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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.317 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Tyrosine mediated nuclear import of CIRBP reveals a flexible NLS recognition by TNPO3

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

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 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TSS	G [auth B]	2-(1H-INDOL-3-YL)ETHANAMINE C10 H12 N2 APJYDQYYACXCRM-UHFFFAOYSA-N
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.317 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.240 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Zhou, Q., Sagmeister, T., Pavkov-Keller, T., Madl, T.

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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

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release