7OZT

Nanobodies restore stability to cancer-associated mutants of tumor suppressor protein p16INK4a

• PDB DOI: https://doi.org/10.2210/pdb7OZT/pdb

• Classification: CELL CYCLE
• Organism(s): Lama glama, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-28 Released: 2022-07-13 
• Deposition Author(s): Pastok, M.W., Burbidge, O., Itzhaki, L., Endicott, J.A., Noble, M.E.M.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.209 
• R-Value Work: 0.180 

Literature

Nanobodies restore stability to cancer-associated mutants of tumor suppressor protein p16INK4a

Burbidge, O., Pastok, M.W., Hodder, S.L., Zenkeviciute, G., Noble, M.E.M., Endicott, J.A., Itzhaki, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.91 kDa 
• Atom Count: 1,970 
• Modelled Residue Count: 247 
• Deposited Residue Count: 307 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Camelid nanobody NB09	A [auth AAA]	132	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase inhibitor 2A	B [auth BBB]	175	Homo sapiens	Mutation(s): 0  Gene Names: CDKN2A, CDKN2, MTS1
UniProt & NIH Common Fund Data Resources
Find proteins for P42771 (Homo sapiens) Explore P42771  Go to UniProtKB:  P42771
PHAROS:  P42771 GTEx:  ENSG00000147889

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.209 
• R-Value Work: 0.180 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.119	α = 90
b = 182.931	β = 90
c = 65.225	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-13 
Deposition Author(s): Pastok, M.W., Burbidge, O., Itzhaki, L., Endicott, J.A., Noble, M.E.M.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N009738/1

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description