[English] 日本語
Yorodumi
- PDB-9hts: Human KHNYN KH domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hts
TitleHuman KHNYN KH domain
ComponentsProtein KHNYN
KeywordsANTIVIRAL PROTEIN / ZAP associated protein
Function / homology
Function and homology information


RNA endonuclease activity / cytoplasmic ribonucleoprotein granule / mRNA binding / nucleus
Similarity search - Function
: / : / : / N4BP1, first type I KH-domain / N4BP1, second type I KH-domain / N4BP1, C-terminal UBA domain / Ribonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain / K Homology domain, type 1 superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsYoule, R.L. / Cottee, M.A. / Taylor, I.A. / Morris, E.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome TrustCC2029 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2029 United Kingdom
Cancer Research UKCC2029 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural and functional characterization of the extended-diKH domain from the antiviral endoribonuclease KHNYN.
Authors: Youle, R.L. / Lista, M.J. / Bouton, C. / Kunzelmann, S. / Wilson, H. / Cottee, M.A. / Purkiss, A.G. / Morris, E.R. / Neil, S.J.D. / Taylor, I.A. / Swanson, C.M.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein KHNYN
B: Protein KHNYN


Theoretical massNumber of molelcules
Total (without water)42,2422
Polymers42,2422
Non-polymers00
Water48627
1
A: Protein KHNYN


Theoretical massNumber of molelcules
Total (without water)21,1211
Polymers21,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein KHNYN


Theoretical massNumber of molelcules
Total (without water)21,1211
Polymers21,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.833, 121.797, 44.547
Angle α, β, γ (deg.)90.000, 108.545, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 12 - 198 / Label seq-ID: 6 - 192

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

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


Mass: 21120.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHNYN, KIAA0323 / Production host: Escherichia coli (E. coli) / References: UniProt: O15037
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris, 250 mM NaCl, 35 % PEG 3000, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.198→60.899 Å / Num. obs: 10852 / % possible obs: 73.3 % / Redundancy: 5.4 % / CC1/2: 0.995 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.26 Å / Num. unique obs: 183 / CC1/2: 0.577

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.198→60.899 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 10.09 / SU ML: 0.242 / Cross valid method: FREE R-VALUE / ESU R Free: 0.34
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 780 7.18 %RANDOM
Rwork0.1961 10083 --
all0.201 ---
obs-10852 73.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.986 Å2
Baniso -1Baniso -2Baniso -3
1--0.175 Å2-0 Å20.137 Å2
2--0.048 Å2-0 Å2
3---0.029 Å2
Refinement stepCycle: LAST / Resolution: 2.198→60.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 0 27 2786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122829
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162664
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.8283844
X-RAY DIFFRACTIONr_angle_other_deg0.4721.7436159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.497517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01410469
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.47210131
X-RAY DIFFRACTIONr_chiral_restr0.0630.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023336
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
X-RAY DIFFRACTIONr_nbd_refined0.2240.2609
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.22418
X-RAY DIFFRACTIONr_nbtor_refined0.180.21386
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.238
X-RAY DIFFRACTIONr_nbd_other0.2420.2159
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.28
X-RAY DIFFRACTIONr_mcbond_it2.4893.0111413
X-RAY DIFFRACTIONr_mcbond_other2.4893.0121413
X-RAY DIFFRACTIONr_mcangle_it3.9465.3931761
X-RAY DIFFRACTIONr_mcangle_other3.9455.3941762
X-RAY DIFFRACTIONr_scbond_it3.3353.4741416
X-RAY DIFFRACTIONr_scbond_other3.3343.4751417
X-RAY DIFFRACTIONr_scangle_it5.4646.1832083
X-RAY DIFFRACTIONr_scangle_other5.4626.1842084
X-RAY DIFFRACTIONr_lrange_it7.65936.1353107
X-RAY DIFFRACTIONr_lrange_other7.65936.1423107
X-RAY DIFFRACTIONr_ncsr_local_group_10.1130.055355
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.112740.05008
12BX-RAY DIFFRACTIONLocal ncs0.112740.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.198-2.2550.508230.29183X-RAY DIFFRACTION18.9862
2.255-2.3170.243240.278256X-RAY DIFFRACTION26.0951
2.317-2.3840.324200.275318X-RAY DIFFRACTION32.6255
2.384-2.4570.336350.231409X-RAY DIFFRACTION44.9848
2.457-2.5380.307420.251495X-RAY DIFFRACTION54.8519
2.538-2.6270.335320.242632X-RAY DIFFRACTION68.1725
2.627-2.7260.312500.252671X-RAY DIFFRACTION83.3526
2.726-2.8370.306720.246764X-RAY DIFFRACTION92.9922
2.837-2.9630.318530.239776X-RAY DIFFRACTION97.7594
2.963-3.1070.31510.205723X-RAY DIFFRACTION98.2234
3.107-3.2750.284480.184703X-RAY DIFFRACTION99.0765
3.275-3.4730.266310.163696X-RAY DIFFRACTION99.1814
3.473-3.7110.233530.169631X-RAY DIFFRACTION99.1304
3.711-4.0080.229530.167575X-RAY DIFFRACTION98.7421
4.008-4.3880.305310.175540X-RAY DIFFRACTION98.9601
4.388-4.9030.2650.158474X-RAY DIFFRACTION99.6303
4.903-5.6550.237280.205444X-RAY DIFFRACTION100
5.655-6.9110.25280.185348X-RAY DIFFRACTION98.9474
6.911-9.7120.16240.163288X-RAY DIFFRACTION98.4227
9.712-60.8990.25170.21157X-RAY DIFFRACTION97.7528

+
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