PDB-2ux0: Structure of the oligomerisation domain of calcium-calmodulin dep...

ID or keywords:

Entry

Database: PDB / ID: 2ux0

Title

Structure of the oligomerisation domain of calcium-calmodulin dependent protein kinase II gamma

Components

CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

Keywords

TRANSFERASE /

CALMODULIN /

PROTEIN KINASE /

OLIGOMERISATION DOMAIN / SERINE- THREONINE KINASE / ATP-BINDING /

KINASE / NUCLEOTIDE-BINDING /

SERINE/THREONINE-PROTEIN KINASE /

TRANSFERASE.

Function / homology

Function and homology information

regulation of skeletal muscle adaptation / calcium-dependent protein serine/threonine phosphatase activity / calcium- and calmodulin-dependent protein kinase complex /

Ca2+/calmodulin-dependent protein kinase / Trafficking of AMPA receptors / Assembly and cell surface presentation of NMDA receptors / calmodulin-dependent protein kinase activity / insulin secretion / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.46 Å

Authors

Bunkoczi, G. / Debreczeni, J.E. / Salah, E. / Gileadi, O. / Rellos, P. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / von Delft, F. ...

Citation

Journal: Plos Biol. / Year: 2010
Title: Structure of the Camkiidelta/Calmodulin Complex Reveals the Molecular Mechanism of Camkii Kinase Activation.
Authors: Rellos, P. / Pike, A.C.W. / Niesen, F.H. / Salah, E. / Lee, W.H. / von Delft, F. / Knapp, S.

History

Deposition	Mar 26, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 10, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 10, 2011	Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy
Revision 1.3	Jan 24, 2018	Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4	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_site 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2ux0.cif.gz	170.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2ux0.ent.gz	136.5 KB	Display	PDB format
PDBx/mmJSON format	2ux0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ux/2ux0 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/2ux0	HTTPS FTP

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Related structure data

Related structure data	2v7oC 2vn9C 2vz6C 2w2cC 2welC 1hkxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5jrb-d 1kn0-d 1h2i-2 5ig3-1 5xs0-1 1h2i-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 (15) #196 - Apr 2016 Lead Poisoning similarity (10) #28 - Apr 2002 Anthrax Toxin similarity (10) #234 - Jun 2019 MDM2 and Cancer similarity (1) #85 - Jan 2007 Importins similarity (2) #148 - Apr 2012 Ras Protein similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #235 - Jul 2019 AMPA Receptor similarity (1) #127 - Jul 2010 Crystallins similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

PDB pages

PDBj /

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NCBI

Related items in Molecule of the Month

#44 - Aug 2003
Calmodulin
similarity (15)
#196 - Apr 2016
Lead Poisoning
similarity (10)
#28 - Apr 2002
Anthrax Toxin
similarity (10)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#85 - Jan 2007
Importins
similarity (2)
#148 - Apr 2012
Ras Protein
similarity (1)
#152 - Aug 2012
cAMP-dependent Protein Kinase
similarity (1)
#243 - Mar 2020
Voltage-gated Sodium Channels
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#235 - Jul 2019
AMPA Receptor
similarity (1)
#127 - Jul 2010
Crystallins
similarity (1)
#195 - Mar 2016
RAF Protein Kinases
similarity (1)
#142 - Oct 2011
PDB Pioneers
similarity (1)

Deposited unit

A: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

B: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

C: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

D: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

E: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

F: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

hetero molecules

98.6 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

B: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

C: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

D: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

E: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

F: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

hetero molecules

A: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

B: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

C: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

D: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

E: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

F: CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA

hetero molecules

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

Unit cell

Length a, b, c (Å)	122.954, 158.363, 103.941
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	389 - 452
2	1	1	2	B	389 - 452
3	1	1	2	C	389 - 452
4	1	1	2	D	389 - 452
5	1	1	2	E	389 - 452
6	1	1	2	F	389 - 452
1	2	1	4	A	453 - 456
2	2	1	4	B	453 - 456
3	2	1	4	C	453 - 456
4	2	1	4	D	453 - 456
5	2	1	4	E	453 - 456
6	2	1	4	F	453 - 456
1	3	1	2	A	457 - 488
2	3	1	2	B	457 - 488
3	3	1	2	C	457 - 488
4	3	1	2	D	457 - 488
5	3	1	2	E	457 - 488
6	3	1	2	F	457 - 488
1	4	1	4	A	489 - 491
2	4	1	4	B	489 - 491
3	4	1	4	C	489 - 491
4	4	1	4	D	489 - 491
5	4	1	4	E	489 - 491
6	4	1	4	F	489 - 491
1	5	1	2	A	492 - 521
2	5	1	2	B	492 - 521
3	5	1	2	C	492 - 521
4	5	1	2	D	492 - 521
5	5	1	2	E	492 - 521
6	5	1	2	F	492 - 521

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.60631, -0.7661, -0.21328), (0.7701, 0.49876, 0.39772), (-0.19832, -0.40539, 0.89237)	-25.2648, -30.38748, -13.51065
2	given	(-0.19034, -0.77142, -0.6072), (0.76619, -0.50342, 0.39939), (-0.61377, -0.38921, 0.68687)	-15.23708, -70.81217, -7.40988
3	given	(-0.58854, 0.00228, -0.80847), (-0.0039, -0.99999, 2.0E-5), (-0.80846, 0.00316, 0.58854)	20.91674, -80.33826, 10.94072
4	given	(-0.18421, 0.77312, -0.60692), (-0.76885, -0.49802, -0.40105), (-0.61232, 0.39275, 0.68615)	46.91051, -49.61198, 23.78858
5	given	(0.6034, 0.77188, -0.20029), (-0.77113, 0.50079, -0.39316), (-0.20317, 0.39168, 0.89739)	36.28653, -9.81225, 18.48212

#1: Protein	CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE (CAM KINASE) II GAMMA Mass: 16375.393 Da / Num. of mol.: 6 / Fragment: OLIGOMERISATION DOMAIN, RESIDUES 387-527 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8N4I3, UniProt: Q13555*PLUS, EC: 2.7.1.123
#2: Chemical	ChemComp-GLY / GLYCINE / Glycine Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN B, LEU 526 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN B, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN C, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN D, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN E, LEU 526 TO ARG ENGINEERED RESIDUE IN CHAIN F, LEU 526 TO ARG
Sequence details	THE L526R MUTATION IS FROM THE ENTRY CLONE THAT HAS BEEN SEQUENCED AFTER IDENTIFICATION OF THE MASS DIFFERENCE

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53 %
Crystal grow	pH: 7 / Details: 0.1 M SPG PH 7.0, 60% MPD

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999
Detector	Type: MARRESEARCH / Detector: CCD / Date: Dec 21, 2006
Radiation	Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 2.46→39.7 Å / Num. obs: 29117 / % possible obs: 78.2 % / Observed criterion σ(I): 0 / Redundancy: 2.63 % / R_merge(I) obs: 0.06 / Net I/σ(I): 11.4
Reflection shell	Resolution: 2.46→2.56 Å / Redundancy: 0.13 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 1.45 / % possible all: 10.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HKX

1hkx

Resolution: 2.46→39.68 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.937 / SU B: 21.332 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.982 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.224	1467	5 %	RANDOM
R_work	0.184	-	-	-
obs	0.186	27628	78.4 %	-

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: 34.13 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.06 Å²	0 Å²	0 Å²
2-	-	-0.54 Å²	0 Å²
3-	-	-	1.6 Å²

Refinement step

Cycle: LAST / Resolution: 2.46→39.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6360	0	25	99	6484

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	6530
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4202
X-RAY DIFFRACTION	r_angle_refined_deg	1.25	1.931	8880
X-RAY DIFFRACTION	r_angle_other_deg	0.91	3	10256
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.101	5	809
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.556	24.63	324
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.891	15	1013
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.557	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	983
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	7405
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1313
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	1152
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	3942
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	3072
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	3530
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	146
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	0.148	0.2	52
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.173	0.2	93
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.124	0.2	21
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	2.82	3	4222
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	4.416	5	6545
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.985	8	2674
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	9.668	11	2335
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

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	738	tight positional	0.04	0.05
2	B	738	tight positional	0.04	0.05
3	C	738	tight positional	0.04	0.05
4	D	738	tight positional	0.03	0.05
5	E	738	tight positional	0.03	0.05
6	F	738	tight positional	0.03	0.05
1	A	909	medium positional	0.41	0.5
2	B	909	medium positional	0.32	0.5
3	C	909	medium positional	0.3	0.5
4	D	909	medium positional	0.37	0.5
5	E	909	medium positional	0.35	0.5
6	F	909	medium positional	0.29	0.5
1	A	738	tight thermal	0.08	0.5
2	B	738	tight thermal	0.08	0.5
3	C	738	tight thermal	0.08	0.5
4	D	738	tight thermal	0.07	0.5
5	E	738	tight thermal	0.07	0.5
6	F	738	tight thermal	0.07	0.5
1	A	909	medium thermal	0.8	2
2	B	909	medium thermal	0.8	2
3	C	909	medium thermal	0.68	2
4	D	909	medium thermal	0.69	2
5	E	909	medium thermal	0.68	2
6	F	909	medium thermal	0.7	2

LS refinement shell

Resolution: 2.46→2.52 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.405	6
R_work	0.475	195

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	0.8671	-0.4611	0.1957	4.7523	0.1366	2.683	0.0954	0.2956	0.0263	-0.5306	-0.2174	0.0038	0.0404	-0.0128	0.122	-0.0117	0.0308	-0.0162	0.0385	-0.0663	-0.0074	-19.9583	-60.0784	3.44
2	4.8976	-1.1448	2.2696	1.0795	-0.3576	4.2911	0.2935	0.7231	-0.3206	-0.296	-0.1607	-0.1682	0.5148	0.5194	-0.1327	0.0501	0.1164	-0.0208	0.0216	-0.0442	-0.0327	8.0281	-74.5189	18.1934
3	2.4896	1.0133	0.3432	2.797	0.9578	2.2059	0.0111	0.3083	0.0183	-0.3548	-0.077	-0.5031	-0.0458	0.7364	0.0659	-0.0577	-0.0105	0.0111	0.2686	0.118	0.1042	32.8026	-54.5353	30.8115
4	2.2781	-0.9349	-1.3501	5.2144	-0.5114	1.9525	0.1247	0.3477	0.2399	-0.4258	-0.162	-1.0571	-0.2836	0.2792	0.0374	0.0659	-0.1293	0.051	0.1317	0.1265	0.3127	29.4705	-20.5273	28.7426
5	3.8401	-0.591	0.9224	1.7424	-1.0745	2.7759	-0.0136	0.4642	0.2853	-0.3601	-0.2132	-0.0801	-0.2188	0.2938	0.2268	0.0629	0.0371	0.0038	0.22	0.073	0.0553	1.9976	-5.6166	14.8346
6	1.5894	1.5899	0.0661	4.1653	0.0282	2.6536	-0.1171	0.3497	0.0817	-0.8201	0.0505	0.2833	-0.1594	-0.1227	0.0667	0.1453	0.0935	-0.1546	0.1644	-0.0422	0.1326	-22.1673	-26.1121	2.3191

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	385 - 521
2	X-RAY DIFFRACTION	2	B	385 - 521
3	X-RAY DIFFRACTION	3	C	385 - 521
4	X-RAY DIFFRACTION	4	D	385 - 521
5	X-RAY DIFFRACTION	5	E	385 - 521
6	X-RAY DIFFRACTION	6	F	385 - 521

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