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), 0.220 (DCC)
R-Value Work:
0.180 (Depositor), 0.190 (DCC)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 247
Deposited Residue Count: 307
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Camelid nanobody NB09	A [auth AAA]	132	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.220 (DCC)
R-Value Work: 0.180 (Depositor), 0.190 (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

View Full Validation Report

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

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.