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- PDB-7vkj: Structure of ESRP1 qRRM3 domain -

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Basic information

Entry
Database: PDB / ID: 7vkj
TitleStructure of ESRP1 qRRM3 domain
ComponentsEpithelial splicing regulatory protein 1
KeywordsRNA BINDING PROTEIN / qRRM domain / RNA binding / circRNA / 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
Epithelial splicing regulatory protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWu, B.X. / Patel, D.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of ESRP1 qRRM3 domain
Authors: Wu, B.X. / Patel, D.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

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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: Epithelial splicing regulatory protein 1
C: Epithelial splicing regulatory protein 1
D: Epithelial splicing regulatory protein 1
E: Epithelial splicing regulatory protein 1
F: Epithelial splicing regulatory protein 1
G: Epithelial splicing regulatory protein 1
H: Epithelial splicing regulatory protein 1


Theoretical massNumber of molelcules
Total (without water)99,8758
Polymers99,8758
Non-polymers00
Water16,826934
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.572, 102.813, 107.141
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.931581308383, 0.22385449457, -0.286435736479), (-0.243942437005, -0.199253671619, -0.949099605824), (-0.269533584734, 0.954037284181, -0.131013385167)11.6003899592, 3.77651486772, 4.008362461
2given(-0.893454954054, -0.0154143266142, 0.448888230645), (0.0336645651313, -0.998897966041, 0.032703982835), (0.447889430698, 0.0443311625584, 0.892989252956)-11.3003514257, -2.1663656298, 1.79824450223
3given(-0.964385695184, 0.192567879761, 0.181322482356), (0.214502989297, 0.168309449615, 0.962112465751), (0.154753670413, 0.966741713621, -0.203621611425)-19.3639773128, -5.34480500746, 10.3034275437
4given(-0.997870490967, 0.0336418426133, 0.0558812104569), (0.0106280742235, 0.929138709435, -0.36957854736), (-0.0643546990891, -0.368197616852, -0.927517648161)-12.0155848312, 19.3251053786, 7.36879656165
5given(0.910353950075, 0.0333614879559, -0.412483571437), (0.162063746614, -0.945873439494, 0.281173929255), (-0.380776873795, -0.322816430159, -0.866486309645)20.1171301821, -2.46027103293, 4.40204721751
6given(-0.935371822268, -0.216495387125, 0.279659259565), (-0.311681660031, 0.130923426047, -0.941123583443), (0.167134966142, -0.967465143489, -0.189939725247)-2.00696251374, 2.28895010497, 4.03064570821
7given(0.973783835702, -0.176816699979, -0.143111480792), (0.118081909556, -0.14480979727, 0.982388306756), (-0.194426603019, -0.973532730432, -0.120134586258)8.15313715786, 9.32910926502, -0.601708220011

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Components

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


Mass: 12484.396 Da / Num. of mol.: 8
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 934 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 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: BL17U1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 2073014 / % possible obs: 93.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 13.77 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.031 / Rrim(I) all: 0.109 / Net I/σ(I): 26.176
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 3.214 / Num. unique obs: 17259 / CC1/2: 0.876 / CC star: 0.966 / Rpim(I) all: 0.278 / Rrim(I) all: 1.006 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VKI

7vki


Resolution: 1.45→29.347 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.176 / SU B: 0.998 / SU ML: 0.039 / Average fsc free: 0.9406 / Average fsc work: 0.9469 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1899 8155 5.001 %
Rwork0.1705 154909 -
all0.171 --
obs-163064 93.163 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å20 Å2
2--0.354 Å2-0 Å2
3----0.143 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 0 934 7504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136708
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156361
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.6489021
X-RAY DIFFRACTIONr_angle_other_deg1.5241.58714577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3785823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15521.21405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.238151181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9381563
X-RAY DIFFRACTIONr_chiral_restr0.1050.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021674
X-RAY DIFFRACTIONr_nbd_refined0.2220.21141
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.26030
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23281
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23338
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2563
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0340.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2490.216
X-RAY DIFFRACTIONr_nbd_other0.2130.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.234
X-RAY DIFFRACTIONr_mcbond_it1.5921.3563313
X-RAY DIFFRACTIONr_mcbond_other1.5871.3553312
X-RAY DIFFRACTIONr_mcangle_it2.4142.034129
X-RAY DIFFRACTIONr_mcangle_other2.4142.0314130
X-RAY DIFFRACTIONr_scbond_it2.7011.7413395
X-RAY DIFFRACTIONr_scbond_other2.7011.7423395
X-RAY DIFFRACTIONr_scangle_it4.2192.4884892
X-RAY DIFFRACTIONr_scangle_other4.2172.4884892
X-RAY DIFFRACTIONr_lrange_it5.5217.8117367
X-RAY DIFFRACTIONr_lrange_other5.41317.1147111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.4880.256060.23111255X-RAY DIFFRACTION92.5628
1.488-1.5280.2336500.21111666X-RAY DIFFRACTION99.0191
1.528-1.5720.2046220.18311503X-RAY DIFFRACTION99.6548
1.572-1.6210.2056140.17311150X-RAY DIFFRACTION99.8472
1.621-1.6740.1975640.16710852X-RAY DIFFRACTION99.8338
1.674-1.7320.185530.16110500X-RAY DIFFRACTION99.6933
1.732-1.7970.2045400.16210106X-RAY DIFFRACTION99.607
1.797-1.870.1914960.1619832X-RAY DIFFRACTION99.9806
1.87-1.9530.2983040.2695461X-RAY DIFFRACTION58.3443
1.953-2.0480.1954430.1689014X-RAY DIFFRACTION100
2.048-2.1580.1854140.1618617X-RAY DIFFRACTION99.9115
2.158-2.2890.2462110.2144231X-RAY DIFFRACTION51.7836
2.289-2.4460.1784170.157594X-RAY DIFFRACTION99.565
2.446-2.640.1673850.1567112X-RAY DIFFRACTION99.6412
2.64-2.890.1733440.166593X-RAY DIFFRACTION99.9568
2.89-3.2270.1642730.1556042X-RAY DIFFRACTION100
3.227-3.7190.1711970.1634012X-RAY DIFFRACTION75.2817
3.719-4.5380.1621900.1473639X-RAY DIFFRACTION79.9374
4.538-6.3450.1932140.1753538X-RAY DIFFRACTION99.4434
6.345-29.3470.1741170.192155X-RAY DIFFRACTION99.6491

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