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- PDB-9kbo: Crystal structure of human Shiftless (SFL) containing phosphoryla... -

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Basic information

Entry
Database: PDB / ID: 9kbo
TitleCrystal structure of human Shiftless (SFL) containing phosphorylation sites Ser249, Thr250, Thr253 and Ser256
ComponentsShiftless antiviral inhibitor of ribosomal frameshifting protein
KeywordsANTIVIRAL PROTEIN / Host factor / Antivirus / -1 PRF / RNA-bingding
Function / homology
Function and homology information


response to type III interferon / response to interferon-beta / regulation of translational termination / response to type I interferon / sequence-specific mRNA binding / negative regulation of viral genome replication / negative regulation of translational frameshifting / response to type II interferon / P-body / ribosome binding ...response to type III interferon / response to interferon-beta / regulation of translational termination / response to type I interferon / sequence-specific mRNA binding / negative regulation of viral genome replication / negative regulation of translational frameshifting / response to type II interferon / P-body / ribosome binding / defense response to virus / viral translational frameshifting / innate immune response / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Shiftless antiviral inhibitor of ribosomal frameshifting / Uncharacterised protein UPF0515
Similarity search - Domain/homology
Shiftless antiviral inhibitor of ribosomal frameshifting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, Z. / Hao, W. / Zhang, Y. / Hou, P. / Cui, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2025
Title: Crystal Structure of a host factor Shiftless(SHFL)
Authors: Li, Z. / Hao, W. / Zhang, Y. / Hou, P. / Cui, S.
History
DepositionOct 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 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: Shiftless antiviral inhibitor of ribosomal frameshifting protein
B: Shiftless antiviral inhibitor of ribosomal frameshifting protein
C: Shiftless antiviral inhibitor of ribosomal frameshifting protein
D: Shiftless antiviral inhibitor of ribosomal frameshifting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,37215
Polymers133,6524
Non-polymers71911
Water8,989499
1
A: Shiftless antiviral inhibitor of ribosomal frameshifting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6094
Polymers33,4131
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Shiftless antiviral inhibitor of ribosomal frameshifting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6094
Polymers33,4131
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Shiftless antiviral inhibitor of ribosomal frameshifting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6094
Polymers33,4131
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Shiftless antiviral inhibitor of ribosomal frameshifting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5443
Polymers33,4131
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.719, 89.411, 82.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Shiftless antiviral inhibitor of ribosomal frameshifting protein / SFL / SHFL / Interferon-regulated antiviral protein / IRAV / Repressor of yield of DENV protein / RyDEN


Mass: 33413.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHFL, C19orf66, FLJ11286, IRAV, RYDEN, SFL / Cell line (production host): High Five / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUL5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 20 % w/v Polyethylene glycol 3350, pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2023
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→39.847 Å / Num. obs: 106364 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 47.589 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.175 / Χ2: 0.98 / Net I/σ(I): 13.4
Reflection shellResolution: 2→5 Å / Num. unique obs: 16829 / CC1/2: 0.1

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.28 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 5157 4.96 %Random
Rwork0.2217 ---
obs0.2248 103986 97.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8153 0 9 499 8661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148421
X-RAY DIFFRACTIONf_angle_d1.4111400
X-RAY DIFFRACTIONf_dihedral_angle_d17.6883308
X-RAY DIFFRACTIONf_chiral_restr0.0641163
X-RAY DIFFRACTIONf_plane_restr0.0171516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.53081040.44391929X-RAY DIFFRACTION58
2.02-2.040.40611400.40082718X-RAY DIFFRACTION83
2.04-2.070.44191670.38673100X-RAY DIFFRACTION92
2.07-2.090.36081790.38193265X-RAY DIFFRACTION98
2.09-2.120.38921660.35863278X-RAY DIFFRACTION98
2.12-2.150.40071950.35163290X-RAY DIFFRACTION100
2.15-2.180.36781830.33623325X-RAY DIFFRACTION99
2.18-2.210.35261730.32823317X-RAY DIFFRACTION100
2.21-2.250.40741750.34783336X-RAY DIFFRACTION99
2.25-2.280.35011920.3223310X-RAY DIFFRACTION99
2.28-2.320.37071760.29923330X-RAY DIFFRACTION100
2.32-2.370.3391780.29933328X-RAY DIFFRACTION99
2.37-2.410.32341820.3013340X-RAY DIFFRACTION99
2.41-2.460.34481630.29123344X-RAY DIFFRACTION99
2.46-2.510.34481640.28243346X-RAY DIFFRACTION99
2.51-2.570.32691730.27213383X-RAY DIFFRACTION99
2.57-2.640.33171920.25873357X-RAY DIFFRACTION100
2.64-2.710.31051790.23973350X-RAY DIFFRACTION100
2.71-2.790.28041990.23033341X-RAY DIFFRACTION100
2.79-2.880.2851920.23243356X-RAY DIFFRACTION100
2.88-2.980.26751530.23193417X-RAY DIFFRACTION100
2.98-3.10.3031610.23893384X-RAY DIFFRACTION100
3.1-3.240.31032010.22463354X-RAY DIFFRACTION100
3.24-3.410.27441820.20883409X-RAY DIFFRACTION100
3.41-3.620.28281460.20023433X-RAY DIFFRACTION100
3.62-3.90.26351940.18823436X-RAY DIFFRACTION100
3.9-4.30.21081540.15633440X-RAY DIFFRACTION100
4.3-4.920.22031500.15493489X-RAY DIFFRACTION100
4.92-6.190.22611460.18253526X-RAY DIFFRACTION100
6.19-39.280.28341980.20673598X-RAY DIFFRACTION98

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