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- PDB-4r3h: The crystal structure of an apo RNA binding protein -

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Basic information

Entry
Database: PDB / ID: 4r3h
TitleThe crystal structure of an apo RNA binding protein
ComponentsYTH domain-containing protein 1
KeywordsRNA BINDING PROTEIN / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / regulation of mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / mRNA export from nucleus / mRNA splicing, via spliceosome ...primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / regulation of mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / 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
YTH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsXu, C. / Liu, K. / Tempel, W. / 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YTH domain-containing protein 1
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,74414
Polymers37,6482
Non-polymers9612
Water2,846158
1
A: YTH domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)18,8246
Polymers18,8241
Non-polymers05
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YTH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9208
Polymers18,8241
Non-polymers967
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.264, 103.026, 41.585
Angle α, β, γ (deg.)90.000, 105.860, 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.: 2
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: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.3 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 25% PEG3350, 0.2M Ammonium Sulphate, 0.1M bis-tris, pH 6.5, vapor diffusion, temperature 293K

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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: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→27.31 Å / Num. obs: 28931 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.8-1.843.30.9011.7496815280.57490.3
9.02-27.313.50.02345.58362400.01495.7

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Processing

Software
NameVersionClassificationNB
Aimless0.2.17data scaling
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MIR / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2194 / WRfactor Rwork: 0.1733 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8008 / SU B: 8.794 / SU ML: 0.129 / SU R Cruickshank DPI: 0.1619 / SU Rfree: 0.1528 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Structure of an isomorphous crystal was solved by molecular replacement using PHASER and coordinates from PDB entry 2YUD. Phase improvement and automated model building were performed with ...Details: Structure of an isomorphous crystal was solved by molecular replacement using PHASER and coordinates from PDB entry 2YUD. Phase improvement and automated model building were performed with ARP/WARP. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1007 4 %THIN SHELLS (SFTOOLS)
Rwork0.1909 ---
obs0.193 24951 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.28 Å2 / Biso mean: 32.1817 Å2 / Biso min: 15.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20.86 Å2
2---1.01 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 16 158 2601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192499
X-RAY DIFFRACTIONr_bond_other_d0.0010.022400
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.953381
X-RAY DIFFRACTIONr_angle_other_deg0.76135513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68823.529102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36615428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9731513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
X-RAY DIFFRACTIONr_mcbond_it1.6341.9811246
X-RAY DIFFRACTIONr_mcbond_other1.6331.9791245
X-RAY DIFFRACTIONr_mcangle_it2.4462.9531551
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 26 -
Rwork0.299 1787 -
all-1813 -
obs--99.07 %
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)
12.30070.7808-0.21833.6135-0.26572.11130.03520.1464-0.1608-0.14130.01560.0720.081-0.0058-0.05080.0425-0.0059-0.0130.0164-0.00140.042621.569522.75121.3514
22.5880.29970.21424.07641.1082.5060.00110.0444-0.0923-0.09190.0895-0.25250.03260.0958-0.09060.0073-0.00340.00670.0077-0.00870.018725.505349.307226.4192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A344 - 507
2X-RAY DIFFRACTION2B344 - 507

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