PDB-2fk9: Human protein kinase C, eta

ID or keywords:

Entry

Database: PDB / ID: 2fk9

Title

Human protein kinase C, eta

Components

protein kinase C, eta type

Keywords

TRANSFERASE / ATP-binding / Kinase / Metal-binding / Nucleotide-binding / Diacylglycerol binding / Serine/threonine-protein kinase / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / positive regulation of B cell receptor signaling pathway / protein kinase C signaling / protein kinase C / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / Effects of PIP2 hydrolysis / positive regulation of macrophage derived foam cell differentiation / positive regulation of keratinocyte differentiation / regulation of bicellular tight junction assembly ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Walker, J.R. / Littler, D.R. / Finerty Jr., P.J. / MacKenzie, F. / Newman, E.M. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Structure of human protein kinase C eta (PKCeta) C2 domain and identification of phosphorylation sites.
Authors: Littler, D.R. / Walker, J.R. / She, Y.M. / Finerty, P.J. / Newman, E.M. / Dhe-Paganon, S.

History

Deposition	Jan 4, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 17, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2fk9.cif.gz	46.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2fk9.ent.gz	33 KB	Display	PDB format
PDBx/mmJSON format	2fk9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2fk9_validation.pdf.gz	428.8 KB	Display	wwPDB validaton report
Full document	2fk9_full_validation.pdf.gz	430.5 KB	Display
Data in XML	2fk9_validation.xml.gz	9 KB	Display
Data in CIF	2fk9_validation.cif.gz	12.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fk/2fk9 ftp://data.pdbj.org/pub/pdb/validation_reports/fk/2fk9	HTTPS FTP

-
Related structure data

Related structure data	1gmiS S: Starting model for refinement
Similar structure data	7knv-d 6ewl-d 4dui-d 3fk3-4 3fk3-3 5h20-1 3fk3-2 2kpt-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#195 - Mar 2016 RAF Protein Kinases similarity (6) #196 - Apr 2016 Lead Poisoning similarity (17) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (6) #148 - Apr 2012 Ras Protein similarity (5) #239 - Nov 2019 Phospholipase A2 similarity (5) #183 - Mar 2015 Phototropin similarity (3)

Deposited unit

A: protein kinase C, eta type

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	45.007, 49.404, 67.508
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	protein kinase C, eta type Mass: 17501.670 Da / Num. of mol.: 1 / Fragment: C2 DOMAIN (residues 1-138) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCH / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: GenBank: 28557781, UniProt: P24723*PLUS, EC: 2.7.1.37
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

protein kinase C, eta type

Mass: 17501.670 Da / Num. of mol.: 1 / Fragment: C2 DOMAIN (residues 1-138)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PRKCH / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: GenBank: 28557781, UniProt: P24723*PLUS, EC: 2.7.1.37

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.61 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 22% PEG3350, 0.2M CaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 20, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.75→19.93 Å / Num. all: 15364 / Num. obs: 15364 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / R_merge(I) obs: 0.068 / Net I/σ(I): 31.3
Reflection shell	Resolution: 1.75→1.81 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.315 / Mean I/σ(I) obs: 3.35 / Num. unique all: 1193 / % possible all: 77.5

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1GMI

1gmi

Resolution: 1.75→19.93 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.941 / SU B: 4.043 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21458	761	5 %	RANDOM
R_work	0.17817	-	-	-
obs	0.17994	14560	97.7 %	-
all	-	15323	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 22.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.36 Å²	0 Å²	0 Å²
2-	-	0.05 Å²	0 Å²
3-	-	-	0.31 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→19.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1109	0	0	132	1241

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	1135
X-RAY DIFFRACTION	r_angle_refined_deg	1.629	1.943	1541
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.341	5	138
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.836	23.962	53
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.952	15	186
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.554	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.14	0.2	175
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	858
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	471
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	776
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	105
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.181	0.2	48
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.115	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	1.973	3	707
X-RAY DIFFRACTION	r_mcangle_it	2.622	4	1122
X-RAY DIFFRACTION	r_scbond_it	3.667	5	478
X-RAY DIFFRACTION	r_scangle_it	5.418	7	419

LS refinement shell

Resolution: 1.752→1.797 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.242	43	-
R_work	0.176	826	-
obs	-	-	76.77 %

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	5.6358	-3.7749	5.0627	5.3283	-3.6677	9.2785	0.067	0.1699	0.2241	-0.4581	-0.427	-0.0804	-0.1053	0.5238	0.3599	0.0047	-0.102	0.019	0.097	0.0199	-0.0282	57.8853	0.1593	-13.7997
2	10.8576	-0.5777	-0.6104	12.1919	-3.1314	2.9744	0.0701	0.3129	-0.4867	-0.4199	-0.0907	-0.3054	0.4295	-0.0615	0.0206	0.1014	0.0524	-0.0129	0.0882	-0.034	0.0582	53.4171	17.3717	-3.4121
3	7.0751	-8.3598	2.0527	10.5296	-0.6857	5.238	0.14	-0.007	0.0538	-0.1756	-0.0829	-0.2847	-0.114	0.4577	-0.0571	0.0471	0.006	-0.0185	0.0365	-0.024	0.0417	46.9638	30.3019	-2.4412
4	23.6643	-0.4595	2.9033	0.3623	-0.7547	1.7363	-0.2966	0.354	1.1237	-0.1439	0.1783	0.172	-0.0182	0.0495	0.1183	0.0128	-0.0046	0.0169	0.0285	-0.0148	0.0555	31.6392	32.7197	-3.5653
5	30.5487	19.2463	-29.2118	32.5924	-25.7979	43.9744	-0.8988	1.6878	0.0388	-0.7726	1.1867	0.7237	1.0725	-2.0077	-0.2879	0.0159	-0.0481	-0.0333	0.1178	-0.0079	0.0396	20.0887	24.3297	3.2399
6	2.7254	-2.3612	-1.8764	12.4966	1.612	7.6657	-0.0053	-0.0727	-0.0304	0.1321	0.1539	0.344	0.2315	-0.2563	-0.1486	0	-0.0284	-0.0022	0.0372	0.044	0.0156	17.3057	26.3801	11.139
7	6.1249	-2.6542	-0.6562	2.6637	-0.1416	1.0234	-0.1314	-0.1306	0.0201	0.1377	0.1582	0.037	-0.0082	-0.0103	-0.0268	0.035	0.007	0.0134	0.0049	-0.0029	0.0119	26.4496	32.0153	7.0359
8	13.16	-8.5632	-2.9549	30.9262	7.5882	6.3134	-0.045	-0.4314	-0.362	0.8112	-0.0832	0.4124	0.7359	-0.0423	0.1282	0.0646	0.0281	0.0137	0.0047	0.0275	-0.0148	44.1928	18.9086	5.5002
9	20.937	-9.2936	-3.1855	12.114	8.9451	7.5843	-0.3573	-0.4163	-0.3714	0.444	0.2161	-0.1061	0.1342	0.1719	0.1411	0.0591	0.0278	-0.0049	0.0389	0.0075	0.0595	40.0914	30.1729	8.0341
10	39.384	-17.5858	2.4755	9.4753	0.0415	0.966	-0.5918	-0.945	1.009	0.3429	0.3861	-0.3204	-0.0978	-0.2588	0.2057	0.0903	0.0134	0.01	0.0957	-0.0302	0.0965	30.5084	37.0294	8.3146
11	19.4595	0.289	-2.8229	0.0613	-0.0143	0.4228	-0.0221	0.6082	0.3686	0.0738	0.0685	-0.0025	-0.1438	-0.0939	-0.0464	0.0325	-0.0028	-0.0057	0.0531	0.0295	0.0346	32.9689	35.9215	0.4796
12	11.2224	-11.8015	-0.5695	19.638	1.3652	0.1101	-0.2443	-0.2042	-0.0078	0.5678	0.1876	-0.3722	0.1091	0.2085	0.0567	0.06	0.0237	-0.0195	0.0756	0.0077	0.0147	48.4475	29.036	2.9262
13	15.5828	-2.5887	-0.3703	7.703	1.1871	3.6771	0.0245	-0.1266	-0.6198	0.4088	0.0317	0.1002	0.3768	-0.0977	-0.0562	0.1447	0.0296	0.0141	0.0288	0.0057	0.0562	47.2881	15.8997	-0.2502
14	4.7309	-1.1901	-4.694	1.9449	3.0434	11.1348	-0.0829	-0.3217	0.0143	0.2292	0.1213	0.0044	0.2758	0.4002	-0.0383	0.0357	0.0172	0.0064	0.0031	0.0153	0.0089	30.6034	26.0058	11.5484
15	9.5785	-3.6267	-5.1203	1.3732	1.9387	2.7371	-0.2435	0.1251	-0.5625	0.1102	-0.0632	0.1501	0.2608	-0.0567	0.3067	0.0562	0.0214	0.0301	0.0104	-0.0037	0.037	35.6365	19.9858	-0.281
16	7.7308	-0.7161	-10.6342	7.8933	-2.7336	16.3949	-0.3418	0.2631	-0.6135	-0.1047	0.0353	-0.0925	0.9184	-0.6152	0.3065	0.0612	-0.0016	-0.007	0.0071	-0.0247	0.0178	46.9737	16.9728	-11.753
17	2.5158	-1.3428	0.4092	6.5083	3.6495	4.6687	0.0501	-0.1051	0.1359	0.003	0.266	-0.3452	-0.0541	0.3028	-0.3161	0.0283	0.0098	0.0091	0.0755	-0.0274	0.0282	50.9776	24.6837	-14.3288
18	12.9532	-4.5582	-3.3997	3.137	1.7474	3.9969	0.0838	0.3748	0.276	-0.2376	-0.042	-0.0626	-0.0698	-0.0727	-0.0418	0.0384	0.0051	-0.0122	0.0499	-0.0198	0.0346	40.1076	28.8387	-10.5404
19	14.3321	7.9983	-10.3411	18.8025	-3.7057	8.4495	-0.229	0.5975	-0.0812	-0.1638	0.1368	0.5611	0.5023	-0.2681	0.0922	0.0501	-0.0454	-0.012	0.0979	-0.0272	0.0698	28.8969	22.4804	-5.0604
20	6.9879	0.6718	-2.6972	1.7984	0.3673	1.911	0.0711	0.1987	0.1625	0.0119	-0.0125	-0.0656	0.095	-0.0278	-0.0586	0.0684	-0.0029	-0.0034	0.039	-0.0031	0.0251	43.1091	27.9449	-6.7695

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	-9 - 5	10 - 24
2	X-RAY DIFFRACTION	2	A	A	6 - 12	25 - 31
3	X-RAY DIFFRACTION	3	A	A	13 - 16	32 - 35
4	X-RAY DIFFRACTION	4	A	A	17 - 22	36 - 41
5	X-RAY DIFFRACTION	5	A	A	23 - 26	42 - 45
6	X-RAY DIFFRACTION	6	A	A	27 - 35	46 - 54
7	X-RAY DIFFRACTION	7	A	A	36 - 46	55 - 65
8	X-RAY DIFFRACTION	8	A	A	47 - 54	66 - 73
9	X-RAY DIFFRACTION	9	A	A	55 - 58	74 - 77
10	X-RAY DIFFRACTION	10	A	A	59 - 62	78 - 81
11	X-RAY DIFFRACTION	11	A	A	63 - 69	82 - 88
12	X-RAY DIFFRACTION	12	A	A	70 - 75	89 - 94
13	X-RAY DIFFRACTION	13	A	A	76 - 83	95 - 102
14	X-RAY DIFFRACTION	14	A	A	84 - 95	103 - 114
15	X-RAY DIFFRACTION	15	A	A	96 - 105	115 - 124
16	X-RAY DIFFRACTION	16	A	A	106 - 110	125 - 129
17	X-RAY DIFFRACTION	17	A	A	111 - 117	130 - 136
18	X-RAY DIFFRACTION	18	A	A	118 - 122	137 - 141
19	X-RAY DIFFRACTION	19	A	A	123 - 127	142 - 146
20	X-RAY DIFFRACTION	20	A	A	128 - 137	147 - 156

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi