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- PDB-7vki: ESRP1 qRRM2 in complex with 12mer-RNA -

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Basic information

Entry
Database: PDB / ID: 7vki
TitleESRP1 qRRM2 in complex with 12mer-RNA
Components
  • Epithelial splicing regulatory protein 1
  • RNA (12-mer)
KeywordsRNA BINDING PROTEIN/RNA / qRRM domain / RNA binding / circRNA / complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of inner ear auditory receptor cell fate specification / FGFR2 alternative splicing / regulation of RNA splicing / RNA splicing / mRNA processing / Signaling by BRAF and RAF1 fusions / nuclear body / ribonucleoprotein complex / mRNA binding / nucleoplasm / nucleus
Similarity search - Function
ESRP1, RNA recognition motif 1 / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Epithelial splicing regulatory protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWu, B.X. / Patel, D.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: ESRP1 controls biogenesis and function of a large abundant multiexon circRNA.
Authors: Liu, D. / Dredge, B.K. / Bert, A.G. / Pillman, K.A. / Toubia, J. / Guo, W. / Dyakov, B.J.A. / Migault, M.M. / Conn, V.M. / Conn, S.J. / Gregory, P.A. / Gingras, A.C. / Patel, D. / Wu, B. / Goodall, G.J.
History
DepositionSep 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epithelial splicing regulatory protein 1
B: RNA (12-mer)


Theoretical massNumber of molelcules
Total (without water)17,1512
Polymers17,1512
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint2 kcal/mol
Surface area7230 Å2
Unit cell
Length a, b, c (Å)86.118, 86.118, 43.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Epithelial splicing regulatory protein 1 / RNA-binding motif protein 35A / RNA-binding protein 35A


Mass: 13210.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRP1, RBM35A / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NXG1
#2: RNA chain RNA (12-mer)


Mass: 3941.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.94989 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94989 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 22615 / % possible obs: 99.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 10.58 Å2 / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.038 / Rrim(I) all: 0.15 / Net I/σ(I): 17.429
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 7 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 4.333 / Num. unique obs: 2200 / CC1/2: 0.933 / CC star: 0.982 / Rpim(I) all: 0.118 / Rrim(I) all: 0.356 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RVJ

2rvj


Resolution: 1.65→28.25 Å / SU ML: 0.1769 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 21.5284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2204 1043 4.96 %
Rwork0.1945 19983 -
obs0.1958 21026 92.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.63 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 66 0 128 1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066979
X-RAY DIFFRACTIONf_angle_d0.86421338
X-RAY DIFFRACTIONf_chiral_restr0.0563152
X-RAY DIFFRACTIONf_plane_restr0.0101164
X-RAY DIFFRACTIONf_dihedral_angle_d26.3154155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.730.25881040.24261779X-RAY DIFFRACTION58.94
1.73-1.840.30551520.23022728X-RAY DIFFRACTION90.03
1.84-1.980.21881590.20613041X-RAY DIFFRACTION99.41
1.98-2.180.20721470.19173071X-RAY DIFFRACTION99.69
2.18-2.50.21721690.20213063X-RAY DIFFRACTION99.94
2.5-3.150.23241780.19873069X-RAY DIFFRACTION99.88
3.15-28.250.18451340.17083232X-RAY DIFFRACTION99.82

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