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- PDB-6lr2: SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-2 CONTAINING P... -

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Basic information

Entry
Database: PDB / ID: 6lr2
TitleSOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-2 CONTAINING PROTEIN 2
ComponentsYTH domain containing protein 2 (YTHDC2)
KeywordsRNA BINDING PROTEIN / MEIOSIS RELATED PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
cDNA FLJ16598 fis, clone TESTI4006473, weakly similar to ATP-dependent RNA helicase A / 3'-5' RNA helicase YTHDC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMuto, Y. / Kobayashi, N. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-CONTAINING PROTEIN 2
Authors: Endo, R. / He, F. / Inoue, M. / Muto, Y. / Kigawa, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJan 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YTH domain containing protein 2 (YTHDC2)


Theoretical massNumber of molelcules
Total (without water)16,1381
Polymers16,1381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7660 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein YTH domain containing protein 2 (YTHDC2)


Mass: 16138.065 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: P060508-16
Production host: Cell-free gateway cloning vector N-term 8xHis eGFP pCellFree_G03 (others)
References: UniProt: Q6ZMY0, UniProt: Q9H6S0*PLUS
Sequence detailsAuthors state that 6L2R has a mutation, L129Q based rs1132529 in dbSNP database.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 3D 13C,15N-SEPARATED NOESY SPECTRA

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Sample preparation

DetailsType: solution
Contents: 1.0 mg/mL [U-99% 13C; U-99% 15N] helicase, 90% H2O/10% D2O
Details: 1mM D-DTT;0.02% NaN3 were used to keep the protein condition
Label: 13C, 15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mg/mL / Component: helicase / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: 20mM D-Tris-HCL (PH7.0); 100mM NaCl; 1mM D-DTT;0.02% NaN3
Ionic strength: 100 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure calculation
KUJIRA0.982N. Kobayashi, T. Kigawa, S. Yokoyamachemical shift assignment
NMRView5.0.4Johnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on 3191 NOE-derived distance contrrains, 71 main chain dihedral angle constraints based on TALOS program and 51 side chain dihedral constraints based on NOE pattern.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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