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Found 1 Document (1.126 seconds)

BMRB: 30099

5K5G

Structure of human islet amyloid polypeptide in complex with an engineered binding protein

Authors

Mirecka, E.A., Feuerstein, S., Gremer, L., Schroeder, G.F., Stoldt, M., Willbold, D., Hoyer, W.

Assembly

Islet amyloid polypeptide, HI18

Entity

1. Islet amyloid polypeptide (polymer, Thiol state: all free), 37 monomers, 3906.277 Da Detail

KCNTATCATQ RLANFLVHSS NNFGAILSST NVGSNTY

2. HI18 (polymer, Thiol state: all disulfide bound), 69 monomers, 7791.555 × 2 Da Detail

MHHHHHHVNS VDNKFNKEME SAGGEIVYLP NLNPDQLCAF IHSIHDDPSQ SANLLAEAKK LNDAQAPKW

Total weight

19489.387 Da

Max. entity weight

7791.555 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	2:CYS38:SG	2:CYS38:SG

Source organism

Homo sapiens , synthetic construct

Exptl. method

solution NMR

Refine. method

SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 60.4 %, Completeness: 48.7 %, Completeness (bb): 51.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	48.7 % (581 of 1193)	51.3 % (315 of 614)	44.7 % (205 of 459)	50.8 % (61 of 120)
Backbone	51.9 % (326 of 628)	57.1 % (121 of 212)	46.2 % (145 of 314)	58.8 % (60 of 102)
Sidechain	47.2 % (315 of 667)	48.3 % (194 of 402)	48.6 % (120 of 247)	5.6 % (1 of 18)
Aromatic	10.6 % (11 of 104)	21.2 % (11 of 52)	0.0 % (0 of 51)	0.0 % (0 of 1)
Methyl	75.0 % (78 of 104)	75.0 % (39 of 52)	75.0 % (39 of 52)

1. Islet amyloid polypeptide

KCNTATCATQ RLANFLVHSS NNFGAILSST NVGSNTY

2. HI18

MHHHHHHVNS VDNKFNKEME SAGGEIVYLP NLNPDQLCAF IHSIHDDPSQ SANLLAEAKK LNDAQAPKW

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.40 mM [U-13C; U-15N] ISLET AMYLOID POLYPEPTIDE, 0.48 mM HI18, 20 mM sodium phosphate, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	HI18	natural abundance	0.48 mM
2	ISLET AMYLOID POLYPEPTIDE	[U-13C; U-15N]	0.40 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.48 mM ISLET AMYLOID POLYPEPTIDE, 0.40 mM [U-13C; U-15N] HI18, 20 mM sodium phosphate, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
6	HI18	[U-13C; U-15N]	0.40 mM
7	ISLET AMYLOID POLYPEPTIDE	natural abundance	0.48 mM
8	sodium phosphate	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.779 ppm	internal	indirect	0.251
¹H	water	protons	4.779 ppm	internal	direct	1.0
¹⁵N	water	protons	4.779 ppm	internal	indirect	0.101

Referencing offset: 0.61 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.779 ppm	internal	indirect	0.251
¹H	water	protons	4.779 ppm	internal	direct	1.0
¹⁵N	water	protons	4.779 ppm	internal	indirect	0.101

Referencing offset: 0.61 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.779 ppm	internal	indirect	0.251
¹H	water	protons	4.779 ppm	internal	direct	1.0
¹⁵N	water	protons	4.779 ppm	internal	indirect	0.101

Referencing offset: 0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5K5G, Strand ID: A, B, C Detail

Release date

2016-09-21

Citation

β-Hairpin of Islet Amyloid Polypeptide Bound to an Aggregation Inhibitor
Mirecka, E.A., Feuerstein, S., Gremer, L., Schroeder, G.F., Stoldt, M., Willbold, D., Hoyer, W.
Sci. Rep. (2016), 6, 33474-33474, PubMed 27641459 , DOI 10.1038/srep33474 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25964 released on 2016-01-25
Title Structure of human islet amyloid polypeptide in complex with an engineered binding protein

Related entities 1. Islet amyloid polypeptide, : 6 : 3 : 9 entities Detail

Related entities 2. HI18, : 1 : 151 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.40 mM [U-13C; U-15N] ISLET AMYLOID POLYPEPTIDE, 0.48 mM HI18, 20 mM sodium phosphate, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	HI18	natural abundance	0.48 mM
2	ISLET AMYLOID POLYPEPTIDE	[U-13C; U-15N]	0.40 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %

2 3D HNCA

Instrument

Varian VNMRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HI18	natural abundance	0.48 mM
2	ISLET AMYLOID POLYPEPTIDE	[U-13C; U-15N]	0.40 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %

3 3D HNHA

Instrument

Varian VNMRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HI18	natural abundance	0.48 mM
2	ISLET AMYLOID POLYPEPTIDE	[U-13C; U-15N]	0.40 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %

4 3D HNCACB

Instrument

Varian VNMRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HI18	natural abundance	0.48 mM
2	ISLET AMYLOID POLYPEPTIDE	[U-13C; U-15N]	0.40 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %

5 3D 1H-15N NOESY

Instrument

Varian VNMRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HI18	natural abundance	0.48 mM
2	ISLET AMYLOID POLYPEPTIDE	[U-13C; U-15N]	0.40 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %

6 3D HNCO

Instrument

Varian VNMRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HI18	natural abundance	0.48 mM
2	ISLET AMYLOID POLYPEPTIDE	[U-13C; U-15N]	0.40 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %

7 3D HCCH-COSY

Instrument

Varian VNMRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HI18	natural abundance	0.48 mM
2	ISLET AMYLOID POLYPEPTIDE	[U-13C; U-15N]	0.40 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %

8 3D 1H-13C NOESY

Instrument

Varian VNMRS - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HI18	natural abundance	0.48 mM
2	ISLET AMYLOID POLYPEPTIDE	[U-13C; U-15N]	0.40 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %

9 2D 1H-15N HSQC

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.48 mM ISLET AMYLOID POLYPEPTIDE, 0.40 mM [U-13C; U-15N] HI18, 20 mM sodium phosphate, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
6	HI18	[U-13C; U-15N]	0.40 mM
7	ISLET AMYLOID POLYPEPTIDE	natural abundance	0.48 mM
8	sodium phosphate	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

10 3D HNCA

Instrument

Varian VNMRS - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
6	HI18	[U-13C; U-15N]	0.40 mM
7	ISLET AMYLOID POLYPEPTIDE	natural abundance	0.48 mM
8	sodium phosphate	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

11 3D HNHA

Instrument

Varian VNMRS - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
6	HI18	[U-13C; U-15N]	0.40 mM
7	ISLET AMYLOID POLYPEPTIDE	natural abundance	0.48 mM
8	sodium phosphate	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

12 3D HNCACB

Instrument

Varian VNMRS - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
6	HI18	[U-13C; U-15N]	0.40 mM
7	ISLET AMYLOID POLYPEPTIDE	natural abundance	0.48 mM
8	sodium phosphate	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

13 3D 1H-15N NOESY

Instrument

Varian VNMRS - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
6	HI18	[U-13C; U-15N]	0.40 mM
7	ISLET AMYLOID POLYPEPTIDE	natural abundance	0.48 mM
8	sodium phosphate	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

14 3D HCCH-COSY

Instrument

Varian VNMRS - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
6	HI18	[U-13C; U-15N]	0.40 mM
7	ISLET AMYLOID POLYPEPTIDE	natural abundance	0.48 mM
8	sodium phosphate	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

15 3D 1H-13C NOESY

Instrument

Varian VNMRS - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
6	HI18	[U-13C; U-15N]	0.40 mM
7	ISLET AMYLOID POLYPEPTIDE	natural abundance	0.48 mM
8	sodium phosphate	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30099_5k5g.nef
Input source #2: Coordindates	5k5g.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
B:28:CYS:SG	C:28:CYS:SG	unknown	unknown	2.236

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

--------10--------20--------30-------
KCNTATCATQRLANFLVHSSNNFGAILSSTNVGSNTY
|||||||||||||||||||||||||||||||||||||
KCNTATCATQRLANFLVHSSNNFGAILSSTNVGSNTY

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

------------------10--------20--------30--------40--------50---------
MHHHHHHVNSVDNKFNKEMESAGGEIVYLPNLNPDQLCAFIHSIHDDPSQSANLLAEAKKLNDAQAPKW
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHHHHHHVNSVDNKFNKEMESAGGEIVYLPNLNPDQLCAFIHSIHDDPSQSANLLAEAKKLNDAQAPKW
--------10--------20--------30--------40--------50--------60---------

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

------------------10--------20--------30--------40--------50---------
MHHHHHHVNSVDNKFNKEMESAGGEIVYLPNLNPDQLCAFIHSIHDDPSQSANLLAEAKKLNDAQAPKW
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHHHHHHVNSVDNKFNKEMESAGGEIVYLPNLNPDQLCAFIHSIHDDPSQSANLLAEAKKLNDAQAPKW
--------10--------20--------30--------40--------50--------60---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	37	100.0
B	B	69	100.0
C	C	69	100.0

Content subtype: combined_30099_5k5g.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	944		56.8 (chain: A, length: 37), 59.4 (chain: B, length: 69), 60.9 (chain: C, length: 69)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	2289 (1)	noe	51.4 (chain: A, length: 37), 59.4 (chain: B, length: 69), 60.9 (chain: C, length: 69)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	32 (32)	.	51.4 (chain: A, length: 37)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	154 (154)	.	60.9 (chain: B, length: 69), 60.9 (chain: C, length: 69)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 56.8%
  - Entity_assembly_ID: B, Chain length: 69, Sequence coverage: 59.4%
  - Entity_assembly_ID: C, Chain length: 69, Sequence coverage: 60.9%
- Total number of assignments
  - ¹H chemical shifts: 526
  - ¹³C chemical shifts: 320
  - ¹⁵N chemical shifts: 98
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
  - Entity_assemble_ID: C
- Peptide bond of PRO
- 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
  - Chain_ID: B
  - Chain_ID: C

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	199	102	51.3
¹³C chemical shifts	152	73	48.0
¹⁵N chemical shifts	45	21	46.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	40	52.6
¹³C chemical shifts	74	36	48.6
¹⁵N chemical shifts	37	20	54.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	123	62	50.4
¹³C chemical shifts	78	37	47.4
¹⁵N chemical shifts	8	1	12.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	13	61.9
¹³C chemical shifts	21	13	61.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	5	31.2
¹³C chemical shifts	16	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	415	211	50.8
¹³C chemical shifts	307	123	40.1
¹⁵N chemical shifts	76	38	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	136	79	58.1
¹³C chemical shifts	138	41	29.7
¹⁵N chemical shifts	65	38	58.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	279	132	47.3
¹³C chemical shifts	169	82	48.5
¹⁵N chemical shifts	11	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	33	26	78.8
¹³C chemical shifts	33	26	78.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	6	16.7
¹³C chemical shifts	35	0	0.0
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	415	213	51.3
¹³C chemical shifts	307	124	40.4
¹⁵N chemical shifts	76	39	51.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	136	81	59.6
¹³C chemical shifts	138	42	30.4
¹⁵N chemical shifts	65	39	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	279	132	47.3
¹³C chemical shifts	169	82	48.5
¹⁵N chemical shifts	11	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	33	26	78.8
¹³C chemical shifts	33	26	78.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	6	16.7
¹³C chemical shifts	35	0	0.0
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 51.4%
  - Entity_assembly_ID: B, Chain length: 69, Sequence coverage: 59.4%
  - Entity_assembly_ID: C, Chain length: 69, Sequence coverage: 60.9%
- Total number of restraints: 2282
- Weight of restraints: 1.0 (2282)
- Potential type of restraints: square-well-parabolic (2282)
- Range of distance target values: 1.6, 5.59 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 51.4%
- Total number of restraints: 32
- Total number of restraints per polymer type: 32
- Weight of restraints: 1.0 (32)
- Potential type of restraints: square-well-parabolic (32)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_4
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 69, Sequence coverage: 60.9%
    - Entity_assembly_ID: C, Chain length: 69, Sequence coverage: 60.9%
  - Total number of restraints: 154
  - Total number of restraints per polymer type: 154
  - Weight of restraints: 1.0 (154)
  - Potential type of restraints: square-well-parabolic (154)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: B
    - Chain_ID: C

Keywords amyloid, beta-hairpin, hormone, signaling protein, type 2 diabetes

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Found 1 Document (1.126 seconds)

BMRB: 30099

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Islet amyloid polypeptide, : 6 : 3 : 9 entities Detail

Related entities 2. HI18, : 1 : 151 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 5 contents Detail