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BMRB: 30305

5W4S

Solution structure of C2 domain from protein kinase C alpha in ternary complex with calcium and V5-pHM peptide

Authors

Yang, Y., Igumenova, T.I.

Assembly

Protein kinase C alpha type (E.C.2.7.11.13), V5-pHM peptide

Entity

1. Protein kinase C alpha type (polymer, Thiol state: not present), 139 monomers, 16215.24 Da Detail

HTEKRGRIYL KAEVTDEKLH VTVRDAKNLI PMDPNGLSDP YVKLKLIPDP KNESKQKTKT IRSTLNPQWN ESFTFKLKPS DKDRRLSVEI WDWDRTTRND FMGSLSFGVS ELMKMPASGW YKLLNQEEGE YYNVPIPEG

2. V5-pHM peptide (polymer, Thiol state: not present), 12 monomers, 1298.186 Da Detail

XDQSDFEGFX YX

3. CALCIUM ION (non-polymer), 40.078 × 2 Da

Total weight

17593.582 Da

Max. entity weight

16215.24 Da

Source organism

Rattus norvegicus

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 8.6 %, Completeness: 6.5 %, Completeness (bb): 7.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	6.5 % (62 of 955)	6.5 % (62 of 955)
Backbone	7.8 % (23 of 294)	7.8 % (23 of 294)
Sidechain	5.9 % (39 of 661)	5.9 % (39 of 661)
Aromatic	14.6 % (12 of 82)	14.6 % (12 of 82)
Methyl	3.1 % (2 of 64)	3.1 % (2 of 64)

1. Protein kinase C alpha type

HTEKRGRIYL KAEVTDEKLH VTVRDAKNLI PMDPNGLSDP YVKLKLIPDP KNESKQKTKT IRSTLNPQWN ESFTFKLKPS DKDRRLSVEI WDWDRTTRND FMGSLSFGVS ELMKMPASGW YKLLNQEEGE YYNVPIPEG

2. V5-pHM peptide

XDQSDFEGFX YX

Show sample condition

Sample #1

Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 296.15 K, pH 6.0, Details 2.225 mM CALCIUM ION, 0.89 mM [U-13C; U-15N] C2 domain of protein kinase C alpha, 6.7 mM MES, 67 mM potassium chloride, 0.2 mg/mL sodium azide, 2 mM V5-pHM peptide, 92% H2O/8% D2O

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

Sample #2

Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 296.15 K, pH 6.0, Details 3.75 mM CALCIUM ION, 1.47 mM [U-13C; U-15N] C2 domain of protein kinase C alpha, 6.7 mM MES, 67 mM potassium chloride, 0.2 mg/mL sodium azide, 0.6 mM V5-pHM peptide, 92% H2O/8% D2O

#	Name	Isotope labeling	Concentration
7	C2 domain of protein kinase C alpha	[U-13C; U-15N]	1.47 mM
8	CALCIUM ION	natural abundance	3.75 mM
9	MES	natural abundance	6.7 mM
10	V5-pHM peptide	natural abundance	0.6 mM
11	potassium chloride	natural abundance	67 mM
12	sodium azide	natural abundance	0.2 mg/mL

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 296.15 K, pH 6.0, Details 2.225 mM CALCIUM ION, 0.89 mM [U-13C; U-15N] C2 domain of protein kinase C alpha, 6.7 mM MES, 67 mM potassium chloride, 0.2 mg/mL sodium azide, 2 mM V5-pHM peptide, 100% D2O

#	Name	Isotope labeling	Concentration
13	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
14	CALCIUM ION	natural abundance	2.225 mM
15	MES	natural abundance	6.7 mM
16	V5-pHM peptide	natural abundance	2 mM
17	potassium chloride	natural abundance	67 mM
18	sodium azide	natural abundance	0.2 mg/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 5W4S, Strand ID: A, B Detail

Release date

2017-06-27

Citation

Structural Basis of Protein Kinase Cα Regulation by the C-Terminal Tail
Yang, Y., Shu, C., Li, P., Igumenova, T.I.
Biophys. J. (2018), 114, 1590-1603, PubMed 29642029 , DOI 10.1016/j.bpj.2017.12.030 , Abstract

Related entities 1. Protein kinase C alpha type, : 1 : 2 : 65 entities Detail

Experiments performed 21 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz Cryoprobe

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 296.15 K, pH 6.0, Details 2.225 mM CALCIUM ION, 0.89 mM [U-13C; U-15N] C2 domain of protein kinase C alpha, 6.7 mM MES, 67 mM potassium chloride, 0.2 mg/mL sodium azide, 2 mM V5-pHM peptide, 92% H2O/8% D2O

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

2 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

3 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 296.15 K, pH 6.0, Details 3.75 mM CALCIUM ION, 1.47 mM [U-13C; U-15N] C2 domain of protein kinase C alpha, 6.7 mM MES, 67 mM potassium chloride, 0.2 mg/mL sodium azide, 0.6 mM V5-pHM peptide, 92% H2O/8% D2O

#	Name	Isotope labeling	Concentration
7	C2 domain of protein kinase C alpha	[U-13C; U-15N]	1.47 mM
8	CALCIUM ION	natural abundance	3.75 mM
9	MES	natural abundance	6.7 mM
10	V5-pHM peptide	natural abundance	0.6 mM
11	potassium chloride	natural abundance	67 mM
12	sodium azide	natural abundance	0.2 mg/mL

4 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

5 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 800 MHz Cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 296.15 K, pH 6.0, Details 2.225 mM CALCIUM ION, 0.89 mM [U-13C; U-15N] C2 domain of protein kinase C alpha, 6.7 mM MES, 67 mM potassium chloride, 0.2 mg/mL sodium azide, 2 mM V5-pHM peptide, 100% D2O

#	Name	Isotope labeling	Concentration
13	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
14	CALCIUM ION	natural abundance	2.225 mM
15	MES	natural abundance	6.7 mM
16	V5-pHM peptide	natural abundance	2 mM
17	potassium chloride	natural abundance	67 mM
18	sodium azide	natural abundance	0.2 mg/mL

6 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 800 MHz Cryoprobe

Sample

#	Name	Isotope labeling	Concentration
13	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
14	CALCIUM ION	natural abundance	2.225 mM
15	MES	natural abundance	6.7 mM
16	V5-pHM peptide	natural abundance	2 mM
17	potassium chloride	natural abundance	67 mM
18	sodium azide	natural abundance	0.2 mg/mL

7 3D HCCH-COSY

Instrument

Bruker AvanceIII - 800 MHz Cryoprobe

Sample

#	Name	Isotope labeling	Concentration
13	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
14	CALCIUM ION	natural abundance	2.225 mM
15	MES	natural abundance	6.7 mM
16	V5-pHM peptide	natural abundance	2 mM
17	potassium chloride	natural abundance	67 mM
18	sodium azide	natural abundance	0.2 mg/mL

8 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

9 3D H(CCO)NH

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

10 3D C(CO)NH

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

11 3D aromatic HCCH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz Cryoprobe

Sample

#	Name	Isotope labeling	Concentration
13	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
14	CALCIUM ION	natural abundance	2.225 mM
15	MES	natural abundance	6.7 mM
16	V5-pHM peptide	natural abundance	2 mM
17	potassium chloride	natural abundance	67 mM
18	sodium azide	natural abundance	0.2 mg/mL

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 800 MHz Cryoprobe

Sample

#	Name	Isotope labeling	Concentration
13	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
14	CALCIUM ION	natural abundance	2.225 mM
15	MES	natural abundance	6.7 mM
16	V5-pHM peptide	natural abundance	2 mM
17	potassium chloride	natural abundance	67 mM
18	sodium azide	natural abundance	0.2 mg/mL

13 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 800 MHz Cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

14 2D [F2-15N,13C filtered] NOESY

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

15 2D [F2-15N,13C filtered] NOESY

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
13	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
14	CALCIUM ION	natural abundance	2.225 mM
15	MES	natural abundance	6.7 mM
16	V5-pHM peptide	natural abundance	2 mM
17	potassium chloride	natural abundance	67 mM
18	sodium azide	natural abundance	0.2 mg/mL

16 2D [F1,F2-15N,13C filtered] NOESY

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

17 2D [F1,F2-15N,13C filtered] NOESY

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
7	C2 domain of protein kinase C alpha	[U-13C; U-15N]	1.47 mM
8	CALCIUM ION	natural abundance	3.75 mM
9	MES	natural abundance	6.7 mM
10	V5-pHM peptide	natural abundance	0.6 mM
11	potassium chloride	natural abundance	67 mM
12	sodium azide	natural abundance	0.2 mg/mL

18 2D [F1,F2-15N,13C filtered] TOCSY

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

19 2D [F1,F2-15N,13C filtered] TOCSY

Instrument

Bruker AvanceIII - 500 MHz RT probe

Sample

#	Name	Isotope labeling	Concentration
7	C2 domain of protein kinase C alpha	[U-13C; U-15N]	1.47 mM
8	CALCIUM ION	natural abundance	3.75 mM
9	MES	natural abundance	6.7 mM
10	V5-pHM peptide	natural abundance	0.6 mM
11	potassium chloride	natural abundance	67 mM
12	sodium azide	natural abundance	0.2 mg/mL

20 3D [F1-15N,13C filtered] 1H-15N NOESY

Instrument

Bruker AvanceIII - 800 MHz Cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
2	CALCIUM ION	natural abundance	2.225 mM
3	MES	natural abundance	6.7 mM
4	V5-pHM peptide	natural abundance	2 mM
5	potassium chloride	natural abundance	67 mM
6	sodium azide	natural abundance	0.2 mg/mL

21 3D [F1-15N,13C filtered] 1H-13C NOESY

Instrument

Bruker AvanceIII - 800 MHz Cryoprobe

Sample

#	Name	Isotope labeling	Concentration
13	C2 domain of protein kinase C alpha	[U-13C; U-15N]	0.89 mM
14	CALCIUM ION	natural abundance	2.225 mM
15	MES	natural abundance	6.7 mM
16	V5-pHM peptide	natural abundance	2 mM
17	potassium chloride	natural abundance	67 mM
18	sodium azide	natural abundance	0.2 mg/mL

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_30305_5w4s.nef
Input source #2: Coordindates	5w4s.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:32:MET:O	3:2:CA:CA	unknown	unknown	n/a
1:33:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a
1:33:ASP:OD1	3:2:CA:CA	unknown	unknown	n/a
1:33:ASP:OD2	3:1:CA:CA	unknown	unknown	n/a
1:39:ASP:OD2	3:1:CA:CA	unknown	unknown	n/a
1:92:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a
1:92:ASP:OD2	3:1:CA:CA	unknown	unknown	n/a
1:92:ASP:OD2	3:2:CA:CA	unknown	unknown	n/a
1:93:TRP:O	3:1:CA:CA	unknown	unknown	n/a
1:94:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a
1:94:ASP:OD1	3:2:CA:CA	unknown	unknown	n/a
1:94:ASP:OD2	3:2:CA:CA	unknown	unknown	n/a
1:100:ASP:OD2	3:2:CA:CA	unknown	unknown	n/a
2:1:ACE:C	2:2:ASP:N	unknown	unknown	n/a
2:9:PHE:C	2:10:SEP:N	unknown	unknown	n/a
2:10:SEP:C	2:11:TYR:N	unknown	unknown	n/a
2:11:TYR:C	2:12:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	648	ACE	ACETYL GROUP	Assigned chemical shifts, Coordinates
B	657	SEP	PHOSPHOSERINE	Assigned chemical shifts, Coordinates
B	659	NH2	AMINO GROUP	Assigned chemical shifts, Coordinates
C	1	CA	CALCIUM ION	None
C	2	CA	CALCIUM ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

---160-------170-------180-------190-------200-------210-------220-------230-------240-------250----
HTEKRGRIYLKAEVTDEKLHVTVRDAKNLIPMDPNGLSDPYVKLKLIPDPKNESKQKTKTIRSTLNPQWNESFTFKLKPSDKDRRLSVEIWDWDRTTRND
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HTEKRGRIYLKAEVTDEKLHVTVRDAKNLIPMDPNGLSDPYVKLKLIPDPKNESKQKTKTIRSTLNPQWNESFTFKLKPSDKDRRLSVEIWDWDRTTRND
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---260-------270-------280-------290---
FMGSLSFGVSELMKMPASGWYKLLNQEEGEYYNVPIPEG
|||||||||||||||||||||||||||||||||||||||
FMGSLSFGVSELMKMPASGWYKLLNQEEGEYYNVPIPEG
-------110-------120-------130---------

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--650-------
XDQSDFEGFXYX
||||||||||||
XDQSDFEGFXYX
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	139	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_30305_5w4s.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	17		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	59		100.0 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 59
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	59	93.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	21	95.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	38	92.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	12	85.7

Covalent bonds

Saveframe: assembly
- Status: OK

Keywords Transferase, phosphorylation

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Found 1 Document (0.817 seconds)

BMRB: 30305

Sample #1

Sample #2

Sample #3

Related entities 1. Protein kinase C alpha type, : 1 : 2 : 65 entities Detail

Experiments performed 21 experiments Detail

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NMR combined restraints 2 contents Detail