BMRBj - BMREntryMaster

Found 1 Document (1.212 seconds)

BMRB: 15450

2JUM

ThrA3-DKP-insulin

Authors

Huang, K., Chan, S., Hua, Q., Chu, Y., Wang, R., Klaproth, B., Jia, W., Whittaker, J., De Meyts, P., Nakagawa, S.H., Steiner, D.F., Katsoyannis, P.G., Weiss, M.A.

Assembly

ThrA3-DKP-insulin

Entity

1. A-chain (polymer, Thiol state: all disulfide bound), 21 monomers, 2385.669 Da Detail

GITEQCCTSI CSLYQLENYC N

2. B-chain (polymer, Thiol state: all disulfide bound), 30 monomers, 3407.868 Da Detail

FVNQHLCGSD LVEALYLVCG ERGFFYTKPT

Total weight

5793.537 Da

Max. entity weight

3407.868 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS6:SG	1:CYS11:SG
2	disulfide	sing	1:CYS7:SG	2:CYS7:SG
3	disulfide	sing	1:CYS20:SG	2:CYS19:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 87.3 %, Completeness (bb): 83.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	87.3 % (261 of 299)	87.3 % (261 of 299)
Backbone	83.8 % (88 of 105)	83.8 % (88 of 105)
Sidechain	89.2 % (173 of 194)	89.2 % (173 of 194)
Aromatic	78.8 % (26 of 33)	78.8 % (26 of 33)
Methyl	92.6 % (25 of 27)	92.6 % (25 of 27)

1. A-chain

GITEQCCTSI CSLYQLENYC N

2. B-chain

FVNQHLCGSD LVEALYLVCG ERGFFYTKPT

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7

#	Name	Isotope labeling	Concentration
1	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
2	D2O		90 %
3	H2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details pD6.6, 25 degree

#	Name	Isotope labeling	Type	Concentration
4	ThrA3-DKP-insulin	natural abundance		1 (±0.2) mM
5	D2O			100 %

Sample #3

Solvent system 20% D-acetic acid/80% H2O, Pressure 1 atm, Temperature 308 K, pH 7, Details pH 1.9, 25 degree

#	Name	Isotope labeling	Concentration
6	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
7	D2O		80 %
8	D-acetic acid	natural abundance	3.1 (±0.2) M

Protein Blocks Logo

Calculated from 15 models in PDB: 2JUM, Strand ID: A, B Detail

Release date

2008-06-25

Citation

The A-chain of insulin contacts the insert domain of the insulin receptor. Photo-cross-linking and mutagenesis of a diabetes-related crevice
Huang, K., Chan, S.J., Hua, Q., Chu, Y., Wang, R., Klaproth, B., Jia, W., Whittaker, J., De Meyts, P., Nakagawa, S.H., Steiner, D.F., Katsoyannis, P.G., Weiss, M.A.
J. Biol. Chem. (2007), 282, 35337-35349, PubMed 17884811 , DOI 10.1074/jbc.M705996200 , Abstract

Related entities 1. A-chain, : 1 : 118 : 102 entities Detail

Related entities 2. B-chain, : 1 : 10 : 1 : 115 : 92 entities Detail

Interaction partners 1. A-chain, : 4 : 1 interactors Detail

More details for 5 interactors identified by 5 citations

Interaction partners 2. B-chain, : 6 : 1 interactors Detail

More details for 7 interactors identified by 7 citations

Experiments performed 15 experiments Detail

1 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7

#	Name	Isotope labeling	Concentration
1	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
2	D2O		90 %
3	H2O	natural abundance	10 %

2 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7

#	Name	Isotope labeling	Concentration
1	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
2	D2O		90 %
3	H2O	natural abundance	10 %

3 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7

#	Name	Isotope labeling	Concentration
1	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
2	D2O		90 %
3	H2O	natural abundance	10 %

4 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, Details pD6.6, 25 degree

#	Name	Isotope labeling	Type	Concentration
4	ThrA3-DKP-insulin	natural abundance		1 (±0.2) mM
5	D2O			100 %

5 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, Details pD6.6, 25 degree

#	Name	Isotope labeling	Type	Concentration
4	ThrA3-DKP-insulin	natural abundance		1 (±0.2) mM
5	D2O			100 %

6 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, Details pD6.6, 25 degree

#	Name	Isotope labeling	Type	Concentration
4	ThrA3-DKP-insulin	natural abundance		1 (±0.2) mM
5	D2O			100 %

7 2D DQF-COSY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 20% D-acetic acid/80% H2O, Pressure 1 atm, Temperature 315 K, Details pH 1.9, 25 degree

#	Name	Isotope labeling	Concentration
6	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
7	D2O		80 %
8	D-acetic acid	natural abundance	3.1 (±0.2) M

8 2D 1H-1H TOCSY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 20% D-acetic acid/80% H2O, Pressure 1 atm, Temperature 315 K, Details pH 1.9, 25 degree

#	Name	Isotope labeling	Concentration
6	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
7	D2O		80 %
8	D-acetic acid	natural abundance	3.1 (±0.2) M

9 2D 1H-1H NOESY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 20% D-acetic acid/80% H2O, Pressure 1 atm, Temperature 315 K, Details pH 1.9, 25 degree

#	Name	Isotope labeling	Concentration
6	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
7	D2O		80 %
8	D-acetic acid	natural abundance	3.1 (±0.2) M

10 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 20% D-acetic acid/80% H2O, Pressure 1 atm, Temperature 308 K, pH 1.9, Details pH 1.9, 25 degree

#	Name	Isotope labeling	Concentration
6	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
7	D2O		80 %
8	D-acetic acid	natural abundance	3.1 (±0.2) M

11 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 20% D-acetic acid/80% H2O, Pressure 1 atm, Temperature 308 K, pH 1.9, Details pH 1.9, 25 degree

#	Name	Isotope labeling	Concentration
6	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
7	D2O		80 %
8	D-acetic acid	natural abundance	3.1 (±0.2) M

12 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 20% D-acetic acid/80% H2O, Pressure 1 atm, Temperature 308 K, pH 1.9, Details pH 1.9, 25 degree

#	Name	Isotope labeling	Concentration
6	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
7	D2O		80 %
8	D-acetic acid	natural abundance	3.1 (±0.2) M

13 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 20% D-acetic acid/80% H2O, Pressure 1 atm, Temperature 308 K, Details pH 1.9, 25 degree

#	Name	Isotope labeling	Concentration
6	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
7	D2O		80 %
8	D-acetic acid	natural abundance	3.1 (±0.2) M

14 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 20% D-acetic acid/80% H2O, Pressure 1 atm, Temperature 308 K, Details pH 1.9, 25 degree

#	Name	Isotope labeling	Concentration
6	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
7	D2O		80 %
8	D-acetic acid	natural abundance	3.1 (±0.2) M

15 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 20% D-acetic acid/80% H2O, Pressure 1 atm, Temperature 308 K, Details pH 1.9, 25 degree

#	Name	Isotope labeling	Concentration
6	ThrA3-DKP-insulin	natural abundance	1 (±0.2) mM
7	D2O		80 %
8	D-acetic acid	natural abundance	3.1 (±0.2) M

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15450_2jum.nef
Input source #2: Coordindates	2jum.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)
A:6:CYS:SG	A:11:CYS:SG	unknown	unknown	2.019
A:7:CYS:SG	B:7:CYS:SG	unknown	unknown	2.019
A:20:CYS:SG	B:19:CYS:SG	unknown	unknown	2.01

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-
GITEQCCTSICSLYQLENYCN
|||||||||||||||||||||
GITEQCCTSICSLYQLENYCN

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

--------10--------20--------30
FVNQHLCGSDLVEALYLVCGERGFFYTKPT
||||||||||||||||||||||||||||||
FVNQHLCGSDLVEALYLVCGERGFFYTKPT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	21	0	0	100.0
B	B	30	0	0	100.0

Content subtype: combined_15450_2jum.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	A_chain	Warning	260		95.2 (chain: A, length: 21), 96.7 (chain: B, length: 30)
1	Distance restraints	Discover_distance_constraints_4	OK	28 (1)	undefined	38.1 (chain: A, length: 21), 73.3 (chain: B, length: 30)
2	Distance restraints	Discover_distance_constraints_6	Warning	279 (1)	noe	28.6 (chain: A, length: 21), 73.3 (chain: B, length: 30)
3	Distance restraints	Discover_distance_constraints_5	Warning	25 (1)	hbond	4.8 (chain: A, length: 21), 46.7 (chain: B, length: 30)
1	Dihedral angle restraints	Discover_dihedral_8	Warning	24 (24)	.	19.0 (chain: A, length: 21), 56.7 (chain: B, length: 30)

Assigned chemical shifts

Saveframe: A_chain
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 95.2%
  - Entity_assembly_ID: B, Chain length: 30, Sequence coverage: 96.7%
- Total number of assignments
  - ¹H chemical shifts: 260
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	119	97	81.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	35	81.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	62	81.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	8	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	4	50.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
28	LYS	HZ1	7.24
28	LYS	HZ2	7.24
28	LYS	HZ3	7.24

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	180	160	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	51	82.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	118	109	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	22	88.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: Discover_distance_constraints_4
- Status: OK
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 38.1%
  - Entity_assembly_ID: B, Chain length: 30, Sequence coverage: 73.3%
- Total number of restraints: 28
- Weight of restraints: 1.0 (28)
- Potential type of restraints: square-well-parabolic (28)
- Range of distance target values: 5.95, 5.95 (Å)
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: Discover_distance_constraints_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 28.6%
    - Entity_assembly_ID: B, Chain length: 30, Sequence coverage: 73.3%
  - Total number of restraints: 279
  - Weight of restraints: 1.0 (279)
  - Potential type of restraints: square-well-parabolic (279)
  - Range of distance target values: 1.85, 4.75 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: Discover_distance_constraints_5
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 4.8%
      - Entity_assembly_ID: B, Chain length: 30, Sequence coverage: 46.7%
    - Total number of restraints: 25
    - Weight of restraints: 1.0 (25)
    - Potential type of restraints: square-well-parabolic (25)
    - Range of distance target values: 2.45, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: Discover_dihedral_8
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 19.0%
  - Entity_assembly_ID: B, Chain length: 30, Sequence coverage: 56.7%
- Total number of restraints: 24
- Total number of restraints per polymer type: 24
- Weight of restraints: 1.0 (24)
- Potential type of restraints: square-well-parabolic (24)
- Dihedral angle restraints per residue
  - Chain_ID: B

Keywords insulin, NMR, ThrA3

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Found 1 Document (1.212 seconds)

BMRB: 15450

Sample #1

Sample #2

Sample #3

Related entities 1. A-chain, : 1 : 118 : 102 entities Detail

Related entities 2. B-chain, : 1 : 10 : 1 : 115 : 92 entities Detail

Interaction partners 1. A-chain, : 4 : 1 interactors Detail

Interaction partners 2. B-chain, : 6 : 1 interactors Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 6 contents Detail