20 Å27.2305 Å2
2--34.9509 Å20 Å2
3----22.7565 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 12 83 2096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132084
X-RAY DIFFRACTIONf_angle_d1.5482829
X-RAY DIFFRACTIONf_dihedral_angle_d13.73752
X-RAY DIFFRACTIONf_chiral_restr0.084325
X-RAY DIFFRACTIONf_plane_restr0.011366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9760.37291480.32072723X-RAY DIFFRACTION99
1.976-2.06590.27041250.24872711X-RAY DIFFRACTION99
2.0659-2.17480.22041450.21992749X-RAY DIFFRACTION99
2.1748-2.31090.28741450.20952701X-RAY DIFFRACTION100
2.3109-2.48920.27231610.21962704X-RAY DIFFRACTION100
2.4892-2.73930.25751470.22432730X-RAY DIFFRACTION100
2.7393-3.1350.2751340.21792748X-RAY DIFFRACTION100
3.135-3.94680.25291440.1972750X-RAY DIFFRACTION100
3.9468-23.68960.22351450.21022529X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3931-0.33250.21980.90840.61053.32040.07640.0223-0.0462-0.0737-0.1199-0.0172-0.0098-0.69040.05350.206-0.0065-0.01160.18860.02560.204212.78414.521430.5582
22.73360.0121-0.09381.65710.56622.46440.01040.3316-0.03520.03140.03790.106-0.0623-0.36080.04360.14860.03170.03090.13610.02210.1656-5.490417.535656.5133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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