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- PDB-4rci: Crystal structure of YTHDF1 YTH domain -

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Basic information

Entry
Database: PDB / ID: 4rci
TitleCrystal structure of YTHDF1 YTH domain
ComponentsYTH domain-containing family protein 1
KeywordsRNA BINDING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of axon guidance / organelle assembly / regulation of antigen processing and presentation / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / mRNA destabilization / positive regulation of translational initiation / immune system process / regulation of mRNA stability / stress granule assembly ...regulation of axon guidance / organelle assembly / regulation of antigen processing and presentation / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / mRNA destabilization / positive regulation of translational initiation / immune system process / regulation of mRNA stability / stress granule assembly / learning / positive regulation of translation / P-body / memory / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA 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
YTH domain-containing family protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsXu, C. / Tempel, W. / Liu, K. / Walker, J.R. / 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 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Sep 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

Downloads & links

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Assembly

Deposited unit
A: YTH domain-containing family protein 1
B: YTH domain-containing family protein 1
C: YTH domain-containing family protein 1
D: YTH domain-containing family protein 1


Theoretical massNumber of molelcules
Total (without water)93,06561
Polymers93,0654
Non-polymers057
Water5,062281
1
A: YTH domain-containing family protein 1


Theoretical massNumber of molelcules
Total (without water)23,26616
Polymers23,2661
Non-polymers015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YTH domain-containing family protein 1


Theoretical massNumber of molelcules
Total (without water)23,26612
Polymers23,2661
Non-polymers011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: YTH domain-containing family protein 1


Theoretical massNumber of molelcules
Total (without water)23,26619
Polymers23,2661
Non-polymers018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: YTH domain-containing family protein 1


Theoretical massNumber of molelcules
Total (without water)23,26614
Polymers23,2661
Non-polymers013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.519, 82.136, 123.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
YTH domain-containing family protein 1 / Dermatomyositis associated with cancer putative autoantigen 1 / DACA-1


Mass: 23266.166 Da / Num. of mol.: 4 / Fragment: UNP residues 361-559
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF1, C20orf21 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9BYJ9
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 57 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 25% PEG-3350, 0.2 M potassium thiocyanate, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979237 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979237 Å / Relative weight: 1
ReflectionResolution: 1.97→48.66 Å / Num. obs: 57668 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.97-2.027.40.9672.329482397799.7
9.03-48.666.10.02557420968598.5

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Processing

Software
NameVersionClassificationNB
Aimless0.2.17data scaling
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4R3I

4r3i


Resolution: 1.97→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2094 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8252 / SU B: 8.836 / SU ML: 0.125 / SU R Cruickshank DPI: 0.1695 / SU Rfree: 0.1526 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ANOTHER STRUCTURE OF THIS CRYSTAL FORM WAS SOLVED BY MOLECULAR REPLACEMENT WITH PHASER AND THE MODEL OF A YTHDC1 CRYSTAL STRUCTURE. PHASES FROM MOLECULAR REPLACEMENT WERE IMPROVED WITH ...Details: ANOTHER STRUCTURE OF THIS CRYSTAL FORM WAS SOLVED BY MOLECULAR REPLACEMENT WITH PHASER AND THE MODEL OF A YTHDC1 CRYSTAL STRUCTURE. PHASES FROM MOLECULAR REPLACEMENT WERE IMPROVED WITH PARROT AND NCS AVERAGING. A PRELIMINARY MODEL WAS BUILD AUTOMATICALLY WITH BUCCANEER. THE MODEL WAS FURTHER REFINED AGAINST DIFFRACTION DATA FROM THE CURRENT CRYSTAL. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY. HISTIDYL-416 SIDE CHAIN DOES NOT MATCH DENSITY WELL IN EITHER PROTEIN CHAIN, EVEN THOUGH THE GENE CONSTRUCT'S SEQUENCE WAS CONFIRMED.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1789 3.1 %THIN SHELLS (SFTOOLS)
Rwork0.189 ---
obs0.1903 57599 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.71 Å2 / Biso mean: 35.4068 Å2 / Biso min: 14.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20 Å2
2---0.38 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 57 281 6163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196062
X-RAY DIFFRACTIONr_bond_other_d0.0010.025436
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9218223
X-RAY DIFFRACTIONr_angle_other_deg0.77312488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7355743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22224.18311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26615999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3821535
X-RAY DIFFRACTIONr_chiral_restr0.080.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021489
X-RAY DIFFRACTIONr_mcbond_it1.1981.2172946
X-RAY DIFFRACTIONr_mcbond_other1.1971.2172945
X-RAY DIFFRACTIONr_mcangle_it1.9291.813668
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 151 -
Rwork0.244 4021 -
all-4172 -
obs--99.62 %
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)
13.11850.14850.363.10380.63732.8310.06510.05940.0125-0.21-0.0735-0.01010.03140.06270.00840.01860.0201-0.00030.17940.03910.14650.266422.105941.4572
24.8883.7292-4.23574.9499-4.55497.0347-0.01260.2436-0.0324-0.42150.28770.30290.4352-0.6078-0.2750.2488-0.0205-0.12510.302-0.00860.329640.0017-1.794940.3927
32.3240.1925-0.36222.88460.5794.9405-0.31820.0454-0.0102-0.1410.28980.17361.0362-0.3010.02840.3397-0.122-0.04720.2170.04130.21466.1438-2.205457.9109
45.85974.5925-3.51127.189-4.81797.8402-0.1517-0.064-0.3313-0.4169-0.0798-0.58420.98890.13040.23140.4799-0.02650.01440.2521-0.07740.246917.9387-1.397434.2974
52.4910.1131-0.04582.07231.12353.1102-0.04980.0652-0.0362-0.10350.02880.10550.0506-0.21770.02090.0106-0.0147-0.01140.18990.01670.113313.070221.728935.9792
67.07545.7134-5.00385.2897-5.44666.5372-0.35110.23320.0066-0.63110.52330.15740.9783-0.9519-0.17220.4558-0.2323-0.01420.4368-0.09720.3343.7715-1.737233.6128
72.5688-0.24080.08673.02590.95623.26480.009-0.0798-0.2149-0.08590.0810.13740.22210.0471-0.090.0314-0.0283-0.04280.15950.05410.185145.2277-2.505163.8015
89.81967.2324-6.76558.8161-6.19847.17680.119-0.0888-0.3807-0.1978-0.3039-0.53730.16790.22560.18490.27690.0408-0.03760.2147-0.05260.226953.7193-1.53339.537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A364 - 533
2X-RAY DIFFRACTION2A534 - 558
3X-RAY DIFFRACTION3B365 - 533
4X-RAY DIFFRACTION4B534 - 559
5X-RAY DIFFRACTION5C364 - 533
6X-RAY DIFFRACTION6C534 - 558
7X-RAY DIFFRACTION7D364 - 533
8X-RAY DIFFRACTION8D534 - 558

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