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- PDB-4ljm: Crystal structure of C-terminal RNA recognition motif of human ETR3 -

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Basic information

Entry
Database: PDB / ID: 4ljm
TitleCrystal structure of C-terminal RNA recognition motif of human ETR3
ComponentsCUGBP Elav-like family member 2
KeywordsRNA BINDING PROTEIN / RRM / RNA binding / RNA / CELF family
Function / homology
Function and homology information


mRNA splice site recognition / pre-mRNA binding / regulation of heart contraction / regulation of alternative mRNA splicing, via spliceosome / RNA processing / mRNA 3'-UTR binding / ribonucleoprotein complex / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKashyap, M. / Sharma, A. / Yogavel, M. / Bhavesh, N.S.
CitationJournal: To be Published
Title: Crystal structure of C-terminal RNA recognition motif of human ETR3
Authors: Kashyap, M. / Sharma, A. / Yogavel, M. / Bhavesh, N.S.
History
DepositionJul 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,8612
Polymers21,8612
Non-polymers00
Water25214
1
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
2
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
Unit cell
Length a, b, c (Å)118.533, 118.533, 118.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.00231, -0.999996, -0.00173), (-0.999997, 0.002309, 0.001041), (-0.001037, 0.001732, -0.999998)29.59717, 29.60011, -88.93753

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Components

#1: Protein CUGBP Elav-like family member 2 / ETR-3


Mass: 10930.555 Da / Num. of mol.: 2 / Fragment: RRM 3 domain, UNP residues 416-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CELF2 / Production host: Escherichia coli (E. coli) / References: UniProt: O95319
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 6.348 Å3/Da / Density % sol: 80.625 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.8M Ammonium citrate dibasic, 0.1M Sodium acetate trihydrate, pH 4.6, 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: Feb 10, 2010
RadiationMonochromator: VariMax Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→48.44 Å / Num. all: 11362 / Num. obs: 10792 / % possible obs: 99.71 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 10.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B7F

1b7f


Resolution: 3→48.44 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.925 / SU B: 17.098 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.268 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20936 542 4.8 %RANDOM
Rwork0.18311 ---
obs0.18434 10792 99.71 %-
all-10823 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.641 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 0 14 1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4951.951744
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0825160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.17325.80662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.62415228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.589152
X-RAY DIFFRACTIONr_chiral_restr0.1730.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021990
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.001→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 36 -
Rwork0.316 767 -
obs--99.88 %
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)Origin x (Å)Origin y (Å)Origin z (Å)
10.80550.6966-0.82292.7174-1.47891.9605-0.0391-0.0056-0.07160.146-0.0663-0.179-0.15610.08970.10540.0517-0.0285-0.02970.04120.02470.0534-4.695713.6644-34.6194
22.4274-0.1635-1.09441.3584-0.01961.37420.03420.0798-0.0896-0.0639-0.0712-0.05290.0472-0.12750.0370.0427-0.0080.01980.0285-0.01740.03615.964134.3895-54.2786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B401 - 481
2X-RAY DIFFRACTION2A401 - 481

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