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- PDB-7z1k: Crystal structure of the SPOC domain of human SHARP (SPEN) in com... -

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Basic information

Entry
Database: PDB / ID: 7z1k
TitleCrystal structure of the SPOC domain of human SHARP (SPEN) in complex with RNA polymerase II CTD heptapeptide phosphorylated on Ser5
Components
  • Msx2-interacting protein
  • SER-TYR-SER-PRO-THR-SEP
KeywordsTRANSCRIPTION / human SHARP / SPOC domain / RNA polymerase II CTD heptapeptide
Function / homology
Function and homology information


random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / RHOBTB1 GTPase cycle / positive regulation of neurogenesis / Notch signaling pathway / transcription repressor complex / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / mRNA binding ...random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / RHOBTB1 GTPase cycle / positive regulation of neurogenesis / Notch signaling pathway / transcription repressor complex / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / mRNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
SHARP, RNA recognition motif 1 / SHARP, RNA recognition motif 2 / SHARP, RNA recognition motif 3 / SHARP, RNA recognition motif 4 / : / : / : / Msx2-interacting protein, RAM7 domain / Msx2-interacting protein, MID domain / Msx2-interacting protein, nuclear receptor-interacting domain ...SHARP, RNA recognition motif 1 / SHARP, RNA recognition motif 2 / SHARP, RNA recognition motif 3 / SHARP, RNA recognition motif 4 / : / : / : / Msx2-interacting protein, RAM7 domain / Msx2-interacting protein, MID domain / Msx2-interacting protein, nuclear receptor-interacting domain / Spen paralogue/orthologue C-terminal, metazoa / SPOC domain profile. / Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / SPOC-like, C-terminal domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Msx2-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsAppel, L. / Grishkovskaya, I. / Slade, D. / Djinovic-Carugo, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Nat Commun / Year: 2023
Title: The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators.
Authors: Appel, L.M. / Franke, V. / Benedum, J. / Grishkovskaya, I. / Strobl, X. / Polyansky, A. / Ammann, G. / Platzer, S. / Neudolt, A. / Wunder, A. / Walch, L. / Kaiser, S. / Zagrovic, B. / ...Authors: Appel, L.M. / Franke, V. / Benedum, J. / Grishkovskaya, I. / Strobl, X. / Polyansky, A. / Ammann, G. / Platzer, S. / Neudolt, A. / Wunder, A. / Walch, L. / Kaiser, S. / Zagrovic, B. / Djinovic-Carugo, K. / Akalin, A. / Slade, D.
History
DepositionFeb 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _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 20, 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
A: Msx2-interacting protein
B: SER-TYR-SER-PRO-THR-SEP


Theoretical massNumber of molelcules
Total (without water)20,4522
Polymers20,4522
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-6 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.327, 60.517, 68.273
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Msx2-interacting protein / SMART/HDAC1-associated repressor protein / SPEN homolog


Mass: 18730.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPEN, KIAA0929, MINT, SHARP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T58
#2: Protein/peptide SER-TYR-SER-PRO-THR-SEP


Mass: 1721.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Potassium thiocyanate, 30% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.55→36.58 Å / Num. obs: 26393 / % possible obs: 98.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.3
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 1257 / CC1/2: 0.203

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OW1

1ow1


Resolution: 1.55→35.23 Å / SU ML: 0.2547 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.6153
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247 1331 5.08 %
Rwork0.2155 24889 -
obs0.217 26220 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.81 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 0 169 1472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441329
X-RAY DIFFRACTIONf_angle_d0.73131814
X-RAY DIFFRACTIONf_chiral_restr0.0467216
X-RAY DIFFRACTIONf_plane_restr0.0076233
X-RAY DIFFRACTIONf_dihedral_angle_d7.8969186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.610.33651260.34942332X-RAY DIFFRACTION94.32
1.61-1.670.3781370.34032433X-RAY DIFFRACTION97.61
1.67-1.750.381340.34922478X-RAY DIFFRACTION99.39
1.75-1.840.37571390.39512485X-RAY DIFFRACTION99.13
1.84-1.950.42231430.3622441X-RAY DIFFRACTION97.99
1.95-2.10.25181160.23482485X-RAY DIFFRACTION98.23
2.1-2.320.25051380.21912469X-RAY DIFFRACTION97.79
2.32-2.650.21071320.19982540X-RAY DIFFRACTION99.63
2.65-3.340.24271280.1892579X-RAY DIFFRACTION99.74
3.34-35.230.19971380.17262647X-RAY DIFFRACTION97.89

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