9KBO | pdb_00009kbo

Crystal structure of human Shiftless (SFL) containing phosphorylation sites Ser249, Thr250, Thr253 and Ser256

PDB DOI: https://doi.org/10.2210/pdb9KBO/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-10-31 Released: 2025-11-19
Deposition Author(s): Zhang, Y., Li, Z., Chong, H., Hou, P., Hao, W., Li, M., Liu, Z., Jia, W., Qin, B., He, Y., Cui, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.286 (Depositor), 0.285 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Phosphorylation of shiftless is important for inhibiting the programmed -1 ribosomal frameshift.

Zhang, Y., Li, Z., Chong, H., Hou, P., Hao, W., Li, M., Liu, Z., Jia, W., Qin, B., He, Y., Cui, S.

(2025) Sci Adv 11: eadw7471-eadw7471

PubMed: 41417896 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adw7471
Primary Citation Related Structures:
9KBO

PubMed Abstract:
Shiftless (SFL) is a broad-spectrum inhibitor of programmed -1 ribosomal frameshift (-1 PRF) and exhibits various antiviral activities. Here, we characterized human SFL structurally and biochemically. The 2.0-angstrom resolution crystal structure of SFL reveals a boat-like module comprising an N-terminal helical bundle and three zinc fingers at the C terminus. A hyperphosphorylation loop (HPL) buried between the helical bundle and the zinc finger 1 harbors four phosphorylated residues (p-S249, p-T250 p-T253, and p-S256), which are important to protein folding. SFL forms monomers in solution and binds the HIV-1 -1 PRF sequence with nanomolar affinity ( K _D = 5.7 nanomolar). Disruption of HPL phosphorylation decreased the RNA binding affinity and undermined the SFL-mediated -1 PRF inhibition of various viruses. Proximity-dependent biotinylation identified three cellular Ser/Thr kinases-EEF2K, NEK9, and PBK-that phosphorylate SFL in cells. These findings shed light on the mechanisms underlying -1 PRF regulation by SFL and provide insights into the role of SFL in virus inhibition.

Organizational Affiliation

NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.

Macromolecule Content

Total Structure Weight: 134.37 kDa
Atom Count: 8,732
Modeled Residue Count: 1,019
Deposited Residue Count: 1,164
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shiftless antiviral inhibitor of ribosomal frameshifting protein	A, B, C, D	291	Homo sapiens	Mutation(s): 0 Gene Names: SHFL, C19orf66, FLJ11286, IRAV, RYDEN, SFL
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUL5 (Homo sapiens) Explore Q9NUL5 Go to UniProtKB: Q9NUL5
PHAROS: Q9NUL5 GTEx: ENSG00000130813
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NUL5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B, C, D	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A, B, C, D	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR