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- PDB-6k6u: Crystal structure of the human YTHDC2 YTH domain -

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Basic information

Entry
Database: PDB / ID: 6k6u
TitleCrystal structure of the human YTHDC2 YTH domain
Components3'-5' RNA helicase YTHDC2
KeywordsHYDROLASE / YTHDC2 / YTH / m6A / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


germline cell cycle switching, mitotic to meiotic cell cycle / ribonucleoprotein granule / positive regulation by host 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 / spermatid development / response to tumor necrosis factor ...germline cell cycle switching, mitotic to meiotic cell cycle / ribonucleoprotein granule / positive regulation by host 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 / spermatid development / response to tumor necrosis factor / 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. / ph1033 like fold / ph1033 like domains / YTH domain / YT521-B-like domain ...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. / ph1033 like fold / ph1033 like domains / 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 / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
3'-5' RNA helicase YTHDC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsMa, C. / Liao, S. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of human YTHDC2 YTH domain.
Authors: Ma, C. / Liao, S. / Zhu, Z.
History
DepositionJun 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)33,1062
Polymers33,1062
Non-polymers00
Water1,40578
1
A: 3'-5' RNA helicase YTHDC2


Theoretical massNumber of molelcules
Total (without water)16,5531
Polymers16,5531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3'-5' RNA helicase YTHDC2


Theoretical massNumber of molelcules
Total (without water)16,5531
Polymers16,5531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.520, 49.520, 119.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 16552.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9H6S0, RNA helicase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Tacsimate,Tris,PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.27→38.07 Å / Num. obs: 13234 / % possible obs: 99.9 % / Redundancy: 13.6 % / Net I/σ(I): 9.3
Reflection shellResolution: 2.27→2.44 Å / Num. unique obs: 2472

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3H
Resolution: 2.27→38.069 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 25.61
RfactorNum. reflection% reflection
Rfree0.2459 699 5.28 %
Rwork0.1952 --
obs0.1978 13234 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.27→38.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 0 78 2180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052157
X-RAY DIFFRACTIONf_angle_d0.7692908
X-RAY DIFFRACTIONf_dihedral_angle_d12.9321271
X-RAY DIFFRACTIONf_chiral_restr0.05300
X-RAY DIFFRACTIONf_plane_restr0.005372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2701-2.44530.27871450.24232472X-RAY DIFFRACTION100
2.4453-2.69140.30641610.25382495X-RAY DIFFRACTION100
2.6914-3.08070.27971260.22452522X-RAY DIFFRACTION100
3.0807-3.88070.23361310.18772510X-RAY DIFFRACTION100
3.8807-38.07410.21821360.16862536X-RAY DIFFRACTION100

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