7OZT | pdb_00007ozt

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.209 (Depositor), 0.208 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42771
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.209 (Depositor), 0.208 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-13

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-07-13
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.