[English] 日本語
Yorodumi
- PDB-9h35: Crystal structure of the YTHDC2 YTH domain -

+
Open data


ID or keywords:

Loading...

-
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 / 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. / 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. / Helicase conserved C-terminal domain / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more