Solution-state NMR structure of the human prion protein
GQGGGTHSQW NKPSKPKTNM KHMAGAAAAG AVVGGLGGYM LGSAMSRPII HFGSDYEDRY YRENMHRYPN QVYYRPMDEY SNQNNFVHDC VNITIKQHTV TTTTKGENFT ETDVKMMERV VEQMCITQYE RESQAYYQRG SS
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS90:SG | 1:CYS125:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 88.7 % (1442 of 1626) | 94.2 % (800 of 849) | 78.9 % (490 of 621) | 97.4 % (152 of 156) |
Backbone | 84.0 % (707 of 842) | 95.6 % (280 of 293) | 71.4 % (294 of 412) | 97.1 % (133 of 137) |
Sidechain | 94.2 % (859 of 912) | 93.5 % (520 of 556) | 95.0 % (320 of 337) | 100.0 % (19 of 19) |
Aromatic | 89.6 % (138 of 154) | 89.6 % (69 of 77) | 89.5 % (68 of 76) | 100.0 % (1 of 1) |
Methyl | 96.1 % (98 of 102) | 94.1 % (48 of 51) | 98.0 % (50 of 51) |
1. entity
GQGGGTHSQW NKPSKPKTNM KHMAGAAAAG AVVGGLGGYM LGSAMSRPII HFGSDYEDRY YRENMHRYPN QVYYRPMDEY SNQNNFVHDC VNITIKQHTV TTTTKGENFT ETDVKMMERV VEQMCITQYE RESQAYYQRG SSSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
5 | D2O | natural abundance | 100 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Varian Uniform NMR System - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Varian Uniform NMR System - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Varian Uniform NMR System - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Varian Uniform NMR System - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Varian Uniform NMR System - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Varian Uniform NMR System - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Varian Uniform NMR System - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Varian Uniform NMR System - 800 MHz
State isotropic, Solvent system 100% D2O, Temperature 298 K
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
5 | D2O | natural abundance | 100 % |
Varian Uniform NMR System - 800 MHz
State isotropic, Solvent system 100% D2O, Temperature 298 K
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
5 | D2O | natural abundance | 100 % |
Varian Uniform NMR System - 800 MHz
State isotropic, Solvent system 100% D2O, Temperature 298 K
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | huPrP | [U-100% 13C; U-100% 15N] | 1.5 mM | |
5 | D2O | natural abundance | 100 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_18426_2lsb.nef |
Input source #2: Coordindates | 2lsb.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 58.476, CB 40.645 ppm | oxidized, CA 59.867, CB 41.888 ppm | 2.027 |
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- TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSS |||||||||||||||||||||||||||||||||||||||||| TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSS -------110-------120-------130-------140--
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 142 | 0 | 0 | 100.0 |
Content subtype: combined_18426_2lsb.nef
Assigned chemical shifts
90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTV ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||||||||||||||||||| .QGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYY.PMD..SNQNNFVHDCVNITIKQHTV 0-------200-------210-------220-------230- TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSS |||||||||||||||||||||||||||||||||||||||||| TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSS
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 849 | 810 | 95.4 |
13C chemical shifts | 621 | 461 | 74.2 |
15N chemical shifts | 164 | 150 | 91.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 293 | 282 | 96.2 |
13C chemical shifts | 284 | 138 | 48.6 |
15N chemical shifts | 137 | 131 | 95.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 556 | 528 | 95.0 |
13C chemical shifts | 337 | 323 | 95.8 |
15N chemical shifts | 27 | 19 | 70.4 |
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 | 77 | 69 | 89.6 |
13C chemical shifts | 76 | 68 | 89.5 |
15N chemical shifts | 1 | 1 | 100.0 |
Covalent bonds
Distance restraints
90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTV || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||||||||||||||||||| .QG.GTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYY.PMD..SNQNNFVHDCVNITIKQHTV 90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 0-------200-------210-------220-------230- TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSS ||||||||||||||||||||||||||||||||||||||||| TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGS 0-------200-------210-------220-------230
Dihedral angle restraints
90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTV ||||||||||||||| ||||||||||||||||||||||||| ||||||||||||||||||| .....................................GYMLGSAMSRPIIHF.SDYEDRYYRENMHRYPNQVYYRPMD...NQNNFVHDCVNITIKQHTV 90------100-------110-------120-------130-------140-------150-------160-------170-------180-------19 0-------200-------210-------220-------230- TTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSS |||||| ||||||||||||||||||||||||||||||||| TTTTKG.NFTETDVKMMERVVEQMCITQYERESQAYYQRG 0-------200-------210-------220---------