PDB-8y68: the crystal structure of apo CASK-CaMK

ID or keywords:

Entry

Database: PDB / ID: 8y68

Title

the crystal structure of apo CASK-CaMK

Components

Peripheral plasma membrane protein CASK

Keywords

TRANSPORT PROTEIN / CASK / CaMK domain

Function / homology

Function and homology information

negative regulation of cellular response to growth factor stimulus / GMP kinase activity / neurexin family protein binding / negative regulation of wound healing / Dopamine Neurotransmitter Release Cycle / regulation of neurotransmitter secretion / nuclear lamina / calcium ion import / Nephrin family interactions / Assembly and cell surface presentation of NMDA receptors ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Li, W. / Feng, W.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: Structural basis for the Ca2+/CaM-mediated regulation of CASK-CaMK
Authors: Li, W.

History

Deposition	Feb 2, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 6, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8y68.cif.gz	267.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8y68.ent.gz	216.6 KB	Display	PDB format
PDBx/mmJSON format	8y68.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8y68_validation.pdf.gz	442.3 KB	Display	wwPDB validaton report
Full document	8y68_full_validation.pdf.gz	450.7 KB	Display
Data in XML	8y68_validation.xml.gz	27.9 KB	Display
Data in CIF	8y68_validation.cif.gz	36.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y6/8y68 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/8y68	HTTPS FTP

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Related structure data

Related structure data	6kmhS S: Starting model for refinement
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	#167 - Nov 2013 SNARE Proteins similarity (2) #134 - Feb 2011 Integrin similarity (1) #199 - Jul 2016 Monellin similarity (1) #19 - Jul 2001 Actin similarity (1)

Deposited unit

A: Peripheral plasma membrane protein CASK

B: Peripheral plasma membrane protein CASK

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

1

A: Peripheral plasma membrane protein CASK

defined by author
Evidence: gel filtration
38.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Peripheral plasma membrane protein CASK

defined by author
38.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.490, 93.680, 139.970
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Peripheral plasma membrane protein CASK / hCASK / Calcium/calmodulin-dependent serine protein kinase / Protein lin-2 homolog Mass: 38177.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2 / Production host: Escherichia coli (E. coli) References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.55 Å³/Da / Density % sol: 51.84 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium citrate tribasic dihydrate, pH 5.0, 10% (v/v) PEG6000.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.2→46.84 Å / Num. obs: 40508 / % possible obs: 99.6 % / Redundancy: 12.8 % / CC_1/2: 0.998 / CC star: 1 / Net I/σ(I): 9.8
Reflection shell	Resolution: 2.2→2.26 Å / Num. unique obs: 2957 / CC_1/2: 0.676

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Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6KMH

6kmh

Resolution: 2.2→46.84 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2638	3797	4.96 %
R_work	0.2381	-	-
obs	0.2395	40386	99.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.2→46.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5024	0	0	116	5140

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5169
X-RAY DIFFRACTION	f_angle_d	0.493	6977
X-RAY DIFFRACTION	f_dihedral_angle_d	21.934	1939
X-RAY DIFFRACTION	f_chiral_restr	0.043	747
X-RAY DIFFRACTION	f_plane_restr	0.004	897

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 (%)
2.2-2.23	0.3633	139	0.4037	2731	X-RAY DIFFRACTION	100
2.23-2.26	0.4786	139	0.4666	2686	X-RAY DIFFRACTION	100
2.26-2.29	0.3831	144	0.3772	2695	X-RAY DIFFRACTION	100
2.29-2.32	0.3843	140	0.3772	2682	X-RAY DIFFRACTION	100
2.32-2.36	0.3292	139	0.3477	2699	X-RAY DIFFRACTION	100
2.36-2.39	0.4347	139	0.3402	2696	X-RAY DIFFRACTION	100
2.39-2.43	0.2882	142	0.3129	2666	X-RAY DIFFRACTION	100
2.43-2.47	0.3025	141	0.2804	2731	X-RAY DIFFRACTION	100
2.47-2.52	0.3167	142	0.2913	2691	X-RAY DIFFRACTION	100
2.52-2.57	0.3265	138	0.2832	2683	X-RAY DIFFRACTION	100
2.57-2.62	0.3166	147	0.2754	2694	X-RAY DIFFRACTION	100
2.62-2.68	0.3369	137	0.2671	2714	X-RAY DIFFRACTION	100
2.68-2.74	0.3319	143	0.2597	2684	X-RAY DIFFRACTION	100
2.74-2.81	0.3091	140	0.25	2729	X-RAY DIFFRACTION	100
2.81-2.88	0.2709	143	0.261	2668	X-RAY DIFFRACTION	100
2.88-2.97	0.3282	146	0.2648	2710	X-RAY DIFFRACTION	100
2.97-3.06	0.2933	139	0.2523	2668	X-RAY DIFFRACTION	100
3.06-3.17	0.304	141	0.229	2737	X-RAY DIFFRACTION	100
3.17-3.3	0.2942	142	0.2353	2678	X-RAY DIFFRACTION	100
3.3-3.45	0.2279	140	0.2272	2714	X-RAY DIFFRACTION	100
3.45-3.63	0.232	138	0.2263	2675	X-RAY DIFFRACTION	100
3.63-3.86	0.2365	139	0.2102	2697	X-RAY DIFFRACTION	100
3.86-4.16	0.2143	134	0.1887	2713	X-RAY DIFFRACTION	100
4.16-4.57	0.1951	143	0.1782	2707	X-RAY DIFFRACTION	100
4.58-5.24	0.2219	137	0.1837	2662	X-RAY DIFFRACTION	99
5.24-6.59	0.1917	141	0.2138	2705	X-RAY DIFFRACTION	100
6.6-46.84	0.245	144	0.2132	2681	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	2.8013	0.4888	-0.4167	5.8856	-1.1918	4.2848	0.2283	-0.1219	0.2728	0.9539	0.0068	-0.2088	-0.5559	0.0909	-0.1606	0.3954	-0.0036	0.01	0.255	0.006	0.3079	-13.5296	15.4843	59.3422
2	3.5172	-1.2683	1.283	2.5064	-0.9436	3.3355	-0.0488	-0.427	0.0966	-0.0088	0.009	-0.5625	-0.2688	0.0958	0.0227	0.2412	-0.042	0.004	0.5273	0.0035	0.4568	25.022	18.4075	35.0412
3	2.4184	-0.8018	0.171	5.4299	-0.7652	3.1355	0.0719	0.1732	-0.1666	-1.2174	0.0434	-0.1074	0.4205	-0.0666	-0.0683	0.4822	-0.0086	0.0002	0.2705	0.0084	0.2295	14.1997	15.214	10.2139
4	3.579	-1.9333	-1.0544	3.4879	1.3845	4.7355	-0.2859	0.0692	-0.1642	-0.6041	-0.1115	-0.7	0.1794	1.1815	0.2605	0.777	0.0056	0.1905	0.6126	0.1007	0.7697	27.8874	10.3914	14.7543
5	4.2088	1.9951	-1.5626	2.2899	-1.2381	4.0588	-0.1599	0.4494	-0.393	-0.0511	0.0708	-0.497	0.3221	0.0186	0.084	0.2516	0.0572	0.0197	0.4699	0.0131	0.5295	-4.6795	11.6823	35.1453

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 99 through 326 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 5 through 98 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 99 through 288 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 289 through 326 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 98 )

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