8CMK | pdb_00008cmk

Transportin-3 TNPO3 in complex with RSY region of CIRBP

PDB DOI: https://doi.org/10.2210/pdb8CMK/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-02-20 Released: 2024-03-06
Deposition Author(s): Zhou, Q., Sagmeister, T., Pavkov-Keller, T., Madl, T.
Funding Organization(s): Austrian Research Promotion Agency, Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free:
0.317 (Depositor), 0.317 (DCC)
R-Value Work:
0.246 (Depositor), 0.246 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structural basis of phosphorylation-independent nuclear import of CIRBP by TNPO3.

Zhou, Q., Sagmeister, T., Hutten, S., Bourgeois, B., Pavkov-Keller, T., Dormann, D., Madl, T.

(2025) Nat Commun 16: 4456-4456

PubMed: 40360518 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-59802-2
Primary Citation Related Structures:
8CMK

PubMed Abstract:
Transportin 3 (TNPO3) is a nuclear import receptor known for its broad substrate specificity, often recognizing arginine-serine (SR/RS) repeat-rich nuclear localization signals (NLS) in SRSF proteins. While serine phosphorylation or glutamate presence has been associated with these NLSs, recent proteomic studies identified TNPO3 cargoes lacking SR/RS repeats. One such example is the cold-inducible RNA-binding protein (CIRBP), which contains a non-classical RSY-NLS. Using X-ray crystallography, here we investigate the TNPO3-CIRBP interaction and find that tyrosines within the RSY-NLS play a key role in binding, independent of phosphorylation. Surprisingly, serine and tyrosine phosphorylation in CIRBP's NLS inhibits TNPO3 binding, suggesting a regulatory mechanism for nuclear import. Our study reveals a non-conventional nuclear import mechanism mediated by TNPO3, which may extend to other known or yet undiscovered TNPO3 cargoes.

Organizational Affiliation

Research Unit Integrative Structural Biology, Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Graz, Austria.

Macromolecule Content

Total Structure Weight: 220.69 kDa
Atom Count: 14,823
Modeled Residue Count: 1,846
Deposited Residue Count: 1,951
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transportin-3	A, B	923	Homo sapiens	Mutation(s): 1 Gene Names: TNPO3, IPO12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5L0 (Homo sapiens) Explore Q9Y5L0 Go to UniProtKB: Q9Y5L0
PHAROS: Q9Y5L0 GTEx: ENSG00000064419
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y5L0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cold-inducible RNA-binding protein	C, D, E	35	Homo sapiens	Mutation(s): 0 Gene Names: CIRBP, A18HNRNP, CIRP
UniProt & NIH Common Fund Data Resources
Find proteins for Q14011 (Homo sapiens) Explore Q14011 Go to UniProtKB: Q14011
PHAROS: Q14011 GTEx: ENSG00000099622
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14011
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TSS Query on TSS Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	2-(1H-INDOL-3-YL)ETHANAMINE C₁₀ H₁₂ N₂ APJYDQYYACXCRM-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.317 (Depositor), 0.317 (DCC)
R-Value Work: 0.246 (Depositor), 0.246 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.526	α = 90
b = 101.805	β = 111.128
c = 114.133	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Austrian Research Promotion Agency	Austria	864690
Austrian Research Promotion Agency	Austria	870454
Austrian Science Fund	Austria	P28854
Austrian Science Fund	Austria	I3792
Austrian Science Fund	Austria	DOC-130
Austrian Science Fund	Austria	W1226