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- PDB-4r3i: The crystal structure of an RNA complex -

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Basic information

Entry
Database: PDB / ID: 4r3i
TitleThe crystal structure of an RNA complex
Components
  • RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')
  • YTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN/RNA / structural genomics / Structural Genomics Consortium / SGC / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / dosage compensation by inactivation of X chromosome / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA splicing, via spliceosome / spermatogenesis / in utero embryonic development / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane
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 / YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsTempel, W. / Xu, C. / Liu, K. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain.
Authors: Xu, C. / Wang, X. / Liu, K. / Roundtree, I.A. / Tempel, W. / Li, Y. / Lu, Z. / He, C. / Min, J.
History
DepositionAug 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 2.0Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTH domain-containing protein 1
B: RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)20,4249
Polymers20,4242
Non-polymers07
Water1,60389
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-9 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.728, 39.748, 56.238
Angle α, β, γ (deg.)90.000, 103.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YTH domain-containing protein 1 / Putative splicing factor YT521 / YT521-B


Mass: 18823.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q96MU7
#2: RNA chain RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')


Mass: 1600.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.9 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 25% PEG3350, 0.2 M amonium sulfate, 0.1 M bis-tris, pH 6.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→34.73 Å / Num. obs: 14029 / % possible obs: 97.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.8-1.843.30.5872.325517730.36990.7
8.99-34.733.20.04123.63661140.02792

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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: a different crystal form of same protein

Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.2466 / WRfactor Rwork: 0.1859 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7846 / SU B: 4.237 / SU ML: 0.128 / SU R Cruickshank DPI: 0.1687 / SU Rfree: 0.1627 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Diffraction data for molecular replacement and early refinement were reduced with HKL3000. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 700 5 %RANDOM
Rwork0.2034 ---
obs0.2064 14013 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.53 Å2 / Biso mean: 21.3503 Å2 / Biso min: 2.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å2-0 Å20.74 Å2
2---1.57 Å2-0 Å2
3---2.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 106 7 89 1477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191430
X-RAY DIFFRACTIONr_bond_other_d0.0010.021308
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9231957
X-RAY DIFFRACTIONr_angle_other_deg0.79233013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95223.63655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70515225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.135157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02326
X-RAY DIFFRACTIONr_mcbond_it1.8262.108655
X-RAY DIFFRACTIONr_mcbond_other1.8252.102654
X-RAY DIFFRACTIONr_mcangle_it2.7493.144817
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 48 -
Rwork0.266 932 -
all-980 -
obs--94.41 %

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