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Found 1 Document (1.83 seconds)

BMRB: 15932

2K7Z

Solution Structure of the Catalytic Domain of Procaspase-8

Authors

Keller, N., Zerbe, O., Mares, J., Gruetter, M.G.

Assembly

Procaspase-8

Entity

1. Procaspase-8 (polymer, Thiol state: all free), 266 monomers, 30308.08 Da Detail

MRGSESQTLD KVYQMKSKPR GYCLIINNHN FAKAREKVPK LHSIRDRNGT HLDAGALTTT FEELHFEIKP HDDCTVEQIY EILKIYQLMD HSNMDCFICC ILSHGDKGII YGTDGQEAPI YELTSQFTGL KCPSLAGKPK VFFIQAAQGD NYQKGIPVET DSEEQPYLEM DLSSPQTRYI PDEADFLLGM ATVNNCVSYR NPAEGTWYIQ SLCQSLRERC PRGDDILTIL TEVNYEVSNK DDKKNMGKQM PQPTFTLRKK LVFPSD

Formula weight

30308.08 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.6 %, Completeness: 73.5 %, Completeness (bb): 81.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.5 % (2305 of 3136)	69.6 % (1144 of 1643)	77.6 % (942 of 1214)	78.5 % (219 of 279)
Backbone	81.9 % (1282 of 1566)	79.9 % (426 of 533)	82.2 % (643 of 782)	84.9 % (213 of 251)
Sidechain	67.6 % (1231 of 1820)	64.7 % (718 of 1110)	74.3 % (507 of 682)	21.4 % (6 of 28)
Aromatic	33.5 % (79 of 236)	33.9 % (40 of 118)	32.5 % (38 of 117)	100.0 % (1 of 1)
Methyl	87.9 % (225 of 256)	87.5 % (112 of 128)	88.3 % (113 of 128)

1. procaspase8

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
1	procaspase8	[U-99% 13C; U-99% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	TRIS	[U-2H]	20 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 2H, 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
7	procaspase8	[U-100% 13C; U-100% 15N; 80% 2H]	0.8 mM
8	DTT	natural abundance	10 mM
9	sodium chloride	natural abundance	100 mM
10	TRIS	[U-2H]	20 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.682 ppm	na	indirect	0.2514495
¹H	water	protons	4.682 ppm	internal	direct	1.0
¹⁵N	water	protons	4.682 ppm	na	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.682 ppm	na	indirect	0.2514495
¹H	water	protons	4.682 ppm	internal	direct	1.0
¹⁵N	water	protons	4.682 ppm	na	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.682 ppm	na	indirect	0.2514495
¹H	water	protons	4.682 ppm	internal	direct	1.0
¹⁵N	water	protons	4.682 ppm	na	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.682 ppm	na	indirect	0.2514495
¹H	water	protons	4.682 ppm	internal	direct	1.0
¹⁵N	water	protons	4.682 ppm	na	indirect	0.1013291

Referencing offset: 0.72 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K7Z, Strand ID: A Detail

Release date

2009-03-10

Citation

Structural and biochemical studies on procaspase-8: new insights on initiator caspase activation
Keller, N., Mares, J., Zerbe, O., Gruetter, M.G.
Structure (2009), 17, 438-448, PubMed 19278658 , DOI 10.1016/j.str.2008.12.019 , Abstract

Related entities 1. Procaspase-8, : 1 : 9 : 177 entities Detail

Interaction partners 1. Procaspase-8, : 110 interactors Detail

More details for 110 interactors identified by 34 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 2H, 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
7	procaspase8	[U-100% 13C; U-100% 15N; 80% 2H]	0.8 mM
8	DTT	natural abundance	10 mM
9	sodium chloride	natural abundance	100 mM
10	TRIS	[U-2H]	20 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
1	procaspase8	[U-99% 13C; U-99% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	TRIS	[U-2H]	20 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 2H, 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
7	procaspase8	[U-100% 13C; U-100% 15N; 80% 2H]	0.8 mM
8	DTT	natural abundance	10 mM
9	sodium chloride	natural abundance	100 mM
10	TRIS	[U-2H]	20 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

4 3D HN(CO)CACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 2H, 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
7	procaspase8	[U-100% 13C; U-100% 15N; 80% 2H]	0.8 mM
8	DTT	natural abundance	10 mM
9	sodium chloride	natural abundance	100 mM
10	TRIS	[U-2H]	20 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 2H, 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
7	procaspase8	[U-100% 13C; U-100% 15N; 80% 2H]	0.8 mM
8	DTT	natural abundance	10 mM
9	sodium chloride	natural abundance	100 mM
10	TRIS	[U-2H]	20 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

6 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 2H, 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
7	procaspase8	[U-100% 13C; U-100% 15N; 80% 2H]	0.8 mM
8	DTT	natural abundance	10 mM
9	sodium chloride	natural abundance	100 mM
10	TRIS	[U-2H]	20 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

7 3D HN(CO)CG

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 2H, 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
7	procaspase8	[U-100% 13C; U-100% 15N; 80% 2H]	0.8 mM
8	DTT	natural abundance	10 mM
9	sodium chloride	natural abundance	100 mM
10	TRIS	[U-2H]	20 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

8 3D HNCG

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 2H, 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
7	procaspase8	[U-100% 13C; U-100% 15N; 80% 2H]	0.8 mM
8	DTT	natural abundance	10 mM
9	sodium chloride	natural abundance	100 mM
10	TRIS	[U-2H]	20 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

9 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
1	procaspase8	[U-99% 13C; U-99% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	TRIS	[U-2H]	20 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 2H, 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
7	procaspase8	[U-100% 13C; U-100% 15N; 80% 2H]	0.8 mM
8	DTT	natural abundance	10 mM
9	sodium chloride	natural abundance	100 mM
10	TRIS	[U-2H]	20 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
1	procaspase8	[U-99% 13C; U-99% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	TRIS	[U-2H]	20 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

12 HN(CACO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 2H, 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
7	procaspase8	[U-100% 13C; U-100% 15N; 80% 2H]	0.8 mM
8	DTT	natural abundance	10 mM
9	sodium chloride	natural abundance	100 mM
10	TRIS	[U-2H]	20 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

13 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
1	procaspase8	[U-99% 13C; U-99% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	TRIS	[U-2H]	20 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

14 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 8.0, Details 13C,15N labelled PC8

#	Name	Isotope labeling	Concentration
1	procaspase8	[U-99% 13C; U-99% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	sodium chloride	natural abundance	100 mM
4	TRIS	[U-2H]	20 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15932_2k7z.nef
Input source #2: Coordindates	2k7z.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Sequence alignments

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

----220-------230-------240-------250-------260-------270-------280-------290-------300-------310---
MRGSESQTLDKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHDDCTVEQIYEILKIYQLMDHSNMDCFICC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MRGSESQTLDKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHDDCTVEQIYEILKIYQLMDHSNMDCFICC
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----320-------330-------340-------350-------360-------370-------380-------390-------400-------410---
ILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQAAQGDNYQKGIPVETDSEEQPYLEMDLSSPQTRYIPDEADFLLGMATVNNCVSYR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQAAQGDNYQKGIPVETDSEEQPYLEMDLSSPQTRYIPDEADFLLGMATVNNCVSYR
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

----420-------430-------440-------450-------460-------470---------
NPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFPSD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFPSD
-------210-------220-------230-------240-------250-------260------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	266	0	0	100.0

Content subtype: combined_15932_2k7z.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2241		82.7 (chain: A, length: 266)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3316 (1)	noe	80.8 (chain: A, length: 266)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 266, Sequence coverage: 82.7%
- Total number of assignments
  - ¹H chemical shifts: 1110
  - ¹³C chemical shifts: 922
  - ¹⁵N chemical shifts: 209
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
248	ARG	HH12	7.635
248	ARG	HH11	6.494
248	ARG	NH1	111.52
260	ARG	HH12	7.635
260	ARG	HH11	6.494
260	ARG	NH1	111.52

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1643	1106	67.3
¹³C chemical shifts	1214	922	75.9
¹⁵N chemical shifts	290	207	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	533	416	78.0
¹³C chemical shifts	532	426	80.1
¹⁵N chemical shifts	251	201	80.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1110	690	62.2
¹³C chemical shifts	682	496	72.7
¹⁵N chemical shifts	39	6	15.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	136	118	86.8
¹³C chemical shifts	136	118	86.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	118	38	32.2
¹³C chemical shifts	117	37	31.6
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 266, Sequence coverage: 80.8%
- Total number of restraints: 3305
- Weight of restraints: 1.0 (3305)
- Potential type of restraints: upper-bound-parabolic (3305)
- Range of distance target values: 2.27, 5.85 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords activation, apoptosis, caspase-8, initiator, NMR, caspase, initiator caspase, procaspase

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Found 1 Document (1.83 seconds)

BMRB: 15932

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Procaspase-8, : 1 : 9 : 177 entities Detail

Interaction partners 1. Procaspase-8, : 110 interactors Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 3 contents Detail