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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：Q00416 New Search
10PDB entries
15Biological assembly
17chain/assembly records
Main Difference Dimensions in This Set
Different construct 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
5MZN Helicase Sen1 Deposited 2017-02-01 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1095–1470（376 aa）
Chain A 1539–1904（366 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 40 GOL GLYCEROL × 12 PEG DI(HYDROXYETHYL)ETHER × 11 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；18% PEG 2K 0.1M MOPS 7.2
Resolution 1.79 Å R-free 0.184
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 B 2052–2063（12 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
6I59 Long wavelength native-SAD phasing of Sen1 helicase Deposited 2018-11-13 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1095–1470（376 aa）
Chain A 1539–1904（366 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 40 GOL GLYCEROL × 12 PEG DI(HYDROXYETHYL)ETHER × 11 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；18% PEG 2K 0.1M MOPS 7.2
Resolution 2.95 Å R-free 0.213
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 C 1882–1895（14 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 D 1882–1895（14 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 D 2053–2064（12 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 E 2053–2064（12 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 F 2053–2064（12 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 D 2181–2193（13 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 E 2181–2193（13 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 F 2181–2193（13 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
8RAM Structure of Sen1 bound RNA Polymerase II pre-termination complex Deposited 2023-12-01 Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric（19） Consistent with all polymers
Chain O 1–2231（2231 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8RAN Structure of Sen1-RNA complex Deposited 2023-12-01 Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric（2） Consistent with all polymers
Chain O 1–2231（2231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
8RAO Structure of Sen1-ADP.BeF3-RNA complex Deposited 2023-12-01 Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric（2） Consistent with all polymers
Chain O 1–2231（2231 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8RAP Structure of Sen1-ADP.BeF3 bound RNA Polymerase II pre-termination complex Deposited 2023-12-01 Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 19-meric（19） Consistent with all polymers
Chain O 1–2231（2231 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å

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.