PDB-8uso: Full-length human CaMKII delta holoenzyme

ID or keywords:

Entry

Database: PDB / ID: 8uso

Title

Full-length human CaMKII delta holoenzyme

Components

calcium/calmodulin-dependent protein kinase

Keywords

TRANSFERASE / CaMKII / Kinase / CAMK2D / Holoenzyme

Function / homology

Function and homology information

organelle / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / calmodulin binding / phosphorylation / ATP binding
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Ozden, C. / Abromson, N.L. / Tomchick, D.R. / Stratton, M.M. / Garman, S.C.

Funding support

United States, 1items

Citation

Journal: To be published
Title: Full-length human CaMKII delta holoenzyme
Authors: Ozden, C. / Abromson, N.L. / Stratton, M.M. / Garman, S.C.

History

Deposition	Oct 28, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8uso.cif.gz	758.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8uso.ent.gz	647.5 KB	Display	PDB format
PDBx/mmJSON format	8uso.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8uso_validation.pdf.gz	477.7 KB	Display	wwPDB validaton report
Full document	8uso_full_validation.pdf.gz	492.4 KB	Display
Data in XML	8uso_validation.xml.gz	48.1 KB	Display
Data in CIF	8uso_validation.cif.gz	67.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/us/8uso ftp://data.pdbj.org/pub/pdb/validation_reports/us/8uso	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#44 - Aug 2003 Calmodulin similarity (4)

Deposited unit

A: calcium/calmodulin-dependent protein kinase

B: calcium/calmodulin-dependent protein kinase

C: calcium/calmodulin-dependent protein kinase

hetero molecules

154 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: calcium/calmodulin-dependent protein kinase

B: calcium/calmodulin-dependent protein kinase

C: calcium/calmodulin-dependent protein kinase

hetero molecules

A: calcium/calmodulin-dependent protein kinase

B: calcium/calmodulin-dependent protein kinase

C: calcium/calmodulin-dependent protein kinase

hetero molecules

A: calcium/calmodulin-dependent protein kinase

B: calcium/calmodulin-dependent protein kinase

C: calcium/calmodulin-dependent protein kinase

hetero molecules

A: calcium/calmodulin-dependent protein kinase

B: calcium/calmodulin-dependent protein kinase

C: calcium/calmodulin-dependent protein kinase

hetero molecules

defined by author&software
615 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	174.984, 174.984, 140.416
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	93
Space group name H-M	P4₂22

Components on special symmetry positions

ID	Model	Components
1	1	A-670- HOH

#1: Protein	calcium/calmodulin-dependent protein kinase Mass: 51173.586 Da / Num. of mol.: 3 / Mutation: D336C, Deletion 316-343 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2D / Production host: Escherichia coli (E. coli) / References: UniProt: D6R938
#2: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₂O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.5 Å³/Da / Density % sol: 64.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M pH 6.5 Bis-Tris, 16% PEG 2K , 0.2 M sodium malonate dibasic

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Data collection

Diffraction

Mean temperature: 100 K / Ambient temp details: 100 K thorughout the collection / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 96528 / % possible obs: 100 % / Redundancy: 20 % / CC_1/2: 0.992 / CC star: 0.998 / R_merge(I) obs: 0.158 / R_pim(I) all: 0.036 / R_rim(I) all: 0.162 / Χ²: 1.05 / Net I/σ(I): 5.3 / Num. measured all: 1932274

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.3-2.34	12.9	1.626	4754	0.611	0.871	0.446	1.691	0.91	99.9
2.34-2.38	15.1	1.537	4761	0.723	0.916	0.396	1.589	0.924	100
2.38-2.43	16.7	1.389	4772	0.811	0.946	0.343	1.432	0.93	100
2.43-2.48	19.2	1.299	4725	0.875	0.966	0.302	1.334	0.927	100
2.48-2.53	20.5	1.245	4782	0.88	0.967	0.281	1.277	0.935	100
2.53-2.59	21	1.03	4748	0.918	0.978	0.23	1.056	0.936	100
2.59-2.66	20	0.869	4794	0.94	0.985	0.198	0.891	0.936	100
2.66-2.73	21.3	0.718	4785	0.953	0.988	0.159	0.736	0.95	100
2.73-2.81	21.7	0.582	4798	0.973	0.993	0.127	0.596	0.953	100
2.81-2.9	21.5	0.466	4773	0.979	0.995	0.103	0.478	0.957	100
2.9-3	20.8	0.363	4792	0.984	0.996	0.081	0.372	0.967	100
3-3.12	21.4	0.28	4839	0.988	0.997	0.062	0.287	0.985	100
3.12-3.26	20.3	0.212	4788	0.992	0.998	0.048	0.217	1.009	100
3.26-3.44	21.7	0.165	4836	0.994	0.999	0.036	0.169	1.071	100
3.44-3.65	21.8	0.124	4814	0.996	0.999	0.027	0.127	1.152	100
3.65-3.93	21	0.092	4851	0.997	0.999	0.02	0.094	1.267	100
3.93-4.33	20.7	0.076	4861	0.997	0.999	0.017	0.078	1.304	100
4.33-4.95	22	0.064	4908	0.997	0.999	0.014	0.066	1.324	100
4.95-6.24	20.5	0.064	4958	0.998	1	0.014	0.066	1.222	100
6.24-50	19.9	0.046	5189	0.997	0.999	0.011	0.048	1.176	99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-3000		data scaling
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→48.53 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2132	2000	2.31 %	RANDOM
R_work	0.1844	-	-	-
obs	0.1851	86683	89.79 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→48.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10458	0	21	302	10781

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	10729
X-RAY DIFFRACTION	f_angle_d	0.503	14515
X-RAY DIFFRACTION	f_dihedral_angle_d	13.597	3988
X-RAY DIFFRACTION	f_chiral_restr	0.041	1571
X-RAY DIFFRACTION	f_plane_restr	0.007	1878

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.36	0.2867	62	0.2159	2630	X-RAY DIFFRACTION	40
2.36-2.42	0.2404	81	0.2215	3427	X-RAY DIFFRACTION	52
2.42-2.49	0.2678	111	0.2222	4719	X-RAY DIFFRACTION	71
2.49-2.57	0.2602	148	0.2214	6272	X-RAY DIFFRACTION	94
2.57-2.67	0.2781	156	0.2165	6586	X-RAY DIFFRACTION	99
2.67-2.77	0.2581	158	0.204	6676	X-RAY DIFFRACTION	100
2.77-2.9	0.2302	158	0.1925	6678	X-RAY DIFFRACTION	100
2.9-3.05	0.2231	158	0.1919	6705	X-RAY DIFFRACTION	100
3.05-3.24	0.2249	159	0.1932	6717	X-RAY DIFFRACTION	100
3.24-3.49	0.2048	158	0.1848	6722	X-RAY DIFFRACTION	100
3.49-3.85	0.1819	160	0.1616	6755	X-RAY DIFFRACTION	100
3.85-4.4	0.187	160	0.1511	6796	X-RAY DIFFRACTION	100
4.4-5.54	0.1526	162	0.1526	6853	X-RAY DIFFRACTION	100
5.55-48.53	0.2392	169	0.2051	7147	X-RAY DIFFRACTION	100

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	3.1141	-1.6769	1.5624	2.2041	0.498	2.4987	0.4379	1.092	-0.2848	-0.6389	-0.5127	0.3039	1.1543	-0.1296	0.0762	1.046	-0.0984	-0.001	0.7073	-0.1629	0.5665	62.6636	135.081	28.7833
2	3.4887	0.2194	-0.6836	0.9428	-0.4892	2.7279	0.1089	-0.1283	-0.1952	-0.1298	-0.1232	-0.0052	0.7005	-0.3022	0.0416	0.4039	-0.2138	0.0264	0.3789	0.0403	0.2654	63.7196	147.8664	50.84
3	3.2509	2.9493	-0.6628	2.6143	-0.6169	0.2531	-0.1241	0.0377	0.1149	-0.1351	0.1907	0.2906	0.1427	-0.3097	-0.0852	0.2444	-0.044	-0.0062	0.4332	0.0154	0.3494	65.9546	172.3265	40.9992
4	3.2711	-0.0108	-0.4393	1.8839	0.8239	3.6685	0.0414	0.0019	0.3653	-0.1032	0.0143	-0.2137	-0.5553	0.3048	-0.0415	0.1781	-0.0523	-0.0121	0.2467	0.0005	0.2369	94.0486	188.6671	32.0307
5	3.4475	-0.1801	0.6947	1.1116	-0.0117	3.8218	0.0062	0.0963	0.4842	0.0415	0.0742	-0.0058	-0.7247	-0.2203	0.0322	0.1827	0.0382	0.0472	0.1534	-0.0074	0.2584	80.0338	187.0575	28.6648
6	3.9204	0.47	0.7536	1.186	0.0856	3.071	-0.0978	0.0688	0.3282	0.0675	0.0113	0.0279	-0.3003	0.5789	0.0604	0.1129	-0.013	0.0247	0.1795	-0.0031	0.2011	85.6806	183.5087	33.5731
7	0.9202	-0.6499	-0.3971	3.0293	1.4816	2.9271	-0.2191	0.3542	-0.0379	0.0136	0.4098	-0.5034	0.2418	0.7648	-0.1434	0.4242	-0.2341	-0.0896	0.546	-0.0672	0.4789	47.9465	135.8707	-3.8175
8	1.7077	0.5704	0.393	2.1991	0.9214	2.1594	0.0137	-0.0444	0.123	-0.0504	-0.0708	0.4142	0.1486	-0.433	0.0585	0.2979	-0.1885	-0.0373	0.3484	0.0005	0.3365	30.0518	149.5412	7.6061
9	0.1175	-0.1776	-0.3705	0.6335	1.0864	1.8953	-0.2217	-0.4842	0.0945	-0.5771	0.2173	0.1962	-0.2567	-0.0423	0.0886	0.4782	-0.1289	-0.102	0.4842	0.0512	0.4195	36.752	162.3824	-4.466
10	1.4394	-0.2844	0.1974	2.1534	-0.1911	2.4905	0.0488	-0.0525	0.2988	0.0637	-0.0912	0.0903	-0.389	-0.1972	0.0228	0.1417	0.0157	0.0191	0.203	-0.0388	0.1657	57.2403	187.4817	16.2205
11	0.9065	-0.0099	0.7451	2.2462	-0.0285	3.2778	-0.0951	-0.1339	0.2055	-0.1192	-0.0086	0.0077	-0.1572	0.1358	0.0036	0.1122	-0.0008	-0.0291	0.1685	-0.0415	0.1582	58.98	184.9396	11.4324
12	4.8938	-0.5958	-0.3696	2.5775	-2.2741	2.8393	-0.1121	-0.1339	-0.3722	-0.0396	-0.1861	-0.747	0.1629	1.1706	0.1103	0.5628	0.039	-0.0973	0.6007	0.0691	0.6227	74.8668	135.2515	-34.3614
13	1.7661	0.2087	0.4162	1.3344	0.3344	3.0419	-0.0894	0.1808	-0.08	-0.0063	0.0592	-0.0461	0.3161	0.1023	0.0389	0.2638	-0.1504	-0.0087	0.2892	-0.051	0.2222	57.0598	146.5118	-45.5363
14	2.8619	-0.8867	0.1241	2.1885	-0.989	1.1197	0.0251	0.1194	0.1101	-0.1462	-0.0685	0.0148	-0.3423	-0.2121	0.043	0.1508	0.0182	0.0108	0.1917	-0.035	0.1965	58.5605	184.209	-19.7742
15	5.08	-0.3687	-0.6548	2.0528	0.1293	2.6855	-0.0864	-0.2109	0.3741	-0.1182	0.0063	-0.1584	-0.5675	0.0607	0.1425	0.2183	0.0214	-0.0099	0.2016	-0.0172	0.145	63.3598	184.9001	-20.0368

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 81 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 284 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 285 through 333 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 334 through 371 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 372 through 414 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 415 through 447 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 6 through 109 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 110 through 284 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 285 through 315 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 316 through 396 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 397 through 447 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 15 through 77 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 78 through 300 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 301 through 372 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 373 through 449 )

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