7VKL

Crystal structure of MmIMP3-KH12 in complex with zipcode RNA

• PDB DOI: https://doi.org/10.2210/pdb7VKL/pdb
• NAKB: 7VKL

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-09-30 Released: 2022-10-05 
• Deposition Author(s): Li, X.J., Wu, B.X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.257 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Literature

Crystal structure of MmIMP3-KH12 in complex with zipcode RNA

Li, X.J., Wu, B.X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 20.85 kDa 
• Atom Count: 1,487 
• Modelled Residue Count: 168 
• Deposited Residue Count: 172 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-like growth factor 2 mRNA-binding protein 3	A	164	Mus musculus	Mutation(s): 0  Gene Names: Igf2bp3, Vickz3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CPN8 (Mus musculus) Explore Q9CPN8  Go to UniProtKB:  Q9CPN8
IMPC:  MGI:1890359

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (8-mer)	B	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.257 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.982	α = 90
b = 62.71	β = 90
c = 65.687	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-05 
Deposition Author(s): Li, X.J., Wu, B.X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-10-05
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description