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- PDB-4p6q: The crystal structure of the Split End protein SHARP adds a new l... -

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Basic information

Entry
Database: PDB / ID: 4p6q
TitleThe crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA Recognition Motifs
ComponentsMsx2-interacting protein
KeywordsTRANSCRIPTION / RNA-recognition Motif / SPEN protein / Steroid RNA Activator / Transcriptional Regulation
Function / homology
Function and homology information


random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / positive regulation of neurogenesis / RHOBTB1 GTPase cycle / 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 / positive regulation of neurogenesis / RHOBTB1 GTPase cycle / 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 / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Msx2-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArieti, F. / Gabus, C. / Tambalo, M. / Huet, T. / Round, A. / Thore, S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationN?316030-128787 Switzerland
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA recognition motifs.
Authors: Arieti, F. / Gabus, C. / Tambalo, M. / Huet, T. / Round, A. / Thore, S.
History
DepositionMar 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id
Revision 2.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Msx2-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1532
Polymers33,0571
Non-polymers961
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-7 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.670, 69.710, 88.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33056.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPEN, KIAA0929, MINT, SHARP / Plasmid: pET42a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q96T58
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15% PEG 8000, 0.1M ammonium sulphate, 0.01M magnesium chloride, 0.05M 2-(N-morpholino)ethanesulfonic acid
PH range: 5.4-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→28.71 Å / Num. obs: 26164 / % possible obs: 99.67 % / Redundancy: 5.38 % / Net I/σ(I): 20.44
Reflection shellHighest resolution: 2 Å / Redundancy: 5.63 % / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE). ...Starting model: Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE).

3md1

2adc

2dnm

2dgu

2cqb

2ytc

4f26

1why

2cpz

2i38

1why

1x55

2lcw

2cpe


Resolution: 2→28.71 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 1989 7.64 %
Rwork0.1924 --
obs0.1959 26035 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 5 156 2483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082376
X-RAY DIFFRACTIONf_angle_d1.0963190
X-RAY DIFFRACTIONf_dihedral_angle_d15.497898
X-RAY DIFFRACTIONf_chiral_restr0.081336
X-RAY DIFFRACTIONf_plane_restr0.004414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.35841390.27951693X-RAY DIFFRACTION100
2.05-2.10540.33971400.26371689X-RAY DIFFRACTION100
2.1054-2.16740.28511400.23461690X-RAY DIFFRACTION100
2.1674-2.23730.32731400.23381692X-RAY DIFFRACTION100
2.2373-2.31720.2771400.22481686X-RAY DIFFRACTION100
2.3172-2.40990.24971430.19911725X-RAY DIFFRACTION100
2.4099-2.51960.23631390.20071693X-RAY DIFFRACTION100
2.5196-2.65230.26491410.20881696X-RAY DIFFRACTION100
2.6523-2.81840.28311430.21791722X-RAY DIFFRACTION100
2.8184-3.03570.24491420.21381725X-RAY DIFFRACTION100
3.0357-3.34080.24761430.19881723X-RAY DIFFRACTION100
3.3408-3.82330.23061420.17511724X-RAY DIFFRACTION99
3.8233-4.81330.20351440.15971735X-RAY DIFFRACTION99
4.8133-28.71320.2081530.18151853X-RAY DIFFRACTION99
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
15.9351-3.8082-0.17495.72720.97195.3782-0.3586-0.0117-0.32030.0864-0.00850.3063-0.1998-0.72170.29460.37010.0771-0.03030.4884-0.19230.4658RRM2-36.1044-0.8271-21.5559
23.0567-0.25534.07877.4635-1.94859.00790.3390.75391.5853-1.0381-0.4126-0.9818-1.18762.0133-0.03060.802-0.01110.18170.9318-0.10080.6535Linker-61.42234.1161-25.5705
36.24350.48031.86133.37270.2836.46740.0421-0.31830.07760.07970.09010.18370.28450.0668-0.04670.21550.0179-0.0110.1488-0.07490.2467RRM3-73.2776-8.6876-27.7561
45.2001-0.4981.30983.5994-0.07925.1484-0.01740.8793-0.1391-0.08430.06-0.2401-0.16420.2697-0.0350.1895-0.04150.00370.2566-0.04590.2118RRM4-79.6478-7.8661-52.1191
51.892.41240.62844.45452.50923.38230.33140.4967-0.36360.1341-0.1391-0.31690.4039-0.1423-0.12410.30060.0093-0.03350.2704-0.08590.3717C-terminal helices-90.9288-21.3687-49.5487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 589:620)
2X-RAY DIFFRACTION2(chain A and resid 412:429)
3X-RAY DIFFRACTION3(chain A and resid 430:513)
4X-RAY DIFFRACTION4(chain A and resid 514:588)
5X-RAY DIFFRACTION5(chain A and resid 589:620)

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