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- PDB-4tlq: Crystal structure of C-terminal RNA recognition motif of human EL... -

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Basic information

Entry
Database: PDB / ID: 4tlq
TitleCrystal structure of C-terminal RNA recognition motif of human ELAV type RNA binding protein-3 at 2.5 Angstrom resolution
ComponentsCUGBP Elav-like family member 2
KeywordsRNA BINDING PROTEIN / RRM
Function / homology
Function and homology information


mRNA splice site recognition / pre-mRNA binding / Flemming body / regulation of heart contraction / regulation of alternative mRNA splicing, via spliceosome / RNA processing / mRNA 3'-UTR binding / ribonucleoprotein complex / intracellular membrane-bounded organelle / RNA binding ...mRNA splice site recognition / pre-mRNA binding / Flemming body / regulation of heart contraction / regulation of alternative mRNA splicing, via spliceosome / RNA processing / mRNA 3'-UTR binding / ribonucleoprotein complex / intracellular membrane-bounded organelle / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
CELF1/2, RNA recognition motif 2 / CELF1/2, RNA recognition motif 3 / CELF1/2, RNA recognition motif 1 / Paraneoplastic encephalomyelitis antigen / 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 ...CELF1/2, RNA recognition motif 2 / CELF1/2, RNA recognition motif 3 / CELF1/2, RNA recognition motif 1 / Paraneoplastic encephalomyelitis antigen / 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
CUGBP Elav-like family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsKashyap, M. / Bhavesh, N.S.
Funding support India, 1items
OrganizationGrant numberCountry
DBT India, Beamline project India
CitationJournal: To Be Published
Title: Crystal structure of C-terminal RNA recognition motif of human ELAV type RNA binding protein-3 at 2.5 Angstrom resolution
Authors: Kashyap, M. / Bhavesh, N.S.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CUGBP Elav-like family member 2
B: CUGBP Elav-like family member 2


Theoretical massNumber of molelcules
Total (without water)21,8612
Polymers21,8612
Non-polymers00
Water1,53185
1
A: CUGBP Elav-like family member 2


Theoretical massNumber of molelcules
Total (without water)10,9311
Polymers10,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CUGBP Elav-like family member 2


Theoretical massNumber of molelcules
Total (without water)10,9311
Polymers10,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.611, 118.611, 118.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein CUGBP Elav-like family member 2 / CELF-2 / Bruno-like protein 3 / CUG triplet repeat RNA-binding protein 2 / CUG-BP2 / CUG-BP- and ...CELF-2 / Bruno-like protein 3 / CUG triplet repeat RNA-binding protein 2 / CUG-BP2 / CUG-BP- and ETR-3-like factor 2 / ELAV-type RNA-binding protein 3 / ETR-3 / Neuroblastoma apoptosis-related RNA-binding protein / hNAPOR / RNA-binding protein BRUNOL-3


Mass: 10930.555 Da / Num. of mol.: 2 / Fragment: UNP residues 429-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CELF2, BRUNOL3, CUGBP2, ETR3, NAPOR / Production host: Escherichia coli (E. coli) / References: UniProt: O95319
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.4 M Ammonium Citrate, 0.1 M Sodium Acetate / PH range: 3.5-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19465 / % possible obs: 99.1 % / Redundancy: 4.8 % / Net I/σ(I): 13.4

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Processing

SoftwareName: PHENIX / Version: 1.8.4_1496 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LJM

4ljm


Resolution: 2.503→37.508 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 1790 10.02 %
Rwork0.1774 --
obs0.1791 17856 91.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.503→37.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 0 85 1378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061335
X-RAY DIFFRACTIONf_angle_d1.1191796
X-RAY DIFFRACTIONf_dihedral_angle_d18.139498
X-RAY DIFFRACTIONf_chiral_restr0.042189
X-RAY DIFFRACTIONf_plane_restr0.007239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5033-2.5710.2664540.216502X-RAY DIFFRACTION38
2.571-2.64660.24841190.24721037X-RAY DIFFRACTION79
2.6466-2.7320.30241260.22721241X-RAY DIFFRACTION93
2.732-2.82960.21351400.22911236X-RAY DIFFRACTION94
2.8296-2.94290.2471480.21511306X-RAY DIFFRACTION97
2.9429-3.07680.21091390.20861280X-RAY DIFFRACTION98
3.0768-3.23890.2161460.17671329X-RAY DIFFRACTION99
3.2389-3.44170.22481500.17171326X-RAY DIFFRACTION98
3.4417-3.70720.1691520.15051340X-RAY DIFFRACTION100
3.7072-4.07990.1491530.15241336X-RAY DIFFRACTION100
4.0799-4.66930.15411540.1341348X-RAY DIFFRACTION100
4.6693-5.87920.15931510.16551367X-RAY DIFFRACTION100
5.8792-37.51230.20361580.19031418X-RAY DIFFRACTION99

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