PDB-8sg2: BIVALENT INTERACTIONS OF PIN1 WITH THE C-TERMINAL TAIL OF PKC

Basic information

• Entry: Database: PDB / ID: 8sg2
• Title: BIVALENT INTERACTIONS OF PIN1 WITH THE C-TERMINAL TAIL OF PKC

Components

• Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
• Protein kinase C beta type

• Keywords: ISOMERASE / bivalent complex / Pin1 / protein kinase C / hydrophobic motif / turn motif

Function / homology

Function:

dibenzo-p-dioxin metabolic process / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / histone H3T6 kinase activity / positive regulation of odontogenesis of dentin-containing tooth / positive regulation of B cell receptor signaling pathway / spectrin / regulation of glucose transmembrane transport / Depolymerization of the Nuclear Lamina / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / protein kinase C / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / negative regulation of glucose transmembrane transport / cellular response to carbohydrate stimulus / diacylglycerol-dependent serine/threonine kinase activity / mitotic nuclear membrane disassembly / cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / response to vitamin D / presynaptic cytosol / regulation of protein localization to nucleus / positive regulation of vascular endothelial growth factor receptor signaling pathway / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / GTPase activating protein binding / regulation of growth / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / lipoprotein transport / regulation of mitotic nuclear division / nuclear androgen receptor binding / regulation of synaptic vesicle exocytosis / negative regulation of SMAD protein signal transduction / B cell activation / regulation of dopamine secretion / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / calyx of Held / calcium channel regulator activity / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / protein peptidyl-prolyl isomerization / response to glucose / positive regulation of protein dephosphorylation / presynaptic modulation of chemical synaptic transmission / negative regulation of insulin receptor signaling pathway / post-translational protein modification / ciliary basal body / nuclear receptor coactivator activity / positive regulation of GTPase activity / regulation of cytokinesis / VEGFR2 mediated cell proliferation / negative regulation of protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / protein kinase C binding / phosphoprotein binding / Activation of NF-kappaB in B cells / brush border membrane / B cell receptor signaling pathway / synapse organization / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / neuron differentiation / positive regulation of insulin secretion / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / intracellular calcium ion homeostasis / G alpha (z) signalling events / positive regulation of angiogenesis / calcium ion transport / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / histone binding / regulation of gene expression / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / adaptive immune response / Regulation of TP53 Activity through Phosphorylation / protein stabilization / response to hypoxia / intracellular signal transduction / nuclear speck / response to xenobiotic stimulus / positive regulation of protein phosphorylation / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse

Domain/homology:

Classical protein kinase C beta, catalytic domain / Protein kinase C, alpha/beta/gamma types / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / Peptidyl-prolyl cis-trans isomerase domain superfamily / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily

Component:

Protein kinase C beta type / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1

• Biological species: Homo sapiens (human)
• Method: SOLUTION NMR / torsion angle dynamics / simulated annealing
• Authors: Dixit, K. / Yang, Y. / Chen, X.R. / Igumenova, T.I.

Funding support

United States, 2items

Organization	Grant number	Country
Welch Foundation	A-1784	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01 GM108998	United States

• Citation: Journal: Elife / Year: 2024; Title: A novel bivalent interaction mode underlies a non-catalytic mechanism for Pin1-mediated protein kinase C regulation.; Authors: Chen, X.R. / Dixit, K. / Yang, Y. / McDermott, M.I. / Imam, H.T. / Bankaitis, V.A. / Igumenova, T.I.

History

Deposition	Apr 11, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Assembly

Deposited unit

A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1

B: Protein kinase C beta type

Summary:

• 21.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	21,124	2
Polymers	21,124	2
Non-polymers	0	0
Water	0	0

1

Summary:

• Idetical with deposited unit
• defined by author
• Evidence: NMR-detected binding experiments provided direct evidence of the complex formation.

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	20 / 50	structures with the lowest energy
Representative	Model #1	lowest energy

Components

#1: Protein

A Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Peptidyl-prolyl cis-trans isomerase Pin1 / PPIase Pin1 / Rotamase Pin1

Details:

Mass: 18271.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Plasmid: PET SUMO / Cell (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13526, peptidylprolyl isomerase

#2: Protein/peptide

B Protein kinase C beta type / PKC-B / PKC-beta

Details:

Mass: 2852.888 Da / Num. of mol.: 1 / Fragment: C-TERMINAL RESIDUES 639-661 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05771, protein kinase C

• Has ligand of interest: Y

Experimental details

Experiment

• Experiment: Method: SOLUTION NMR

NMR experiment

Conditions-ID	Experiment-ID	Solution-ID	Sample state	Spectrometer-ID	Type
1	1	1	isotropic	1	2D [15N,1H] HSQC
1	2	1	isotropic	1	2D 1H-15N HSQC NH2
1	3	1	isotropic	1	3D HNCO
1	4	1	isotropic	2	3D HN(CA)CB
1	5	1	isotropic	1	3D C(CO)NH
1	6	1	isotropic	2	3D CBCA(CO)NH
1	7	1	isotropic	2	3D HN(CA)CO
1	8	1	isotropic	2	3D HNHA
1	9	1	isotropic	2	3D HNHB
1	10	1	isotropic	1	3D H(CCO)NH
1	11	1	isotropic	1	3D 15N-EDITED NOESY- HSQC
1	12	1	isotropic	1	3D [F1] 13C,15N-FILTERED NOESY-15N-HSQC
2	13	2	isotropic	1	3D [F1] 13C,15N-FILTERED NOESY-13C-HSQC
2	14	2	isotropic	1	3D 13C-EDITED NOESY- HSQC
2	15	2	isotropic	2	3D 13Caro-EDITED NOESY- HSQC
2	16	2	isotropic	1	2D CT [13C, 1H] HSQC
2	17	2	isotropic	1	2D CT 1H-13C AROMATIC HSQC
2	18	2	isotropic	1	3D (H)CCH-TOCSY
2	19	2	isotropic	1	3D (H)CCH-COSY
1	20	1	isotropic	2	2D (HB)CB(CGCDCE)HE
1	21	1	isotropic	2	2D (HB)CB(CGCD)HD
1	22	3	isotropic	1	2D [F1] 13C, 15N- FILTERED NOESY
1	23	3	isotropic	1	2D [F2] 13C,15N- FILTERED NOESY
1	24	3	isotropic	2	2D [F1,F2] 13C,15N-FILTERED NOESY
1	25	3	isotropic	1	2D [F1,F2] 13C,15N-FILTERED TOCSY
1	26	4	isotropic	1	3D [F1] 13C,15N-FILTERED NOESY-15N-HSQC
1	27	4	isotropic	1	3D [F1] 13C, 15N-FILTERED NOESY- 13Caro-HSQC
1	28	5	isotropic	1	2D [F1] 13C,15N- FILTERED NOESY
1	29	5	isotropic	1	2D [F2] 13C,15N- FILTERED NOESY
1	30	5	isotropic	1	2D [F1,F2] 13C,15N-FILTERED NOESY
1	31	5	isotropic	1	2D [F1,F2] 13C,15N-FILTERED TOCSY
1	32	6	isotropic	1	3D [F1] 13C,15N-FILTERED NOESY-15N-HSQC
1	33	6	isotropic	1	3D [F1] 13C, 15N-FILTERED NOESY- 13Caro-HSQC
1	34	6	isotropic	1	3D [F1] 13C, 15N-FILTERED NOESY- 13Cali-HSQC
1	35	6	isotropic	1	2D [15N,1H] HSQC
1	36	6	isotropic	1	2D CT [13C, 1H] HSQC
1	37	6	isotropic	3	3D HN(CA)CB
1	38	7	isotropic	1	3D [F1] 13C,15N-FILTERED NOESY-15N-HSQC
1	39	7	isotropic	1	3D [F1] 13C,15N-FILTERED NOESY-13C-HSQC
1	40	7	isotropic	1	2D [15N,1H] HSQC
1	41	7	isotropic	1	2D CT [13C, 1H] HSQC
1	42	8	isotropic	1	3D [F1] 13C,15N-FILTERED NOESY-15N-HSQC
1	43	8	isotropic	1	3D [F1] 13C,15N-FILTERED NOESY-13C-HSQC
1	44	9	isotropic	1	2D [F1] 13C, 15N- FILTERED NOESY
1	45	9	isotropic	1	2D [F2] 13C, 15N- FILTERED NOESY
1	46	9	isotropic	1	2D [F1,F2] 13C,15N-FILTERED NOESY
1	47	9	isotropic	1	2D [F1,F2] 13C,15N-FILTERED TOCSY

Sample preparation

Details

Type	Solution-ID	Contents	Details	Label	Solvent system
solution	1	1.05 mM [U-13C; U-15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1, 0.9 mM The C-terminal tail of PKC, 10 mM [U-100% 2H] imidazole, 100 mM potassium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 92% H2O/8% D2O	[U-13C, 15N-Pin1+pV5bII] The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, 8% D2O, and 0.02% NaN3	[U-13C, 15N-Pin1+pV5bII]	92% H2O/8% D2O
solution	2	1.05 mM [U-13C; U-15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1, 0.9 mM The C-terminal tail of PKC, 10 mM [U-100% 2H] imidazole, 100 mM potassium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 100% D2O	[U-13C, 15N-Pin1+pV5bII]-D2O The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, and 0.02% NaN3	[U-13C, 15N-Pin1+pV5bII]-D2O	100% D2O
solution	3	1 mM [U-13C; U-15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1, 1.3 mM The C-terminal tail of PKC, 10 mM [U-100% 2H] imidazole, 100 mM potassium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 92% H2O/8% D2O	[U-13C, 15N-Pin1-saturated-pV5bII] The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, and 0.02% NaN	[U-13C, 15N-Pin1-saturated-pV5bII]	92% H2O/8% D2O
solution	4	0.8 mM [U-13C; U-15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1, 5.5 mM The C-terminal tail of PKC, 10 mM [U-100% 2H] imidazole, 100 mM potassium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 92% H2O/8% D2O	[U-13C, 15N-PPIase+pHMbII] The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, 8% D2O, and 0.02% NaN3	[U-13C, 15N-PPIase+pHMbII]	92% H2O/8% D2O
solution	5	0.5 mM [U-13C; U-15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1, 1.8 mM The C-terminal tail of PKC, 10 mM [U-100% 2H] imidazole, 100 mM potassium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 92% H2O/8% D2O	[U-13C, 15N-PPIase-saturated-pHMbII] The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, 8% D2O, and 0.02% NaN3	[U-13C, 15N-PPIase-saturated-pHMbII]	92% H2O/8% D2O
solution	6	0.5 mM [U-13C; U-15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1, 2.5 mM The C-terminal tail of PKC, 10 mM [U-100% 2H] imidazole, 100 mM potassium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 92% H2O/8% D2O	[na-PPIase+selective residues-13C,15N pHMbII] The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, 8% D2O, and 0.02% NaN3	PPIase+[U-13C,15N Phe]pHMbII	92% H2O/8% D2O
solution	7	1 mM [U-13C; U-15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1, 1.5 mM The C-terminal tail of PKC, 10 mM [U-100% 2H] imidazole, 100 mM potassium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 92% H2O/8% D2O	[na-Pin1+selective residues-13C,15N pTMbII] The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, 8% D2O, and 0.02% NaN3	Pin1+[U-13C,15N Pro, Ile, Val]pTMbII	92% H2O/8% D2O
solution	8	1.3 mM [U-13C; U-15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1, 1 mM The C-terminal tail of PKC, 10 mM [U-100% 2H] imidazole, 100 mM potassium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 92% H2O/8% D2O	[U-13C, 15N-Pin1+Ext-pV5bII] The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, 8% D2O, and 0.02% NaN3	[U-13C, 15N-Pin1+Ext-pV5bII]	92% H2O/8% D2O
solution	9	0.8 mM [U-13C; U-15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1, 1.3 mM The C-terminal tail of PKC, 10 mM [U-100% 2H] imidazole, 100 mM potassium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 92% H2O/8% D2O	[U-13C, 15N-Pin1-saturated-Ext-pV5bII] The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, 8% D2O, and 0.02% NaN3	[U-13C, 15N-Pin1-saturated-Ext-pV5bII]	92% H2O/8% D2O

Sample

Conc. (mg/ml)	Component	Isotopic labeling	Solution-ID
1.05 mM	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1	[U-13C; U-15N]	1
0.9 mM	The C-terminal tail of PKC	natural abundance	1
10 mM	imidazole	[U-100% 2H]	1
100 mM	potassium chloride	natural abundance	1
1 mM	TCEP	natural abundance	1
0.02 % w/v	sodium azide	natural abundance	1
1.05 mM	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1	[U-13C; U-15N]	2
0.9 mM	The C-terminal tail of PKC	natural abundance	2
10 mM	imidazole	[U-100% 2H]	2
100 mM	potassium chloride	natural abundance	2
1 mM	TCEP	natural abundance	2
0.02 % w/v	sodium azide	natural abundance	2
1 mM	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1	[U-13C; U-15N]	3
1.3 mM	The C-terminal tail of PKC	natural abundance	3
10 mM	imidazole	[U-100% 2H]	3
100 mM	potassium chloride	natural abundance	3
1 mM	TCEP	natural abundance	3
0.02 % w/v	sodium azide	natural abundance	3
0.8 mM	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1	[U-13C; U-15N]	4
5.5 mM	The C-terminal tail of PKC	natural abundance	4
10 mM	imidazole	[U-100% 2H]	4
100 mM	potassium chloride	natural abundance	4
1 mM	TCEP	natural abundance	4
0.02 % w/v	sodium azide	natural abundance	4
0.5 mM	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1	[U-13C; U-15N]	5
1.8 mM	The C-terminal tail of PKC	natural abundance	5
10 mM	imidazole	[U-100% 2H]	5
100 mM	potassium chloride	natural abundance	5
1 mM	TCEP	natural abundance	5
0.02 % w/v	sodium azide	natural abundance	5
0.5 mM	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1	[U-13C; U-15N]	6
2.5 mM	The C-terminal tail of PKC	natural abundance	6
10 mM	imidazole	[U-100% 2H]	6
100 mM	potassium chloride	natural abundance	6
1 mM	TCEP	natural abundance	6
0.02 % w/v	sodium azide	natural abundance	6
1 mM	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1	[U-13C; U-15N]	7
1.5 mM	The C-terminal tail of PKC	natural abundance	7
10 mM	imidazole	[U-100% 2H]	7
100 mM	potassium chloride	natural abundance	7
1 mM	TCEP	natural abundance	7
0.02 % w/v	sodium azide	natural abundance	7
1.3 mM	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1	[U-13C; U-15N]	8
1 mM	The C-terminal tail of PKC	natural abundance	8
10 mM	imidazole	[U-100% 2H]	8
100 mM	potassium chloride	natural abundance	8
1 mM	TCEP	natural abundance	8
0.02 % w/v	sodium azide	natural abundance	8
0.8 mM	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1	[U-13C; U-15N]	9
1.3 mM	The C-terminal tail of PKC	natural abundance	9
10 mM	imidazole	[U-100% 2H]	9
100 mM	potassium chloride	natural abundance	9
1 mM	TCEP	natural abundance	9
0.02 % w/v	sodium azide	natural abundance	9

Sample conditions

Ionic strength: 0.1 M / pH: 6.66 / PH err: 0.02 / Pressure: 1 atm / Pressure err: 0.001 / Temperature: 298 K / Temperature err: 0.2

Conditions-ID	Details	Label
1	The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, 8% D2O, and 0.02% NaN3	condition_1
2	The NMR buffer contained 10 mM D4-imidazole at pH 6.6, 100 mM KCl, 1 mM TCEP, 100% D2O, and 0.02% NaN3	condition_2

NMR measurement

NMR spectrometer

Type	Manufacturer	Model	Field strength (MHz)	Spectrometer-ID	Details
Bruker AVANCE	Bruker	AVANCE	800	1	cryoprobe
Bruker AVANCE	Bruker	AVANCE	600	2	cryoprobe
Bruker AVANCE	Bruker	AVANCE	500	3	room temperature probe

Processing

NMR software

Name	Developer	Classification
X-PLOR NIH	SCHWIETERS, KUSZEWSKI, Tjandra and Clore	refinement
CYANA	Guntert, Mumenthaler, and Wuthrich	structure calculation
CcpNmr Analysis	CCPN	chemical shift assignment
NMRDraw	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax	peak picking
NMRPipe	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax	processing

Refinement

Method	Software ordinal	Details
torsion angle dynamics	2	STRUCTURE DETERMINATION
simulated annealing	1	water-refinement

• NMR representative: Selection criteria: lowest energy
• NMR ensemble: Conformer selection criteria: structures with the lowest energy; Conformers calculated total number: 50 / Conformers submitted total number: 20