9mu7

Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk

Method: ELECTRON MICROSCOPY D_max: 171.0 Å Quality: GOOD

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

DNA-directed RNA polymerase II subunit RPB1

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain A； UniProt 7–1476	Not recorded	DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

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 9MU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain A 7–1476（1470 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain A 7–1476（1470 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB1_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1470； UniProt 7–1476

DNA-directed RNA polymerase II subunit RPB2

OrganismNot specified

UniProt P08266

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain B； UniProt 13–1176	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9MU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain B 13–1176（1164 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain B 13–1176（1164 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB2_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1164； UniProt 13–1176

DNA-directed RNA polymerase II subunit RPB3

OrganismNot specified

UniProt O97183

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain C； UniProt 2–270	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9MU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain C 2–270（269 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain C 2–270（269 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O97183_DROME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–269； UniProt 2–270

DNA-directed RNA polymerase II subunit Rpb4

OrganismNot specified

UniProt Q9VEA5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain D； UniProt 10–139	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	RPB4_DROME
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–130； UniProt 10–139

DNA-directed RNA polymerases I, II, and III subunit RPABC2

OrganismNot specified

UniProt Q24320

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain F； UniProt 47–130	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9MU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain F 47–130（84 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain F 47–130（84 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPAB2_DROME
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–84； UniProt 47–130

DNA-directed RNA polymerase II subunit RPB7

OrganismNot specified

UniProt Q9VFB5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain G； UniProt 1–173	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q9VFB5_DROME
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–173； UniProt 1–173

DNA-directed RNA polymerases I, II, and III subunit RPABC3

OrganismNot specified

UniProt Q9VNZ3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain H； UniProt 2–148	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9MU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain H 2–148（147 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain H 2–148（147 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9VNZ3_DROME
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain H； PDBConstruct 1–147； UniProt 2–148

DNA-directed RNA polymerase II subunit RPB9

OrganismNot specified

UniProt P36958

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain I； UniProt 14–129	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9MU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain I 14–129（116 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain I 14–129（116 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB9_DROME
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain I； PDBConstruct 1–116； UniProt 14–129

DNA-directed RNA polymerases I, II, and III subunit RPABC5

OrganismNot specified

UniProt Q9VC49

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain J； UniProt 1–67	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9MU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain J 1–67（67 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain J 1–67（67 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPAB5_DROME
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain J； PDBConstruct 1–67； UniProt 1–67

DNA-directed RNA polymerase II subunit RPB11

OrganismNot specified

UniProt Q9VJE4

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain K； UniProt 1–116	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9MU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain K 1–116（116 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain K 1–116（116 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB11_DROME
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain K； PDBConstruct 1–116； UniProt 1–116

DNA-directed RNA polymerase II subunit RPB12

OrganismNot specified

UniProt Q6IGE3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain L； UniProt 12–57	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） RNA × 1 Template DNA × 1 Non-template DNA × 1 DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9MU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain L 12–57（46 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain L 12–57（46 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6IGE3_DROME
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain L； PDBConstruct 1–46； UniProt 12–57

DNA-directed RNA polymerase II subunit RPB5

OrganismNot specified

UniProt Q7JZF5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 DNA 2 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain E； UniProt 1–210	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerase II subunit Rpb4 × 1 （Q9VEA5） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q9VFB5） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） RNA × 1 Template DNA × 1 Non-template DNA × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9MU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain E 1–210（210 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain E 1–210（210 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q7JZF5_DROME
Isoform	—
PDB entities	15
Chains and sequence ranges	Author chain E； PDBConstruct 1–210； UniProt 1–210

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	9mu7
Deposition date deposition_date	2025-01-13
Structure title title	Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk
Keywords keywords	polymerase, Pol II, transcription, mRNA; TRANSCRIPTION
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	52.23 Å
Radius of gyration Rg (electron density) rg_electron	51.57 Å
Forward intensity I(0) i0	3669610000.00
Molecular weight molecular_weight	485340.0 kDa
Excluded volume excluded_volume	597990 Å³
Envelope volume envelope_volume	861350 Å³
Hydration-shell volume shell_volume	130890 Å³
Envelope diameter envelope_diameter	173.6 Å
Shell Rg shell_rg	60.56 Å
Envelope Rg envelope_rg	51.57 Å
Shape Rg shape_rg	51.58 Å
Total Rg total_rg	51.76 Å
Total atoms total_atoms	33887
Residues n_residues	4091
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	171.0 Å
Rg (real space) rg_real	52.03 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	3.6700e+09
I(0) uncertainty (real space) i0_real_error	5.7980e+07
Rg (reciprocal space) rg_reciprocal	52.39 Å
I(0) (reciprocal space) i0_reciprocal	3671000000.0000
Solution quality estimate total_estimate	0.8743
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	68.4 Å
Skewness Skewness skewness	0.197
Kurtosis Kurtosis kurtosis	-0.408
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	701400000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.873

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (16)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase II subunit RPB1
Molecular weight formula_weight	166420.4 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	33887

SKAPLRQVKRVQFGILSPDEIRRMSVTEGGVQFAETMEGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKPVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKEIVMKSRGQPRKRLAYVYDLCKGKTICEGGEDMDLTKENQQPDPNKKPGHGGCGHYQPSIRRTGLDLTAEWKHQNEDSQEKKIVVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYPGAKYIVRDNGERIDLRFHPKSSDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLPTWDAKMPQPCILKPRPLWTGKQIFSLIIPGNVNMIRTHSTHPDEEDEGPYKWISPGDTKVMVEHGELIMGILCKKSLGTSAGSLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTPGNTLRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVGQLIQLRYGEDGLCGELVEFQNMPTVKLSNKSFEKRFKFDWSNERLMKKVFTDDVIKEMTDSSEAIQELEAEWDRLVSDRDSLRQIFPNGESKVVLPCNLQRMIWNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVIVTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRIRIMNNEENKFQDEDEAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIVITETGEFKAIGEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVRKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGVSENIIMGQLPKMGTGCFDLLLDAEKCRFGI

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase II subunit RPB2
Molecular weight formula_weight	132640.1 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ENAEEISHELWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVETPPRFSLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPVETQHQKTFIGKIPIMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDGKYAFKTEIRSCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNFIGARGARPGVTKDKRIKYAKEILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPRQLHNTLWGMLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGRICRPLLIVENGSLLLKKTHVEMLKERDYNNYSWQVLVASGVVEYIDTLEEETVMIAMSPYDLKQDKDYAYCTTYTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPMKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGFFRSVFYRSYKDSENKRVGDQEENFEKPHRGTCQGMRNAHYDKLDDDGIIAPGIRVSGDDVVIGKTITLPENDDELDSNTKRFSKRDASTFLRNSETGIVDQVMLTLNSEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMAFTCEGLAPDIIINPHAIPSRMTIGHLIECLQGKLGSNKGEIGDATPFNDAVNVQKISTFLQEYGYHLRGNEVMYNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRVHICNFCGLIAIANLRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMVT

Entity 3 Entity 3 polymer

Description description	DNA-directed RNA polymerase II subunit RPB3
Molecular weight formula_weight	30676.2 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

PYANQPSVQITELTDDNVKFVLEDTELSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFLAHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSNAKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLYPKPDEWPKSEHTELEDDQYEAPYNWEAKPNKFFFNVESAGALKPENIVVMGVQVLKNKLSNLQTQLSHESQN

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase II subunit Rpb4
Molecular weight formula_weight	15180.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

VDEDAADLQFPKEFENAETLLISEVHMLLDHRKRQNESADEEQEFSEVFMKTYAYTDSFRKFKNKETIMSARSLLMQKKLHKFELAALGNLCPEAPEEAKALIPSLEGRFEDEELRQILDDIGTKRSLQY

Entity 5 Entity 5 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC2
Molecular weight formula_weight	9736.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

GGVPKSKRITTKYMTKYERARVLGTRALQIAMCAPIMVELDGETDPLQIAMKELKQKKIPIIIRRYLPDHSYEDWSIDELIMVD

Entity 6 Entity 6 polymer

Description description	DNA-directed RNA polymerase II subunit RPB7
Molecular weight formula_weight	19127.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MFYHISLEQEILLHPRYFGPQLLETVKQKLYSEVEGTCTGKYGFVIAVTTIDQIGSGVIQPGQGFVVYPVKYKAIVFRPFKGEVLDAVVKQINKVGMFAEIGPLSCFISHHSIPADMQFCPNGNPPCYKSKDEDVVISGEDKIRLKIVGTRVDATGIFAIGTLMDDYLGLVSN

Entity 7 Entity 7 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC3
Molecular weight formula_weight	16946.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

AGVLFEDIFNVKDMDPEGKKFDRVSRLHCESESFKMDLILDINSWLYPMELGDKFRLVLATTLREDGCPDSGEYNPMEHEGTRADSFEYVMYGKIYRIEGDEAHNEASRLSAYVSFGGLLMRLQGDANNLHGFEVDQHMYLLMKRLA

Entity 8 Entity 8 polymer

Description description	DNA-directed RNA polymerase II subunit RPB9
Molecular weight formula_weight	13786.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

GFVGIRFCQECNNMLYPKEDKENKILLYACRNCDYKQEADSNCIYVNKIMHEIDELTHIVPDVISDPTLPRTEDHACPKCSHREAVFFQAQTRRAEEEMRLYYVCTNQNCTHRWTE

Entity 9 Entity 9 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC5
Molecular weight formula_weight	7671.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MIIPIRCFTCGKVIGNKWESYLGLLQAEYTEGDALDALGLKRYCCRRMLLGHVDLIEKLLNYAPLEK

Entity 10 Entity 10 polymer

Description description	DNA-directed RNA polymerase II subunit RPB11
Molecular weight formula_weight	13288.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MNAPPTFESFLLYEGEKKIIKELDTKVTNAAIFTINKEDHTLGNMIRNQLLKDPNVLFAGYKVPHPLEHKFVIRIQTTADYSPQEAFMNAITDLLAELSLFEERFKDAIKEKKEGG

Entity 11 Entity 11 polymer

Description description	DNA-directed RNA polymerase II subunit RPB12
Molecular weight formula_weight	5647.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

TAMTYICGECHHENEMRPRDPIRCRECGYRIMYKKRTKRLVVFDAR

Entity 12 Entity 12 polymer

Description description	RNA
Molecular weight formula_weight	3247.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R

AAAAAAAAAA

Entity 13 Entity 13 polymer

Description description	Template DNA
Molecular weight formula_weight	15134.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTT

Entity 14 Entity 14 polymer

Description description	Non-template DNA
Molecular weight formula_weight	12170.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Entity 15 Entity 15 polymer

Description description	DNA-directed RNA polymerase II subunit RPB5
Molecular weight formula_weight	24518.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MDDEAETYKLWRIRKTIMQLSHDRGYLVTQDELDQTLEQFKEMFGDKPSEKRPARSDLIVLVAHNDDPTDQMFVFFPEEPKIGIKTIKTYCTRMQEENIHRAIVVVQGGMTPSAKQSLVDMAPKYILEQFLESELLINITEHELVPEHVVMTVEEKQELLSRYKLKENMLMRIQAGDPVARYFGLKRGQVVKIIRSSETAGRYISYRLVC

Entity 16 Entity 16 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.440 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.44 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	70116

fit	/app/data/saxs_computation/mu/9mu7/9mu7.fit
pddf	/app/data/pr_computation/mu/9mu7/9mu7.pr.out
profile	/app/data/saxs_computation/mu/9mu7/9mu7.dat

Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk

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

DNA-directed RNA polymerase II subunit RPB1

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB2

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB3

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit Rpb4

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases I, II, and III subunit RPABC2

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB7

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases I, II, and III subunit RPABC3

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB9

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases I, II, and III subunit RPABC5

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB11

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB12

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB5

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (16)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

Entity 10 Entity 10 polymer

Polymer Polymer

Entity 11 Entity 11 polymer

Polymer Polymer

Entity 12 Entity 12 polymer

Polymer Polymer

Entity 13 Entity 13 polymer

Polymer Polymer

Entity 14 Entity 14 polymer

Polymer Polymer

Entity 15 Entity 15 polymer

Polymer Polymer

Entity 16 Entity 16 non-polymer