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- PDB-4a8x: Structure of the core ASAP complex -

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Basic information

Entry
Database: PDB / ID: 4a8x
TitleStructure of the core ASAP complex
Components
  • HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18
  • HOOK-LIKE, ISOFORM A
  • RNA-BINDING PROTEIN WITH SERINE-RICH DOMAIN 1
KeywordsTRANSCRIPTION / SPLICING / RNA PROCESSING / NONSENSE MEDIATED DECAY / NMD / HDAC / HISTONE DEACETYLATION
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / ASAP complex / mRNA Splicing - Major Pathway / mRNA Splicing - Major Pathway / HDACs deacetylate histones / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / precatalytic spliceosome ...Apoptotic cleavage of cellular proteins / ASAP complex / mRNA Splicing - Major Pathway / mRNA Splicing - Major Pathway / HDACs deacetylate histones / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / histone deacetylase complex / negative regulation of mRNA splicing, via spliceosome / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / mRNA processing / transcription corepressor activity / transcription regulator complex / nucleic acid binding / regulation of autophagy / nuclear speck / positive regulation of apoptotic process / DNA-templated transcription / regulation of DNA-templated transcription / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
RNPS1, RNA recognition motif / Acin1, RNSP1-SAP18 binding (RSB) motif / Acinus, RNA recognition motif / : / RNSP1-SAP18 binding (RSB) motif / ASAP complex, SAP18 subunit / Sin3 associated polypeptide p18 / Histone deacetylase complex subunit SAP18 / Sin3 associated polypeptide p18 superfamily / Sin3 associated polypeptide p18 (SAP18) ...RNPS1, RNA recognition motif / Acin1, RNSP1-SAP18 binding (RSB) motif / Acinus, RNA recognition motif / : / RNSP1-SAP18 binding (RSB) motif / ASAP complex, SAP18 subunit / Sin3 associated polypeptide p18 / Histone deacetylase complex subunit SAP18 / Sin3 associated polypeptide p18 superfamily / Sin3 associated polypeptide p18 (SAP18) / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Ubiquitin-like (UB roll) / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone deacetylase complex subunit SAP18 / RNA-binding protein with serine-rich domain 1 / Acinus, isoform A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
DROSOPHILA MELANOGASTER (fruit fly)
MUS 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 21, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-BINDING PROTEIN WITH SERINE-RICH DOMAIN 1
B: HOOK-LIKE, ISOFORM A
C: HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18


Theoretical massNumber of molelcules
Total (without water)29,7473
Polymers29,7473
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-22.6 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.868, 73.331, 50.754
Angle α, β, γ (deg.)90.00, 110.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA-BINDING PROTEIN WITH SERINE-RICH DOMAIN 1 / RNPS1 / SR-RELATED PROTEIN LDC2


Mass: 10051.624 Da / Num. of mol.: 1 / Fragment: RRM DOMAIN, RESIDUES 122-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET SERIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q15287
#2: Protein/peptide HOOK-LIKE, ISOFORM A / ACINUS / HOOK-LIKE / ISOFORM B / LD23757P


Mass: 4707.469 Da / Num. of mol.: 1 / Fragment: RSB DOMAIN, RESIDUES 648-687
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PET SERIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9VJ12
#3: Protein HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18 / SAP18 / 18 KDA SIN3-ASSOCIATED POLYPEPTIDE / SIN3-ASSOCIATED POLYPEPTIDE P18


Mass: 14988.154 Da / Num. of mol.: 1 / Fragment: RESIDUES 14-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET SERIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O55128
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSM ARE RESIDUALS FROM TAG CLEAVAGE

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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: 2.28 Å3/Da / Density % sol: 46.13 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM TRIS PH 7.5 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2010
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: 25760 / % possible obs: 98.9 % / Observed criterion σ(I): 3.8 / Redundancy: 7.5 % / Biso Wilson estimate: 32.27 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.1 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1RK8 AND 4A6Q

1rk8

4a6q


Resolution: 1.9→36.289 Å / SU ML: 0.54 / σ(F): 0 / Phase error: 23.08 / Stereochemistry target values: ML
Details: DISORDERED SIDE CHAIN WERE TRUNCATED AT C ALPHA. THE 96-100 LOOP OF SAP18 (CHAIN C) DISPLAYS POOR DENSITY AND WAS MODELED BASED ON ENTRY 4A6Q
RfactorNum. reflection% reflection
Rfree0.2256 1078 5.1 %
Rwork0.1856 --
obs0.1877 21016 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.834 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-5.6 Å20 Å2-2.773 Å2
2--8.4548 Å2-0 Å2
3---0.6614 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 0 179 2042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121926
X-RAY DIFFRACTIONf_angle_d1.2782615
X-RAY DIFFRACTIONf_dihedral_angle_d12.667711
X-RAY DIFFRACTIONf_chiral_restr0.077293
X-RAY DIFFRACTIONf_plane_restr0.007335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.98650.30471300.26752486X-RAY DIFFRACTION100
1.9865-2.09120.27231370.21542463X-RAY DIFFRACTION100
2.0912-2.22220.2411380.19342483X-RAY DIFFRACTION100
2.2222-2.39380.27521280.19212482X-RAY DIFFRACTION100
2.3938-2.63460.25051410.20332492X-RAY DIFFRACTION100
2.6346-3.01570.25521260.19862500X-RAY DIFFRACTION100
3.0157-3.79880.23951320.18232495X-RAY DIFFRACTION100
3.7988-36.29590.17751460.16332537X-RAY DIFFRACTION100
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)
11.6657-0.2089-0.02633.0539-1.45271.16380.08510.2624-0.14430.0915-0.0754-0.30250.32440.34190.00870.20260.00760.01230.1969-0.07140.182122.90515.67745.197
21.8572-1.1860.61673.4624-1.58882.454-0.088-0.48540.36020.8590.20310.0792-0.63420.1909-0.51960.2761-0.0210.09430.2007-0.04250.18512.991818.47849.0734
32.2926-0.30461.10412.9728-0.6832.33150.08880.3965-0.0283-0.55770.04610.48720.10960.01820.05590.1946-0.0536-0.06290.23170.00340.23384.475518.3519-13.2414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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