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- PDB-9hts: human KHNYN KH domain -

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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.
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: To Be Published
Title: human KHNYN KH domain
Authors: Youle, R.L. / Cottee, M.A. / Taylor, I.A.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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

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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: 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

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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

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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

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