3nfi

Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49

Method: X-RAY DIFFRACTION D_max: 115.4 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase I subunit RPA49

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 171–403	Fragment：UNP residues 171-403 Mutation：L178M, L261M Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；24% PEG 3350, 50 mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.224
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 171–403	Fragment：UNP residues 171-403 Mutation：L178M, L261M Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；24% PEG 3350, 50 mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.224
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 171–403	Fragment：UNP residues 171-403 Mutation：L178M, L261M Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；24% PEG 3350, 50 mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.224
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 171–403	Fragment：UNP residues 171-403 Mutation：L178M, L261M Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；24% PEG 3350, 50 mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.224
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 171–403	Fragment：UNP residues 171-403 Mutation：L178M, L261M Non-standard monomer：Yes (specific site not provided by mmCIF)	PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；24% PEG 3350, 50 mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.224

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3NFI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3NFH Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49 (P4) Deposited 2010-06-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 154–399（246 aa） Fragment：UNP residues 154-399	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；26% PEG 4000, 200 mM lithium sulfate monohydrate, 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.17 Å R-free 0.225
3NFH Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49 (P4) Deposited 2010-06-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 154–399（246 aa） Fragment：UNP residues 154-399	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；26% PEG 4000, 200 mM lithium sulfate monohydrate, 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.17 Å R-free 0.225
4C2M Structure of RNA polymerase I at 2.8 A resolution Deposited 2013-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 7 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；10% PEG4000, 300MM AMMONIUM ACETATE, 50MM HEPES PH 7.5, 5MM TCEP	Resolution 2.80 Å R-free 0.210
4C2M Structure of RNA polymerase I at 2.8 A resolution Deposited 2013-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain 2 1–415（415 aa）	Not recorded	ZN ZINC ION × 7 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；10% PEG4000, 300MM AMMONIUM ACETATE, 50MM HEPES PH 7.5, 5MM TCEP	Resolution 2.80 Å R-free 0.210
4C3H Structure of 14-subunit RNA polymerase I at 3.27 A resolution, crystal form C2-93 Deposited 2013-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions 24% ETHYLENGLYCOL, 0.1M MES PH 6.8	Resolution 3.27 Å R-free 0.226
4C3I Structure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100 Deposited 2013-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain M 1–415（415 aa）	Not recorded	SO4 SULFATE ION × 3 ZN ZINC ION × 7 MG MAGNESIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 10% MPD, 0.1M TRIS HCL PH 7.4	Resolution 3.00 Å R-free 0.231
4C3J Structure of 14-subunit RNA polymerase I at 3.35 A resolution, crystal form C2-90 Deposited 2013-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions 10% MPD, 0.1M TRIS HCL, PH 7.5	Resolution 3.35 Å R-free 0.220
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain AM 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP	Resolution 5.50 Å R-free 0.235
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain BM 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP	Resolution 5.50 Å R-free 0.235
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain CM 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP	Resolution 5.50 Å R-free 0.235
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain DM 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP	Resolution 5.50 Å R-free 0.235
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain EM 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP	Resolution 5.50 Å R-free 0.235
4YM7 RNA polymerase I structure with an alternative dimer hinge Deposited 2015-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain FM 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 6000, 3% MPD, 100 mM Hepes, 300 mM di-ammonium-tartrate, 3 mM TCEP	Resolution 5.50 Å R-free 0.235
5G5L RNA polymerase I-Rrn3 complex at 4.8 A resolution Deposited 2016-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer 150MM NACL, 5MM HEPES, 1MM MGCL2, 0.01 MM ZNCL2, 5 MM DTT；pH 7.8；150MM NACL, 5MM HEPES, 1MM MGCL2, 0.01 MM ZNCL2, 5 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITROBOT MARK IV, METHOD- 4.5 MICROLITERS OF SAMPLE WAS APPLIED TO GLOW- DISCHARGED QUANTIFOIL R 2- 1 HOLEY CARBON GRIDS, WHICH WERE THEN BLOTTED FOR 8.5S AND PLUNGE- FROZEN IN LIQUID ETHANE.	Resolution 4.80 Å
5LMX Monomeric RNA polymerase I at 4.9 A resolution Deposited 2016-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
5M3F Yeast RNA polymerase I elongation complex at 3.8A Deposited 2016-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 13, blotting time 8.5s	Resolution 3.80 Å
5M3M Free monomeric RNA polymerase I at 4.0A resolution Deposited 2016-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 7 SO4 SULFATE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；blot force 13, blotting time 8.5s	Resolution 4.00 Å
5M5W RNA Polymerase I open complex Deposited 2016-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；2.5 ul of sample 15 seconds wait time Blot for 8 seconds	Resolution 3.80 Å
5M5X RNA Polymerase I elongation complex 1 Deposited 2016-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；2.5 ul of sample 15 seconds wait time Blot time for 8 seconds	Resolution 4.00 Å
5M5Y RNA Polymerase I elongation complex 2 Deposited 2016-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；2.5 ul of sample 15 seconds wait time Blot for 8 seconds	Resolution 4.00 Å
5M64 RNA Polymerase I elongation complex with A49 tandem winged helix domain Deposited 2016-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；2.5 ul of sample 15 seconds wait time Blot for 8 seconds	Resolution 4.60 Å
5N5Y Cryo-EM structure of RNA polymerase I in complex with Rrn3 and Core Factor (Orientation III) Deposited 2017-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 8 SO4 SULFATE ION × 5 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.70 Å
5N5Z Cryo-EM structure of RNA polymerase I in complex with Rrn3 and Core Factor (Orientation II) Deposited 2017-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.70 Å
5N60 Cryo-EM structure of RNA polymerase I in complex with Rrn3 and Core Factor (Orientation I) Deposited 2017-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.70 Å
5N61 RNA polymerase I initially transcribing complex Deposited 2017-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OA1 RNA polymerase I pre-initiation complex Deposited 2017-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
5W5Y RNA polymerase I Initial Transcribing Complex Deposited 2017-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
5W64 RNA Polymerase I Initial Transcribing Complex State 1 Deposited 2017-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
5W65 RNA polymerase I Initial Transcribing Complex State 2 Deposited 2017-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
5W66 RNA polymerase I Initial Transcribing Complex State 3 Deposited 2017-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6H67 Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) Deposited 2018-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6H68 Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) with fully-ordered A49 Deposited 2018-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
6HKO Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP Deposited 2018-09-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain M 1–415（415 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 6 G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；30 seconds incubation 3 seconds blotting blotting force 3	Resolution 3.42 Å
6RQH RNA Polymerase I Closed Conformation 1 (CC1) Deposited 2019-05-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain M 1–415（415 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6RQL RNA Polymerase I Closed Conformation 2 (CC2) Deposited 2019-05-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain M 1–415（415 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
6RQT RNA Polymerase I-tWH-Rrn3-DNA Deposited 2019-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
6RRD RNA Polymerase I Pre-initiation complex DNA opening intermediate 1 Deposited 2019-05-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6RUI RNA Polymerase I Pre-initiation complex DNA opening intermediate 2 Deposited 2019-05-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6RUO RNA Polymerase I Open Complex conformation 1 Deposited 2019-05-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6RWE RNA Polymerase I Open Complex conformation 2 Deposited 2019-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6TPS early intermediate RNA Polymerase I Pre-initiation complex - eiPIC Deposited 2019-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
9G1V Yeast RNA polymerase I elongation complex stalled by an apurinic site Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric	Chain M 1–415（415 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 2.70 Å
9G23 Yeast RNA polymerase I elongation complex stalled by an apurinic site bound to nucleotide analog AMPCPP at A-site Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 3.40 Å
9G24 Yeast RNA polymerase I elongation complex stalled by an apurinic site bound to nucleotide analog AMPCPP at E-site Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 6 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 3.50 Å
9G26 Yeast RNA polymerase I elongation complex stalled by an apurinic site, closed state Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric	Chain M 1–415（415 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 3.40 Å
9G29 Yeast RNA polymerase I elongation complex stalled by an apurinic site with the C-terminal of A12 in the funnel Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 17-meric	Chain M 1–415（415 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 3.30 Å
9G2C Yeast RNA polymerase I elongation complex stalled by an apurinic site, open state Deposited 2024-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric	Chain M 1–415（415 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 3.50 Å

40 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPA49_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–237； UniProt 171–403 Author chain B； PDBConstruct 5–237； UniProt 171–403 Author chain C； PDBConstruct 5–237； UniProt 171–403 Author chain D； PDBConstruct 5–237； UniProt 171–403 Author chain E； PDBConstruct 5–237； UniProt 171–403

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3nfi
Deposition date deposition_date	2010-06-10
Structure title title	Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49
Keywords keywords	winged helix, transcription, RNA polymerase, DNA binding, DNA BINDING PROTEIN; DNA BINDING PROTEIN, TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	37.05 Å
Radius of gyration Rg (electron density) rg_electron	36.22 Å
Forward intensity I(0) i0	212455000.00
Molecular weight molecular_weight	124920.0 kDa
Excluded volume excluded_volume	159570 Å³
Envelope volume envelope_volume	218960 Å³
Hydration-shell volume shell_volume	49577 Å³
Envelope diameter envelope_diameter	120.1 Å
Shell Rg shell_rg	43.48 Å
Envelope Rg envelope_rg	35.34 Å
Shape Rg shape_rg	36.22 Å
Total Rg total_rg	36.74 Å
Total atoms total_atoms	8729
Residues n_residues	1071
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	115.4 Å
Rg (real space) rg_real	36.87 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	2.1250e+08
I(0) uncertainty (real space) i0_real_error	3.2930e+06
Rg (reciprocal space) rg_reciprocal	36.99 Å
I(0) (reciprocal space) i0_reciprocal	212500000.0000
Solution quality estimate total_estimate	0.9076
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	51.0 Å
Skewness Skewness skewness	0.093
Kurtosis Kurtosis kurtosis	-0.640
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42500000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase I subunit RPA49
Molecular weight formula_weight	27141.7 kDa
EC 编号 ec_number	2.7.7.6
Mutation mutation	L178M, L261M
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	9695

GSHMDLPTRAQMDEITSNDRPTPLANIDATDVEQIYPIESIIPKKELQFIRVSSILKEADKEKKLELFPYQNNSKYVAKKLDSLTQPSQMTKLQMLYYLSLLLGVYENRRVNNKTKLLERLNSPPEILVDGILSRFTVIKPGQFGRSKDRSYFIDPQNEDKILCYILAIIMHLDNFIVEITPLAHELNLKPSKVVSLFRVLGAIVKGATVAQAEAFGIPKSTAASYKIATMKVPFKL

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
Molecular weight formula_weight	354.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	786

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3nfia1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.86 — RNA polymerase I subunit A49, winged helix domain

Domain ID domain_id	d3nfia2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.86 — RNA polymerase I subunit A49, winged helix domain

Domain ID domain_id	d3nfib1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.86 — RNA polymerase I subunit A49, winged helix domain

Domain ID domain_id	d3nfib2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.86 — RNA polymerase I subunit A49, winged helix domain

Domain ID domain_id	d3nfic1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.86 — RNA polymerase I subunit A49, winged helix domain

Domain ID domain_id	d3nfic2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.86 — RNA polymerase I subunit A49, winged helix domain

Domain ID domain_id	d3nfid1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.86 — RNA polymerase I subunit A49, winged helix domain

Domain ID domain_id	d3nfid2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.86 — RNA polymerase I subunit A49, winged helix domain

Domain ID domain_id	d3nfie1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.86 — RNA polymerase I subunit A49, winged helix domain

Domain ID domain_id	d3nfie2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.86 — RNA polymerase I subunit A49, winged helix domain

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8. Citations (1)

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Unit-cell length a length_a	85.110 Å
Unit-cell length b length_b	78.100 Å
Unit-cell length c length_c	100.670 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	10

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	27.820 Å
R factor r_factor	0.1903
R_work r_work	0.1886
R_free r_free	0.2235

fit	/app/data/saxs_computation/nf/3nfi/3nfi.fit
pddf	/app/data/pr_computation/nf/3nfi/3nfi.pr.out
profile	/app/data/saxs_computation/nf/3nfi/3nfi.dat