1F5Q | pdb_00001f5q

CRYSTAL STRUCTURE OF MURINE GAMMA HERPESVIRUS CYCLIN COMPLEXED TO HUMAN CYCLIN DEPENDENT KINASE 2

PDB DOI: https://doi.org/10.2210/pdb1F5Q/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens, Murid gammaherpesvirus 4
Expression System: Spodoptera frugiperda, Escherichia coli
Mutation(s): No

Deposited: 2000-06-15 Released: 2000-12-27
Deposition Author(s): Card, G.L., Knowles, P., Laman, H., Jones, N., McDonald, N.Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.278 (Depositor)
R-Value Work:
0.234 (Depositor)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a gamma-herpesvirus cyclin-cdk complex.

Card, G.L., Knowles, P., Laman, H., Jones, N., McDonald, N.Q.

(2000) EMBO J 19: 2877-2888

PubMed: 10856233 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/emboj/19.12.2877
Primary Citation Related Structures:
1F5Q

PubMed Abstract:
Several gamma-herpesviruses encode proteins related to the mammalian cyclins, regulatory subunits of cyclin-dependent kinases (cdks) essential for cell cycle progression. We report a 2.5 A crystal structure of a full-length oncogenic viral cyclin from gamma-herpesvirus 68 complexed with cdk2. The viral cyclin binds cdk2 with an orientation different from cyclin A and makes several novel interactions at the interface, yet it activates cdk2 by triggering conformational changes similar to cyclin A. Sequences within the viral cyclin N-terminus lock part of the cdk2 T-loop within the core of the complex. These sequences and others are conserved amongst the viral and cellular D-type cyclins, suggesting that this structure has wider implications for other cyclin-cdk complexes. The observed resistance of this viral cyclin-cdk complex to inhibition by the p27(KIP:) cdk inhibitor is explained by sequence and conformational variation in the cyclin rendering the p27(KIP:)-binding site on the cyclin subunit non-functional.

Organizational Affiliation

Structural Biology and Gene Expression Laboratories, Imperial Cancer Research Fund, 44 Lincoln's Inn Fields, Holborn, London WC2A 3PX, UK.

Macromolecule Content

Total Structure Weight: 126.12 kDa
Atom Count: 8,723
Modeled Residue Count: 1,079
Deposited Residue Count: 1,100
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN DEPENDENT KINASE 2	A, C	298	Homo sapiens	Mutation(s): 0 EC: 2.7.1 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941 Go to UniProtKB: P24941
PHAROS: P24941 GTEx: ENSG00000123374
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24941
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GAMMA HERPESVIRUS CYCLIN	B, D	252	Murid gammaherpesvirus 4	Mutation(s): 0
UniProt
Find proteins for P89883 (Murid herpesvirus 4) Explore P89883 Go to UniProtKB: P89883
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P89883
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.278 (Depositor)
R-Value Work: 0.234 (Depositor)
R-Value Observed: 0.234 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.59	α = 90
b = 73.45	β = 102.18
c = 107.67	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-12-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-12-27
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations