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- PDB-4lmz: Structural insight into RNA recognition by RRM1+2 domain of human... -

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Basic information

Entry
Database: PDB / ID: 4lmz
TitleStructural insight into RNA recognition by RRM1+2 domain of human ETR-3 protein
Components
  • CUGBP Elav-like family member 2
  • RNA (5'-R(*GP*CP*UP*GP*CP*GP*UP*AP*UP*UP*GP*UP*UP*UP*G)-3')
KeywordsRNA BINDING PROTEIN / CELF family / ETR-3 / GRE / RNA recognition motif / RNA binding
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
RNA / RNA (> 10) / CUGBP Elav-like family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsBhatt, H. / Manickam, Y. / Bhavesh, N.S.
CitationJournal: TO BE PUBLISHED
Title: sequence specific RNA recognition of ETR3 RRM 1-2 domains
Authors: Bhatt, H. / Manickam, Y. / Bhavesh, N.S.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA (5'-R(*GP*CP*UP*GP*CP*GP*UP*AP*UP*UP*GP*UP*UP*UP*G)-3')
A: CUGBP Elav-like family member 2


Theoretical massNumber of molelcules
Total (without water)24,9772
Polymers24,9772
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-10 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.006, 70.134, 133.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: RNA chain RNA (5'-R(*GP*CP*UP*GP*CP*GP*UP*AP*UP*UP*GP*UP*UP*UP*G)-3')


Mass: 4763.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: this sequence occurs naturally in humans
#2: 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: 20213.293 Da / Num. of mol.: 1
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

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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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M NaCl, Tris-HCl, 35% (v/v) 2-methyl 2,4-pentandiol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 22, 2012 / Details: VariMax HR optics
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.78→44.322 Å / Num. all: 5715 / Num. obs: 5715 / % possible obs: 100 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1
Reflection shellResolution: 2.78→2.85 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NMR

3nmr


Resolution: 2.78→44.322 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 32.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2925 552 9.66 %Ramdom
Rwork0.2441 ---
obs0.2486 5715 99.83 %-
all-5715 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→44.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1345 103 0 0 1448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041507
X-RAY DIFFRACTIONf_angle_d0.8742054
X-RAY DIFFRACTIONf_dihedral_angle_d15.715576
X-RAY DIFFRACTIONf_chiral_restr0.063226
X-RAY DIFFRACTIONf_plane_restr0.005257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7975-3.0790.37691350.31911251X-RAY DIFFRACTION100
3.079-3.52440.30171320.27741274X-RAY DIFFRACTION100
3.5244-4.43970.2541410.23051283X-RAY DIFFRACTION100
4.4397-44.32730.29511440.22181355X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.6171 Å / Origin y: 12.5047 Å / Origin z: -8.0639 Å
111213212223313233
T0.2933 Å20.0599 Å2-0.0871 Å2-0.3086 Å20.0214 Å2--0.2766 Å2
L-0.1506 °2-0.2958 °20.8602 °2--0.0366 °2-0.6195 °2--1.1575 °2
S-0.0689 Å °-0.0777 Å °0.108 Å °-0.052 Å °0.0574 Å °0.0871 Å °-0.7118 Å °-0.4594 Å °0.0321 Å °
Refinement TLS groupSelection details: all

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