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- PDB-4rcm: Crystal structure of the Pho92 YTH domain in complex with m6A -

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Basic information

Entry
Database: PDB / ID: 4rcm
TitleCrystal structure of the Pho92 YTH domain in complex with m6A
Components
  • Methylated RNA-binding protein 1
  • RNA (5'-R(*UP*G)-D(*(6MZ)P*CP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / Structural Genomics / Structural Genomics Consortium / SGC / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


: / N6-methyladenosine-containing RNA reader activity / mRNA destabilization / regulation of mRNA stability / mRNA 3'-UTR binding / mRNA binding / cytoplasm
Similarity search - Function
ph1033 like fold / ph1033 like domains / YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
RNA / Methylated RNA-binding protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsTempel, W. / Xu, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins.
Authors: Xu, C. / Liu, K. / Ahmed, H. / Loppnau, P. / Schapira, M. / Min, J.
History
DepositionSep 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 2.0Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylated RNA-binding protein 1
B: Methylated RNA-binding protein 1
D: RNA (5'-R(*UP*G)-D(*(6MZ)P*CP*U)-3')
E: RNA (5'-R(*UP*G)-D(*(6MZ)P*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)41,74823
Polymers41,7484
Non-polymers019
Water1,76598
1
A: Methylated RNA-binding protein 1
D: RNA (5'-R(*UP*G)-D(*(6MZ)P*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)20,87411
Polymers20,8742
Non-polymers09
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methylated RNA-binding protein 1
E: RNA (5'-R(*UP*G)-D(*(6MZ)P*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)20,87412
Polymers20,8742
Non-polymers010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.430, 57.171, 66.725
Angle α, β, γ (deg.)90.00, 103.08, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein Methylated RNA-binding protein 1 / PHOsphate metabolism protein 92 / YTH domain-containing protein PHO92


Mass: 19313.057 Da / Num. of mol.: 2 / Fragment: UNP residues 141-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: PHO92, MRB1, YDR374C / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q06390
#2: RNA chain RNA (5'-R(*UP*G)-D(*(6MZ)P*CP*U)-3')


Mass: 1560.995 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 19 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.84 Å3/Da / Density % sol: 33.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG-3350, 0.2 M potassium isocyanate, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→38.4 Å / Num. obs: 27985 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.8-1.840.3914.14918151192.9
9.01-38.40.02935.379124397.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.17data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4R3H AND 4RCI

4r3h

4rci


Resolution: 1.8→32.97 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.2485 / WRfactor Rwork: 0.1999 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.747 / SU B: 4.912 / SU ML: 0.143 / SU R Cruickshank DPI: 0.1674 / SU Rfree: 0.1578 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: AN ENSEMBLE OF CRYSTALLOGRAPHIC MODELS OF HUMAN YTHDC1 AND YTHDF1 WAS USED AS SEARCH MODEL FOR MOLECULAR REPLACEMENT. PARROT WAS USED FOR DENSITY MODIFICATION. ARP/WARP WAS USED FOR PHASE ...Details: AN ENSEMBLE OF CRYSTALLOGRAPHIC MODELS OF HUMAN YTHDC1 AND YTHDF1 WAS USED AS SEARCH MODEL FOR MOLECULAR REPLACEMENT. PARROT WAS USED FOR DENSITY MODIFICATION. ARP/WARP WAS USED FOR PHASE IMPROVEMENT AND AUTOMATED MODEL BUILDING. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 1149 4.1 %THIN SHELLS (SFTOOLS)
Rwork0.218 ---
obs0.22 27964 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.6 Å2 / Biso mean: 19.2124 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å2-0 Å20.13 Å2
2---1.59 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 40 19 98 2701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192732
X-RAY DIFFRACTIONr_bond_other_d0.0010.022534
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9493723
X-RAY DIFFRACTIONr_angle_other_deg0.83835828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5055345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5623.305118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29615453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.851515
X-RAY DIFFRACTIONr_chiral_restr0.1010.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
X-RAY DIFFRACTIONr_mcbond_it2.1361.8421314
X-RAY DIFFRACTIONr_mcbond_other2.1351.841313
X-RAY DIFFRACTIONr_mcangle_it3.232.7431645
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.423 1921 -
obs--94.17 %

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