2rf4

Crystal structure of the RNA Polymerase I subcomplex A14/43

Method: X-RAY DIFFRACTION D_max: 94.9 Å Quality: GOOD

▼

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

DNA-directed RNA polymerase I subunit RPA4

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–172 Chain A； UniProt 210–251	Non-standard monomer：Yes (specific site not provided by mmCIF)	DNA-directed RNA polymerase I subunit RPA4 × 1 （P50106）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；18 % (w/v) PEG 3350, 350 mM potassium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.10 Å R-free 0.285
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–172 Chain C； UniProt 210–251	Non-standard monomer：Yes (specific site not provided by mmCIF)	DNA-directed RNA polymerase I subunit RPA4 × 1 （P50106）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；18 % (w/v) PEG 3350, 350 mM potassium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.10 Å R-free 0.285
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 2–172 Chain E； UniProt 210–251	Non-standard monomer：Yes (specific site not provided by mmCIF)	DNA-directed RNA polymerase I subunit RPA4 × 1 （P50106）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；18 % (w/v) PEG 3350, 350 mM potassium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.10 Å R-free 0.285

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 2RF4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 G 1–326（326 aa） Chain O 1–326（326 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 4 1–326（326 aa） Chain V 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 AG 1–326（326 aa） Chain AO 1–326（326 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 BG 1–326（326 aa） Chain BO 1–326（326 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 CG 1–326（326 aa） Chain CO 1–326（326 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 DG 1–326（326 aa） Chain DO 1–326（326 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 EG 1–326（326 aa） Chain EO 1–326（326 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 FG 1–326（326 aa） Chain FO 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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
6HLQ Yeast RNA polymerase I* elongation complex bound to nucleotide analog GMPCPP Deposited 2018-09-11	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 × 12 PDB declaration: pentadecameric	Chain G 1–326（326 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 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 3.18 Å
6HLR Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (core focused) Deposited 2018-09-11	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 × 12 PDB declaration: pentadecameric	Chain G 1–326（326 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 3.18 Å
6HLS Yeast apo RNA polymerase I* Deposited 2018-09-11	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 × 12 PDB declaration: dodecameric	Chain G 1–326（326 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；30 seconds incubation 3 seconds blotting blotting force 3	Resolution 3.21 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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
9G1X Yeast RNA polymerase I elongation complex stalled by an apurinic site, 11-subunit 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 × 11 PDB declaration: 14-meric	Chain G 1–326（326 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 3.50 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 G 1–326（326 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 G 1–326（326 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 G 1–326（326 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
9G27 Yeast RNA polymerase I elongation complex stalled by an apurinic site, pre-translocation 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 × 12 PDB declaration: 15-meric	Chain G 1–326（326 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 2.80 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 G 1–326（326 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
9G2B Yeast RNA polymerase I elongation complex stalled by an apurinic site, 12-subunit 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 × 12 PDB declaration: 15-meric	Chain G 1–326（326 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 3.20 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 G 1–326（326 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

45 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPA43_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–172； UniProt 2–172 Author chain A； PDBConstruct 173–214； UniProt 210–251 Author chain C； PDBConstruct 2–172； UniProt 2–172 Author chain C； PDBConstruct 173–214； UniProt 210–251 Author chain E； PDBConstruct 2–172； UniProt 2–172 Author chain E； PDBConstruct 173–214； UniProt 210–251

DNA-directed RNA polymerase I subunit RPA4

Saccharomyces cerevisiae

UniProt P50106

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–52 Chain B； UniProt 78–112	Not recorded	DNA-directed RNA polymerase I subunit RPA4 × 1 （P46669）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；18 % (w/v) PEG 3350, 350 mM potassium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.10 Å R-free 0.285
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–52 Chain D； UniProt 78–112	Not recorded	DNA-directed RNA polymerase I subunit RPA4 × 1 （P46669）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；18 % (w/v) PEG 3350, 350 mM potassium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.10 Å R-free 0.285
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 1–52 Chain F； UniProt 78–112	Not recorded	DNA-directed RNA polymerase I subunit RPA4 × 1 （P46669）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；18 % (w/v) PEG 3350, 350 mM potassium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.10 Å R-free 0.285

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2RF4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 D 1–137（137 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 S 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 AD 1–137（137 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 BD 1–137（137 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 CD 1–137（137 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 DD 1–137（137 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 ED 1–137（137 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 FD 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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
6HLQ Yeast RNA polymerase I* elongation complex bound to nucleotide analog GMPCPP Deposited 2018-09-11	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 × 12 PDB declaration: pentadecameric	Chain D 1–137（137 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 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 3.18 Å
6HLR Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (core focused) Deposited 2018-09-11	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 × 12 PDB declaration: pentadecameric	Chain D 1–137（137 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 3.18 Å
6HLS Yeast apo RNA polymerase I* Deposited 2018-09-11	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 × 12 PDB declaration: dodecameric	Chain D 1–137（137 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；30 seconds incubation 3 seconds blotting blotting force 3	Resolution 3.21 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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
9G1X Yeast RNA polymerase I elongation complex stalled by an apurinic site, 11-subunit 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 × 11 PDB declaration: 14-meric	Chain D 1–137（137 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 3.50 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 D 1–137（137 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 D 1–137（137 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 D 1–137（137 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
9G27 Yeast RNA polymerase I elongation complex stalled by an apurinic site, pre-translocation 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 × 12 PDB declaration: 15-meric	Chain D 1–137（137 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 2.80 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 D 1–137（137 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
9G2B Yeast RNA polymerase I elongation complex stalled by an apurinic site, 12-subunit 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 × 12 PDB declaration: 15-meric	Chain D 1–137（137 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen METHANE	Resolution 3.20 Å

44 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPA14_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–52； UniProt 1–52 Author chain B； PDBConstruct 53–87； UniProt 78–112 Author chain D； PDBConstruct 1–52； UniProt 1–52 Author chain D； PDBConstruct 53–87； UniProt 78–112 Author chain F； PDBConstruct 1–52； UniProt 1–52 Author chain F； PDBConstruct 53–87； UniProt 78–112

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2rf4
Deposition date deposition_date	2007-09-28
Structure title title	Crystal structure of the RNA Polymerase I subcomplex A14/43
Keywords keywords	;Transferase DNA/RNA, DNA-binding, Phosphorylation, RNA Polymerase I, Pol I, PolI, RPolI, Nuclear Protein, Nucleolar Protein, Transcription, Transferase, DDRP, Rpb4/7, Ribosome biogenesis, DNA-directed RNA polymerase, Nucleus ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	29.86 Å
Radius of gyration Rg (electron density) rg_electron	28.96 Å
Forward intensity I(0) i0	98001300.00
Molecular weight molecular_weight	78719.0 kDa
Excluded volume excluded_volume	98900 Å³
Envelope volume envelope_volume	131570 Å³
Hydration-shell volume shell_volume	37724 Å³
Envelope diameter envelope_diameter	102.7 Å
Shell Rg shell_rg	36.28 Å
Envelope Rg envelope_rg	28.74 Å
Shape Rg shape_rg	28.97 Å
Total Rg total_rg	29.70 Å
Total atoms total_atoms	5530
Residues n_residues	693
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

▼

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

Maximum dimension Dmax dmax	94.9 Å
Rg (real space) rg_real	29.76 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	9.8000e+07
I(0) uncertainty (real space) i0_real_error	1.5580e+06
Rg (reciprocal space) rg_reciprocal	29.80 Å
I(0) (reciprocal space) i0_reciprocal	98000000.0000
Solution quality estimate total_estimate	0.8968
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.4 Å
Skewness Skewness skewness	0.229
Kurtosis Kurtosis kurtosis	-0.357
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24370000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.942

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase I subunit RPA4
Molecular weight formula_weight	24223.1 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	5530

MSQVKRANENRETARFIKKHKKQVTNPIDEKNGTSNCIVRVPIALYVSLAPMYLENPLQGVMKQHLNPLVMKYNNKVGGVVLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGFTWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGRVVSVDGTLIS

来源 Source

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

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase I subunit RPA4
Molecular weight formula_weight	9675.9 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

MMKGSRRTGNNTATTLNTPVVIHATQLPQHVSTDEVLQFLESFIDEKENIIDIDTNLSSSISQLKRIQRDFKGLPPAQDFSAAPIQV

来源 Source

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

▼

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2rf4a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
Family Family family	d.230.1.2 — RNA polymerase I subunit A43, N-terminal domain

Domain ID domain_id	d2rf4a2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d2rf4b_
Class class	g — Small proteins
Fold Fold fold	g.98 — RNA polymerase I subunit A14-like
Superfamily Superfamily superfamily	g.98.1 — RNA polymerase I subunit A14-like
Family Family family	g.98.1.1 — RNA polymerase I subunit A14

Domain ID domain_id	d2rf4c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
Family Family family	d.230.1.2 — RNA polymerase I subunit A43, N-terminal domain

Domain ID domain_id	d2rf4c2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d2rf4d_
Class class	g — Small proteins
Fold Fold fold	g.98 — RNA polymerase I subunit A14-like
Superfamily Superfamily superfamily	g.98.1 — RNA polymerase I subunit A14-like
Family Family family	g.98.1.1 — RNA polymerase I subunit A14

Domain ID domain_id	d2rf4e1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
Family Family family	d.230.1.2 — RNA polymerase I subunit A43, N-terminal domain

Domain ID domain_id	d2rf4e2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d2rf4f_
Class class	g — Small proteins
Fold Fold fold	g.98 — RNA polymerase I subunit A14-like
Superfamily Superfamily superfamily	g.98.1 — RNA polymerase I subunit A14-like
Family Family family	g.98.1.1 — RNA polymerase I subunit A14

CATH v4.4 (9 domains)

Domain ID domain_id	2rf4A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

Domain ID domain_id	2rf4A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2rf4B01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3390 —

Domain ID domain_id	2rf4C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

Domain ID domain_id	2rf4C02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2rf4D01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3390 —

Domain ID domain_id	2rf4E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

Domain ID domain_id	2rf4E02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2rf4F01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3390 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	229.857 Å
Unit-cell length b length_b	63.942 Å
Unit-cell length c length_c	65.395 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2524
R_free r_free	0.2854

fit	/app/data/saxs_computation/rf/2rf4/2rf4.fit
pddf	/app/data/pr_computation/rf/2rf4/2rf4.pr.out
profile	/app/data/saxs_computation/rf/2rf4/2rf4.dat

Crystal structure of the RNA Polymerase I subcomplex A14/43

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

DNA-directed RNA polymerase I subunit RPA4

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase I subunit RPA4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)