BMRBj - BMREntryMaster

Found 1 Document (0.993 seconds)

BMRB: 25987

2NBP

Solution structure of the T119M variant of transthyretin in its monomeric state

Authors

Kim, J., Oroz, J., Zweckstetter, M.

Assembly

transthyretin

Entity

1. transthyretin (polymer, Thiol state: all free), 127 monomers, 13793.37 Da Detail

GPTGTGESKC PLMVKVLDAV RGSPAINVAV HVFRKAADDT WEPFASGKTS ESGELHGLTT EEEFVEGIYK VEIDTKSYWK ALGISPMHEH AEVVFTANDS GPRRYTIAAM LSPYSYSTMA VVTNPKE

Formula weight

13793.37 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 82.2 %, Completeness (bb): 79.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.2 % (1162 of 1414)	89.9 % (652 of 725)	69.9 % (395 of 565)	92.7 % (115 of 124)
Backbone	79.9 % (596 of 746)	93.8 % (240 of 256)	66.0 % (245 of 371)	93.3 % (111 of 119)
Sidechain	86.4 % (678 of 785)	87.8 % (412 of 469)	84.2 % (262 of 311)	80.0 % (4 of 5)
Aromatic	66.7 % (80 of 120)	85.0 % (51 of 60)	46.6 % (27 of 58)	100.0 % (2 of 2)
Methyl	97.8 % (135 of 138)	100.0 % (69 of 69)	95.7 % (66 of 69)

1. T119M M-TTR

GPTGTGESKC PLMVKVLDAV RGSPAINVAV HVFRKAADDT WEPFASGKTS ESGELHGLTT EEEFVEGIYK VEIDTKSYWK ALGISPMHEH AEVVFTANDS GPRRYTIAAM LSPYSYSTMA VVTNPKE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

LACS Plot; CA

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2016-03-16

Citation

Structure of Monomeric Transthyretin Carrying the Clinically Important T119M Mutation
Kim, J., Oroz, J., Zweckstetter, M.
Angew. Chem Int Ed Engl. (2016), 55, 16168-16171, PubMed 27885756 , DOI 10.1002/anie.201608516 , Abstract

Related entities 1. transthyretin, : 1 : 9 : 150 entities Detail

Interaction partners 1. transthyretin, : 50 interactors Detail

More details for 50 interactors identified by 11 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Oxford Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

3 2D 1H-13C HSQC aromatic

Instrument

Oxford Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

4 3D HNCA

Instrument

Oxford Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

5 3D HN(CO)CA

Instrument

Oxford Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

6 3D HNCACB

Instrument

Oxford Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

7 3D CBCA(CO)NH

Instrument

Oxford Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

9 3D 1H-15N NOESY

Instrument

Oxford Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

11 3D 1H-13C NOESY aromatic

Instrument

Oxford Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	T119M M-TTR	[U-13C; U-15N]	protein	0.6 ~ 1.2 mM
2	MES	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	natural abundance		5 mM
5	DSS	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25987_2nbp.nef
Input source #2: Coordindates	2nbp.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GPTGTGESKCPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTSESGELHGLTTEEEFVEGIYKVEIDTKSYWKALGISPMHEHAEVVFTANDS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPTGTGESKCPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTSESGELHGLTTEEEFVEGIYKVEIDTKSYWKALGISPMHEHAEVVFTANDS

-------110-------120-------
GPRRYTIAAMLSPYSYSTMAVVTNPKE
|||||||||||||||||||||||||||
GPRRYTIAAMLSPYSYSTMAVVTNPKE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	127	0	0	100.0

Content subtype: combined_25987_2nbp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1147		97.6 (chain: A, length: 127)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2918 (1)	noe	95.3 (chain: A, length: 127)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	144 (1)	hbond	36.2 (chain: A, length: 127)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	214 (214)	.	89.8 (chain: A, length: 127)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 97.6%
- Total number of assignments
  - ¹H chemical shifts: 652
  - ¹³C chemical shifts: 381
  - ¹⁵N chemical shifts: 114
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 95.3%
- Total number of restraints: 2908
- Weight of restraints: 1.0 (2908)
- Potential type of restraints: upper-bound-parabolic (2908)
- Range of distance target values: 2.26, 5.5 (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
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 36.2%
  - Total number of restraints: 144
  - Weight of restraints: 1.0 (144)
  - Potential type of restraints: upper-bound-parabolic (144)
  - Range of distance target values: 1.8, 3.0 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 89.8%
- Total number of restraints: 214
- Total number of restraints per polymer type: 214
- Weight of restraints: 1.0 (214)
- Potential type of restraints: square-well-parabolic (214)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NMR, aggregation, amyloid, monomer, transthyretin