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- PDB-9h35: Crystal structure of the YTHDC2 YTH domain -

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Basic information

Entry
Database: PDB / ID: 9h35
TitleCrystal structure of the YTHDC2 YTH domain
Components3'-5' RNA helicase YTHDC2
KeywordsRNA BINDING PROTEIN / YTHDC1 / inhibitor / complex / reader
Function / homology
Function and homology information


germline cell cycle switching, mitotic to meiotic cell cycle / ribonucleoprotein granule / host-mediated activation of viral genome replication / 3'-5' RNA helicase activity / N6-methyladenosine-containing RNA reader activity / oocyte development / ATP-dependent activity, acting on RNA / RNA polymerase binding / response to tumor necrosis factor / spermatid development ...germline cell cycle switching, mitotic to meiotic cell cycle / ribonucleoprotein granule / host-mediated activation of viral genome replication / 3'-5' RNA helicase activity / N6-methyladenosine-containing RNA reader activity / oocyte development / ATP-dependent activity, acting on RNA / RNA polymerase binding / response to tumor necrosis factor / spermatid development / response to interleukin-1 / meiotic cell cycle / helicase activity / RNA helicase / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / ATP binding
Similarity search - Function
DExH-box ATP-dependent RNA helicase, R3H domain / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. / YTH domain / YT521-B-like domain / YTH domain profile. / : ...DExH-box ATP-dependent RNA helicase, R3H domain / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. / YTH domain / YT521-B-like domain / YTH domain profile. / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
3'-5' RNA helicase YTHDC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsBedi, R.K. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of the YTHDC2 YTH domain
Authors: Bedi, R.K. / Caflisch, A.
History
DepositionOct 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3'-5' RNA helicase YTHDC2
B: 3'-5' RNA helicase YTHDC2
C: 3'-5' RNA helicase YTHDC2
D: 3'-5' RNA helicase YTHDC2


Theoretical massNumber of molelcules
Total (without water)65,0824
Polymers65,0824
Non-polymers00
Water68538
1
A: 3'-5' RNA helicase YTHDC2


Theoretical massNumber of molelcules
Total (without water)16,2701
Polymers16,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3'-5' RNA helicase YTHDC2


Theoretical massNumber of molelcules
Total (without water)16,2701
Polymers16,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3'-5' RNA helicase YTHDC2


Theoretical massNumber of molelcules
Total (without water)16,2701
Polymers16,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3'-5' RNA helicase YTHDC2


Theoretical massNumber of molelcules
Total (without water)16,2701
Polymers16,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.972, 115.972, 205.847
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-1521-

HOH

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Components

#1: Protein
3'-5' RNA helicase YTHDC2 / YTH domain-containing protein 2 / hYTHDC2


Mass: 16270.419 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H6S0, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 50 mM ammonium sulfate, 5 mM BIS-TRIS pH 6.5, 30 % PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96863 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.68→48.8 Å / Num. obs: 43492 / % possible obs: 100 % / Redundancy: 10.71 % / Biso Wilson estimate: 77.47 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.75
Reflection shellResolution: 2.68→2.86 Å / Num. unique obs: 7664 / CC1/2: 0.585

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→48.79 Å / SU ML: 0.5319 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2843 1137 4.8 %
Rwork0.2268 22541 -
obs0.2294 23678 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.44 Å2
Refinement stepCycle: LAST / Resolution: 2.68→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 0 38 4170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874240
X-RAY DIFFRACTIONf_angle_d0.98625752
X-RAY DIFFRACTIONf_chiral_restr0.0549612
X-RAY DIFFRACTIONf_plane_restr0.0071742
X-RAY DIFFRACTIONf_dihedral_angle_d16.05211472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.80.51741400.48542726X-RAY DIFFRACTION99.65
2.8-2.950.42021530.35372759X-RAY DIFFRACTION99.79
2.95-3.130.34471350.28712762X-RAY DIFFRACTION99.69
3.13-3.380.36681220.28672778X-RAY DIFFRACTION99.9
3.38-3.720.31051560.25042770X-RAY DIFFRACTION99.97
3.72-4.250.24661640.19712807X-RAY DIFFRACTION100
4.25-5.360.25261410.18072865X-RAY DIFFRACTION100
5.36-48.790.23761260.20143074X-RAY DIFFRACTION99.91

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