[English] 日本語
Yorodumi
- PDB-9cs9: KHNYN KH1-KH2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cs9
TitleKHNYN KH1-KH2
ComponentsProtein KHNYN
KeywordsANTIVIRAL PROTEIN / KH
Function / homologyRibonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain / K Homology domain, type 1 superfamily / RNA endonuclease activity / cytoplasmic ribonucleoprotein granule / mRNA binding / nucleus / Protein KHNYN
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYeoh, Z.C. / Ohi, M.D. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170660-01 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: A minimal complex of KHNYN and zinc-finger antiviral protein binds and degrades single-stranded RNA.
Authors: Yeoh, Z.C. / Meagher, J.L. / Kang, C.Y. / Bieniasz, P.D. / Smith, J.L. / Ohi, M.D.
History
DepositionJul 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein KHNYN
B: Protein KHNYN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8896
Polymers41,5052
Non-polymers3844
Water81145
1
A: Protein KHNYN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9453
Polymers20,7521
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein KHNYN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9453
Polymers20,7521
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.269, 82.269, 177.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Protein KHNYN / KH and NYN domain-containing protein


Mass: 20752.457 Da / Num. of mol.: 2 / Fragment: KH1 and KH2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHNYN, KIAA0323 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15037
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris pH 8.0, 1.4 M Li2SO4, 5% methanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.5→48.63 Å / Num. obs: 40169 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 58.7 Å2 / CC1/2: 0.999 / Net I/σ(I): 0.15
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 12.4 % / Num. unique obs: 21967 / CC1/2: 0.876 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
Coot0.9.8.93model building
PHENIX1.20.1-4487-000refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.63 Å / SU ML: 0.3793 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2401 2359 5.87 %
Rwork0.1981 37810 -
obs0.2005 40169 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.13 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 20 45 2814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892849
X-RAY DIFFRACTIONf_angle_d0.99033876
X-RAY DIFFRACTIONf_chiral_restr0.0578429
X-RAY DIFFRACTIONf_plane_restr0.0092508
X-RAY DIFFRACTIONf_dihedral_angle_d17.38621053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.36431400.34222232X-RAY DIFFRACTION99.92
2.55-2.610.34721390.30882196X-RAY DIFFRACTION99.91
2.61-2.670.3251430.29032237X-RAY DIFFRACTION100
2.67-2.730.37941360.28192223X-RAY DIFFRACTION100
2.73-2.810.44831400.28122213X-RAY DIFFRACTION100
2.81-2.890.35031350.28542229X-RAY DIFFRACTION99.96
2.89-2.980.30331410.27812255X-RAY DIFFRACTION100
2.98-3.090.36891320.29932203X-RAY DIFFRACTION99.87
3.09-3.210.34561430.28332230X-RAY DIFFRACTION99.92
3.21-3.360.29031360.23382228X-RAY DIFFRACTION99.92
3.36-3.540.23591330.19642232X-RAY DIFFRACTION100
3.54-3.760.2791410.18832240X-RAY DIFFRACTION99.96
3.76-4.050.20871390.16672192X-RAY DIFFRACTION99.96
4.05-4.460.17911380.15622227X-RAY DIFFRACTION100
4.46-5.10.16531410.13772235X-RAY DIFFRACTION99.96
5.1-6.420.19931410.1742221X-RAY DIFFRACTION100
6.42-48.630.16921410.14942217X-RAY DIFFRACTION99.45

+
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