PrP226* - Solution-state NMR structure of truncated human prion protein
GQGGGTHSQW NKPSKPKTNM KHMAGAAAAG AVVGGLGGYM LGSAMSRPII HFGSDYEDRY YRENMHRYPN QVYYRPMDEY SNQNNFVHDC VNITIKQHTV TTTTKGENFT ETDVKMMERV VEQMCITQYE RESQAYYGGH HHHHH
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 81.1 % (1345 of 1659) | 86.9 % (750 of 863) | 70.5 % (450 of 638) | 91.8 % (145 of 158) |
Backbone | 76.7 % (660 of 860) | 90.0 % (270 of 300) | 61.9 % (260 of 420) | 92.9 % (130 of 140) |
Sidechain | 86.0 % (799 of 929) | 85.3 % (480 of 563) | 87.4 % (304 of 348) | 83.3 % (15 of 18) |
Aromatic | 75.3 % (134 of 178) | 75.3 % (67 of 89) | 75.0 % (66 of 88) | 100.0 % (1 of 1) |
Methyl | 99.0 % (101 of 102) | 98.0 % (50 of 51) | 100.0 % (51 of 51) |
1. entity 1
GQGGGTHSQW NKPSKPKTNM KHMAGAAAAG AVVGGLGGYM LGSAMSRPII HFGSDYEDRY YRENMHRYPN QVYYRPMDEY SNQNNFVHDC VNITIKQHTV TTTTKGENFT ETDVKMMERV VEQMCITQYE RESQAYYGGH HHHHHSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | indirect | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | indirect | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | indirect | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Agilent VNMRS - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.9, Details 0.9 mM (13C, 15N)-doubly labeled PrP226*, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PrP226 | [U-13C; U-15N] | 0.9 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_34003_5l6r.nef |
Input source #2: Coordindates | 5l6r.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 (Ã…) |
---|---|---|---|---|
A:179:CYS:SG | A:214:CYS:SG | oxidized, CA 58.599, CB 40.615 ppm | oxidized, CA 59.898, CB 41.992 ppm | 2.032 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTV |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTV --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 0-------200-------210-------220-------230---- TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYGGHHHHHH ||||||||||||||||||||||||||||||||||||||||||||| TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYGGHHHHHH -------110-------120-------130-------140-----
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 145 | 0 | 0 | 100.0 |
Content subtype: combined_34003_5l6r.nef
Assigned chemical shifts
90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTV ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||| | |||||||||||||||||| GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSR.IIHFGSDYEDRYYRENMHRYPNQVYY.PMD..S.QNNFVHDCVNITIKQHTV 90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 0-------200-------210-------220-------230---- TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYGGHHHHHH ||||||||||||||||||||||||||||||||||||||| TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYGG 0-------200-------210-------220--------
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 863 | 744 | 86.2 |
13C chemical shifts | 638 | 427 | 66.9 |
15N chemical shifts | 165 | 143 | 86.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 300 | 270 | 90.0 |
13C chemical shifts | 290 | 127 | 43.8 |
15N chemical shifts | 140 | 129 | 92.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 563 | 474 | 84.2 |
13C chemical shifts | 348 | 300 | 86.2 |
15N chemical shifts | 25 | 14 | 56.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 60 | 60 | 100.0 |
13C chemical shifts | 60 | 60 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 89 | 67 | 75.3 |
13C chemical shifts | 88 | 66 | 75.0 |
15N chemical shifts | 1 | 1 | 100.0 |
Covalent bonds
Distance restraints
90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTV || ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||| |||||||||||||||||| GQ..GTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSR.IIHFGSDYEDRYYRENMHRYPNQVYY.PMD....QNNFVHDCVNITIKQHTV 90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 0-------200-------210-------220-------230---- TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYGGHHHHHH ||||||||||||||||||||||||||||||||||||||| TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYGG 0-------200-------210-------220--------
Dihedral angle restraints
90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTV ||||||||||||||||||||||||||||||||||||||| ||||||||||||| .....................................GYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRP...........HDCVNITIKQHTV 90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 0-------200-------210-------220-------230---- TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYGGHHHHHH |||||| |||||||||||||||||||||||||||||||| TTTTKG.NFTETDVKMMERVVEQMCITQYERESQAYYGG 0-------200-------210-------220--------