PDB-1w98: The structural basis of CDK2 activation by cyclin E

ID or keywords:

Entry

Database: PDB / ID: 1w98

Title

The structural basis of CDK2 activation by cyclin E

Components

CELL DIVISION PROTEIN KINASE 2
G1/S-SPECIFIC CYCLIN E1

Keywords

TRANSFERASE / CELL CYCLE

Function / homology

Function and homology information

cyclin E1-CDK2 complex / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / PTK6 Regulates Cell Cycle / positive regulation of mesenchymal stem cell proliferation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / homologous chromosome pairing at meiosis / p53-Dependent G1 DNA Damage Response / RHOBTB3 ATPase cycle / G0 and Early G1 / cyclin-dependent protein serine/threonine kinase regulator activity ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Lowe, E.D. / Honda, R. / Dubinina, E. / Skamnaki, V. / Cook, A. / Johnson, L.N.

Citation

Journal: Embo J. / Year: 2005
Title: The Structure of Cyclin E1/Cdk2: Implications for Cdk2 Activation and Cdk2-Independent Roles
Authors: Honda, R. / Lowe, E.D. / Dubinina, E. / Skamnaki, V. / Cook, A. / Brown, N. / Johnson, L.N.

History

Deposition	Oct 7, 2004	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 2, 2005	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1w98.cif.gz	144.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	1w98_validation.pdf.gz	441.7 KB	Display	wwPDB validaton report
Full document	1w98_full_validation.pdf.gz	459.4 KB	Display
Data in XML	1w98_validation.xml.gz	30.3 KB	Display
Data in CIF	1w98_validation.cif.gz	44.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w9/1w98 ftp://data.pdbj.org/pub/pdb/validation_reports/w9/1w98	HTTPS FTP

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Related structure data

Related structure data	1jstS 1aq1 1b38 1b39 1buh 1ckp 1di8 1dm2 1e1v 1e1x 1e9h 1f5q 1fin 1fq1 1fvt 1fvv 1g5s 1gih 1gii 1gij 1gy3 1gz8 1h00 1h01 1h07 1h08 1h0v 1h0w 1h1p 1h1q 1h1r 1h1s 1h24 1h25 1h26 1h27 1h28 1hck 1hcl 1jsu 1jsv 1jvp 1ke5 1ke6 1ke7 1ke8 1ke9 1ogu 1oi9 1oiq 1oir 1oit 1oiu 1oiy 1okv 1okw 1ol1 1ol2 1p2a 1p5e 1pf8 1pkd 1pw2 1pxi 1pxj 1pxk 1pxl 1pxm 1pxn 1pxo 1pxp 1pye 1qmz 1r78 1urc 1urw 1v1k 1vyw 1vyz 1w0x 1w8c 2c5v S: Starting model for refinement
Similar structure data	6l9j-2 5l2w-d 4fev-9 2wze-1 4n91-2 1ol2-2 4gki-13 2wys-2 2f2c-d 2wze-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#236 - Aug 2019 Cyclin and Cyclin-dependent Kinase similarity (18) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #47 - Nov 2003 Simian Virus 40 similarity (6) #31 - Jul 2002 p53 Tumor Suppressor similarity (2) #213 - Sep 2017 Sirtuins similarity (2) #67 - Jul 2005 TATA-Binding Protein similarity (3) #150 - Jun 2012 Sliding Clamps similarity (1) #122 - Feb 2010 Enhanceosome similarity (2) #221 - May 2018 Human Papillomavirus and Vaccines similarity (2) #234 - Jun 2019 MDM2 and Cancer similarity (2) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#236 - Aug 2019
Cyclin and Cyclin-dependent Kinase
similarity (18)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#47 - Nov 2003
Simian Virus 40
similarity (6)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (2)
#213 - Sep 2017
Sirtuins
similarity (2)
#67 - Jul 2005
TATA-Binding Protein
similarity (3)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (2)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (2)
#234 - Jun 2019
MDM2 and Cancer
similarity (2)
#34 - Oct 2002
Dihydrofolate Reductase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)

Deposited unit

A: CELL DIVISION PROTEIN KINASE 2

B: G1/S-SPECIFIC CYCLIN E1

66.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	99.620, 99.620, 149.987
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	CELL DIVISION PROTEIN KINASE 2 / CYCLIN DEPENDENT KINASE 2 / P33 PROTEIN KINASE Mass: 34030.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: PHOSPHOTHREONINE AT POSITION 160 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24941, EC: 2.7.1.37
#2: Protein	G1/S-SPECIFIC CYCLIN E1 / CYCLIN E Mass: 32909.371 Da / Num. of mol.: 1 Fragment: FRAGMENT DERIVED FROM ELASTASE CLEAVAGE, RESIDUES 96-378 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P24864
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	AN ADDITIONAL SER RESIDUE FROM THE EXPRESSION CONSTRUCT IS PRESENT AT POSITION 0 THIS FRAGMENT ...AN ADDITIONAL SER RESIDUE FROM THE EXPRESSION CONSTRUCT IS PRESENT AT POSITION 0 THIS FRAGMENT CONTAINS ONLY RESIDUES 81-363

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56 % Description: MR SEARCH MODEL MODIFIED TO CONTAIN ONLY THE N- TERMINAL CYCLIN BOX DOMAIN OF CYCLIN A
Crystal grow	pH: 7.5 Details: PCDK2/CYCLIN E (6-8 MG/ML), 1 MM AMPPNP, 10-15% PEG3350, 0.2 M SODIUM CITRATE PH7.5, pH 7.50

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0091
Detector	Type: ADSC CCD / Detector: CCD / Date: Aug 1, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0091 Å / Relative weight: 1
Reflection	Resolution: 2.13→34.28 Å / Num. obs: 39329 / % possible obs: 94.2 % / Observed criterion σ(I): 1.5 / Redundancy: 4 % / R_merge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shell	Resolution: 2.13→2.21 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / % possible all: 53.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0003	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JST

1jst

Resolution: 2.15→83.05 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.933 / SU B: 11 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.246	1984	5 %	RANDOM
R_work	0.181	-	-	-
obs	0.185	37310	94.2 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 45.24 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.72 Å²	0 Å²	0 Å²
2-	-	0.72 Å²	0 Å²
3-	-	-	-1.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→83.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4617	0	0	547	5164

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	4735
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.69	1.955	6429
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.585	5	566
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.556	23.886	211
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.051	15	838
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.457	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	722
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3526
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	2512
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	3179
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.22	0.2	485
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.282	0.2	67
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.247	0.2	34
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.874	1.5	2943
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.411	2	4622
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.232	3	2076
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.258	4.5	1807
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.15→2.21 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.339	80
R_work	0.216	1221

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.6884	0.6915	0.1559	2.1184	0.2471	1.6687	0.1494	0.0254	0.0071	0.1109	-0.1012	-0.1828	0.1328	0.3431	-0.0482	-0.1216	0.0091	-0.0078	0.06	0.0005	-0.0209	41.5961	14.0014	-4.6329
2	2.1599	1.2777	1.7982	0.7963	1.4639	5.4475	0.0216	0.1963	-0.2821	-0.2257	0.2108	-0.1016	0.0418	0.7312	-0.2324	-0.1083	0.0085	0.0347	0.0369	-0.0188	0.0403	36.8728	18.4936	-19.9836
3	4.8356	3.3298	2.1744	5.8134	-0.3235	1.9194	0.1605	0.172	-0.1823	0.2181	0.0494	0.0404	0.0701	0.1385	-0.2099	-0.082	0.0221	0.0241	-0.0266	0.0051	-0.0073	21.9271	8.7975	-15.5924
4	1.6741	0.3178	-0.4521	1.6352	0.1993	0.9277	0.0385	0.1727	0.196	-0.114	0.0252	-0.0104	-0.1376	0.0344	-0.0637	-0.0466	-0.018	0.0112	-0.0111	0.0436	-0.0645	21.7795	29.458	-19.7737
5	1.0444	-0.4202	0.2606	1.2222	0.0088	1.3654	0.018	-0.0245	-0.0131	-0.0125	0.0352	0.1136	0.0664	-0.0807	-0.0532	-0.0573	-0.0348	-0.0059	-0.0009	0.02	-0.0313	6.8578	18.5636	-13.701
6	18.0814	-10.7407	8.1121	9.1165	-1.2103	8.3981	0.6676	0.219	0.4086	-1.3147	-0.2452	-0.2352	0.221	0.3144	-0.4224	0	-0.0542	0.1027	-0.0551	0.0161	-0.0932	28.6065	6.5788	-32.4256
7	1.9268	-0.0083	1.0351	0.9356	0.1934	2.4609	0.3921	0.153	-0.2734	0.1568	0.0717	-0.1425	0.5435	0.2436	-0.4638	0.0729	0.1229	-0.1669	-0.0715	-0.0848	-0.0029	35.8152	-10.6859	-11.9726
8	7.9995	-0.7951	6.5976	6.3782	2.8594	7.4029	0.0973	0.4679	1.1882	-0.178	-0.102	-0.0228	-0.1833	0.4288	0.0047	-0.0827	0.0598	0.0793	0.071	-0.0208	-0.0424	35.7795	1.5776	-19.1421
9	2.541	0.8802	2.515	0.773	1.3697	4.6919	0.6373	0.5949	-0.3946	0.185	0.1855	-0.0719	0.8437	0.3939	-0.8228	0.0887	0.1625	-0.1893	-0.0352	-0.1058	-0.065	23.4223	-13.293	-29.136
10	6.4955	-15.0552	-8.9283	48.5023	43.4068	50.1833	-0.3146	0.2246	-0.2796	-0.2289	-1.3606	4.1171	-0.9269	-1.9428	1.6752	-0.0105	0.0007	0.11	0.1424	0.2222	0.0296	27.5062	23.4914	-41.3511
11	10.6433	10.1698	11.2689	18.146	17.7864	17.7761	-0.6242	1.0286	2.2491	-1.4192	-0.5952	2.3239	-2.2409	-0.3675	1.2194	0.1046	0.0989	-0.1581	0.1278	0.1723	0.2184	11.824	3.1492	-30.5756

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 57
2	X-RAY DIFFRACTION	1	A	67 - 82
3	X-RAY DIFFRACTION	2	A	58 - 66
4	X-RAY DIFFRACTION	3	A	122 - 127
5	X-RAY DIFFRACTION	3	A	146 - 164
6	X-RAY DIFFRACTION	4	A	83 - 121
7	X-RAY DIFFRACTION	4	A	128 - 145
8	X-RAY DIFFRACTION	4	A	245 - 288
9	X-RAY DIFFRACTION	4	A	190 - 202
10	X-RAY DIFFRACTION	5	A	165 - 189
11	X-RAY DIFFRACTION	5	A	203 - 244
12	X-RAY DIFFRACTION	6	B	88 - 113
13	X-RAY DIFFRACTION	7	B	114 - 223
14	X-RAY DIFFRACTION	8	B	224 - 230
15	X-RAY DIFFRACTION	9	B	231 - 243
16	X-RAY DIFFRACTION	9	B	257 - 357
17	X-RAY DIFFRACTION	10	A	289 - 297
18	X-RAY DIFFRACTION	11	B	244 - 256

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