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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P53617 New Search
14PDB entries
19Biological assembly
19chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2LO6 Structure of Nrd1 CID bound to phosphorylated RNAP II CTD Deposited 2012-01-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–153（153 aa） Fragment：CID domain residues 1-154
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；293 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 2 mM [U-100% 13C; U-100% 15N] Nrd1 polypeptide, 2.3 mM phosphopeptide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2M88 NMR structure of a two-domain RNA-binding fragment of Nrd1 Deposited 2013-05-08 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 307–491（185 aa） Fragment：UNP residues 307-491
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；293 K；Pressure ambient
NMR measurement conditions pH 8；293 K；Pressure ambient
NMR measurement conditions pH 8；293 K；Pressure ambient
NMR sample composition 0.4 mM [U-13C; U-15N] Nrd1, 50 mM sodium phosphate, 300 mM sodium chloride, 10 mM beta-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N; U-80% 2H] Nrd1, 50 mM sodium phosphate, 300 mM sodium chloride, 10 mM beta-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM [U-13C; U-15N; U-2H] Nrd1, 50 mM sodium phosphate, 300 mM sodium chloride, 10 mM beta-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MOW Structure of Nrd1p CID - Trf4p NIM complex Deposited 2014-05-06 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–153（153 aa） Fragment：CID (UNP residues 1-153)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；293.15 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 1.5 mM Trf4p, 1 mM [U-99% 13C; U-99% 15N] Nrd1p, 100 mM sodium chloride, 50 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3CLJ Structure of the RNA polymerase II CTD-interacting domain of Nrd1 Deposited 2008-03-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 6–151（146 aa） Fragment：CTD-interacting domain, unp residues 6-151
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100 mM Na-citrate buffer, 1.4 M (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.220
5O1T Solution structure of the RNA binding domain of Nrd1 Deposited 2017-05-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 290–468（179 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 59.1；Pressure 1
NMR sample composition 600 uM [U-100% 13C; U-100% 15N] Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 800 uM Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 400 uM [U-100% 13C; U-100% 15N] expect for Phe and Leu residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 400 uM [U-100% 13C; U-100% 15N] expect for Ile residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 400 uM [U-100% 13C; U-100% 15N] expect for Arg residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5O1W Structure of Nrd1 RNA binding domain Deposited 2017-05-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 301–489（189 aa） Fragment：UNP residues 301-489
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；12% PEG 8000, 0.1 M Bicine pH 9
Resolution 2.30 Å R-free 0.233
5O1X Structure of Nrd1 RNA binding domain Deposited 2017-05-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 290–468（179 aa） Fragment：UNP residues 290-468
Not recorded EDO 1,2-ETHANEDIOL × 7 SCN THIOCYANATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M Potassium Thiocyanate, 23% PEG 3350
Resolution 1.60 Å R-free 0.208
5O1Y Structure of Nrd1 RNA binding domain in complex with RNA (GUAA) Deposited 2017-05-19 Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric（2） Consistent with all polymers
Chain A 290–468（179 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；1M Sodium Potassium Phosphate pH 7.4
Resolution 2.45 Å R-free 0.217
5O1Z Structure of Nrd1 RNA binding domain in complex with RNA (CGUAAA) Deposited 2017-05-19 Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric（2） Consistent with all polymers
Chain A 290–468（179 aa） Fragment：UNP residues 290-468
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；1M Sodium Potassium Phosphate pH 7.4
Resolution 3.40 Å R-free 0.216
5O20 Structure of Nrd1 RNA binding domain in complex with RNA (UUAGUAAUCC) Deposited 2017-05-19 Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric（2） Consistent with all polymers
Chain A 290–468（179 aa）
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；1M Sodium Potassium Phosphate pH 7.4
Resolution 3.53 Å R-free 0.269
6GC3 Structure of Nrd1 CID - Sen1 NIM complex Deposited 2018-04-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–153（153 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；293 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] CTD-interacting domain of Nrd1, 1.5 mM ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6O3W Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM1 Deposited 2019-02-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 6–156（151 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；sodium citrate, lithium chloride, PEG 6000
Resolution 2.10 Å R-free 0.204
6O3W Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM1 Deposited 2019-02-27 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 6–156（151 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；sodium citrate, lithium chloride, PEG 6000
Resolution 2.10 Å R-free 0.204
6O3X Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM2 Deposited 2019-02-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 6–156（151 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium citrate, lithium chloride, PEG 6000
Resolution 1.99 Å R-free 0.226
6O3X Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM2 Deposited 2019-02-27 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 6–156（151 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium citrate, lithium chloride, PEG 6000
Resolution 1.99 Å R-free 0.226
6O3X Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM2 Deposited 2019-02-27 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 6–156（151 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium citrate, lithium chloride, PEG 6000
Resolution 1.99 Å R-free 0.226
6O3Y Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM3 Deposited 2019-02-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 6–156（151 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；sodium citrate, lithium chloride, PEG 6000
Resolution 2.80 Å R-free 0.300
6O3Y Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM3 Deposited 2019-02-27 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 6–156（151 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；sodium citrate, lithium chloride, PEG 6000
Resolution 2.80 Å R-free 0.300
6O3Y Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM3 Deposited 2019-02-27 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 6–156（151 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；sodium citrate, lithium chloride, PEG 6000
Resolution 2.80 Å R-free 0.300

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.