Structure of C-terminal domain of human polymerase Rev1 in complex with PolD3 RIR-motif
NLAGAVEFND VKTLLREWIT TISDPMEEDI LQVVKYCTDL IEEKDLEKLD LVIKYMKRLM QQSVESVWNM AFDFILDNVQ VVLQQTYGST LKVT
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 76.7 % (1026 of 1337) | 82.7 % (573 of 693) | 67.3 % (350 of 520) | 83.1 % (103 of 124) |
Backbone | 72.3 % (476 of 658) | 83.0 % (185 of 223) | 61.3 % (200 of 326) | 83.5 % (91 of 109) |
Sidechain | 81.8 % (642 of 785) | 82.6 % (388 of 470) | 80.7 % (242 of 300) | 80.0 % (12 of 15) |
Aromatic | 51.0 % (50 of 98) | 61.2 % (30 of 49) | 38.3 % (18 of 47) | 100.0 % (2 of 2) |
Methyl | 96.4 % (135 of 140) | 95.7 % (67 of 70) | 97.1 % (68 of 70) |
1. Rev1-CT
NLAGAVEFND VKTLLREWIT TISDPMEEDI LQVVKYCTDL IEEKDLEKLD LVIKYMKRLM QQSVESVWNM AFDFILDNVQ VVLQQTYGST LKVT2. PolD3
KGNMMSNFFG KAAMNKSolvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.868 ppm | internal | direct | 1.0 |
15N | water | protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.868 ppm | internal | direct | 1.0 |
15N | water | protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.868 ppm | internal | direct | 1.0 |
15N | water | protons | 0.0 ppm | internal | indirect | 0.1013291 |
Varian Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 273 K, pH 7.0, Details a 15N/13C-labeled hRev1-CT with excess of an unlabeled PolD3 peptide
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Rev1-CT | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PolD3 | natural abundance | 0.5 ~ 0.8 mM | |
3 | potassium phosphate | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | DTT | natural abundance | 2 mM | |
6 | EDTA | natural abundance | 0.5 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_25559_2n1g.nef |
Input source #2: Coordindates | 2n1g.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
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
--1160---1170------1180------1190------1200------1210------1220------1230------1240------1250- NLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| NLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT --------10--------20--------30--------40--------50--------60--------70--------80--------90----
-------240------ KGNMMSNFFGKAAMNK |||||||||||||||| KGNMMSNFFGKAAMNK --------10------
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 94 | 0 | 0 | 100.0 |
B | B | 16 | 0 | 0 | 100.0 |
Content subtype: combined_25559_2n1g.nef
Assigned chemical shifts
--1160---1170------1180------1190------1200------1210------1220------1230------1240------1250- NLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| NLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
1170 | THR | HG1 | 4.848 |
1177 | THR | HG1 | 5.038 |
1178 | THR | HG1 | 5.344 |
1194 | CYS | HG | 2.676 |
1195 | THR | HG1 | 4.861 |
1201 | LYS | HZ1 | 7.53 |
1201 | LYS | HZ2 | 7.53 |
1201 | LYS | HZ3 | 7.53 |
1243 | THR | HG1 | 4.861 |
1251 | THR | HG1 | 4.395 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 590 | 576 | 97.6 |
13C chemical shifts | 449 | 338 | 75.3 |
15N chemical shifts | 107 | 103 | 96.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 189 | 186 | 98.4 |
13C chemical shifts | 188 | 96 | 51.1 |
15N chemical shifts | 93 | 91 | 97.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 401 | 390 | 97.3 |
13C chemical shifts | 261 | 242 | 92.7 |
15N chemical shifts | 14 | 12 | 85.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 72 | 72 | 100.0 |
13C chemical shifts | 72 | 72 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 39 | 30 | 76.9 |
13C chemical shifts | 37 | 18 | 48.6 |
15N chemical shifts | 2 | 2 | 100.0 |
Distance restraints
--1160---1170------1180------1190------1200------1210------1220------1230------1240------1250- NLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| NLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT
-------240------ KGNMMSNFFGKAAMNK |||||||||||||| ..NMMSNFFGKAAMNK
--1160---1170------1180------1190------1200------1210------1220------1230------1240------1250- NLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT | | |||||||||||||||| || |||||||||||||| |||||||||||||||| |||||||||||||||||||| .L..A.EFNDVKTLLREWITTI....EE.ILQVVKYCTDLIEE....KLDLVIKYMKRLMQQS....WNMAFDFILDNVQVVLQQTY --1160---1170------1180------1190------1200------1210------1220------1230------1240----