7nky

RNA Polymerase II-Spt4/5-nucleosome-FACT structure

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase II subunit RPB1

OrganismNot specified

UniProt P04050

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPB1_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain A; PDBConstruct 1–1733; UniProt 1–1733

DNA-directed RNA polymerase II subunit RPB2

OrganismNot specified

UniProt P08518

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPB2_YEAST
Isoform —
PDB entities 5
Chains and sequence ranges Author chain B; PDBConstruct 1–1224; UniProt 1–1224

DNA-directed RNA polymerase II subunit RPB3

OrganismNot specified

UniProt P16370

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPB3_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain C; PDBConstruct 1–318; UniProt 1–318

DNA-directed RNA polymerases I, II, and III subunit RPABC1

OrganismNot specified

UniProt P20434

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPAB1_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain E; PDBConstruct 1–215; UniProt 1–215

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

OrganismNot specified

UniProt P20435

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPAB2_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain F; PDBConstruct 1–155; UniProt 1–155

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

OrganismNot specified

UniProt P20436

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPAB3_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain H; PDBConstruct 1–146; UniProt 1–146

DNA-directed RNA polymerase II subunit RPB9

OrganismNot specified

UniProt P27999

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPB9_YEAST
Isoform —
PDB entities 10
Chains and sequence ranges Author chain I; PDBConstruct 1–122; UniProt 1–122

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

OrganismNot specified

UniProt P22139

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPAB5_YEAST
Isoform —
PDB entities 11
Chains and sequence ranges Author chain J; PDBConstruct 1–70; UniProt 1–70

DNA-directed RNA polymerase II subunit RPB11

OrganismNot specified

UniProt P38902

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPB11_YEAST
Isoform —
PDB entities 12
Chains and sequence ranges Author chain K; PDBConstruct 1–120; UniProt 1–120

DNA-directed RNA polymerases I, II, and III subunit RPABC4

OrganismNot specified

UniProt P40422

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPAB4_YEAST
Isoform —
PDB entities 13
Chains and sequence ranges Author chain L; PDBConstruct 1–70; UniProt 1–70

Chromatin elongation factor SPT4

Saccharomyces cerevisiae

UniProt A0A6A5PX04

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A6A5PX04_YEASX
Isoform —
PDB entities 14
Chains and sequence ranges Author chain Y; PDBConstruct 1–102; UniProt 1–102

Transcription elongation factor SPT5

Saccharomyces cerevisiae

UniProt A0A6L0ZFJ2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A6L0ZFJ2_YEASX
Isoform —
PDB entities 15
Chains and sequence ranges Author chain Z; PDBConstruct 1–1063; UniProt 1–1063

DNA-directed RNA polymerase II subunit RPB4

OrganismNot specified

UniProt P20433

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPB4_YEAST
Isoform —
PDB entities 16
Chains and sequence ranges Author chain D; PDBConstruct 1–221; UniProt 1–221

DNA-directed RNA polymerase II subunit RPB7

OrganismNot specified

UniProt P34087

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RPB7_YEAST
Isoform —
PDB entities 17
Chains and sequence ranges Author chain G; PDBConstruct 1–171; UniProt 1–171

FACT complex subunit POB3

Saccharomyces cerevisiae

UniProt A0A6A5PUM6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A6A5PUM6_YEASX
Isoform —
PDB entities 18
Chains and sequence ranges Author chain O; PDBConstruct 1–552; UniProt 1–552

FACT complex subunit SPT16

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P32558

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name SPT16_YEAST
Isoform —
PDB entities 19
Chains and sequence ranges Author chain Q; PDBConstruct 1–1035; UniProt 1–1035

Histone H3.2

Xenopus laevis

UniProt P84233

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name H32_XENLA
Isoform —
PDB entities 20
Chains and sequence ranges Author chain a; PDBConstruct 1–136; UniProt 1–136 Author chain e; PDBConstruct 1–136; UniProt 1–136

Histone H4

Xenopus laevis

UniProt P62799

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H2A type 1 × 2 (P06897) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name H4_XENLA
Isoform —
PDB entities 21
Chains and sequence ranges Author chain b; PDBConstruct 1–103; UniProt 1–103 Author chain f; PDBConstruct 1–103; UniProt 1–103

Histone H2A type 1

Xenopus laevis

UniProt P06897

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2B 1.1 × 2 (P02281) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name H2A1_XENLA
Isoform —
PDB entities 22
Chains and sequence ranges Author chain c; PDBConstruct 1–130; UniProt 1–130 Author chain g; PDBConstruct 1–130; UniProt 1–130

Histone H2B 1.1

Xenopus laevis

UniProt P02281

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 24 DNA 2 RNA 1 ;RNA (5'-R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') ; × 1 DNA (138-MER) × 1 DNA (148-MER) × 1 DNA-directed RNA polymerase II subunit RPB1 × 1 (P04050) DNA-directed RNA polymerase II subunit RPB2 × 1 (P08518) DNA-directed RNA polymerase II subunit RPB3 × 1 (P16370) DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 (P20434) DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 (P20435) DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 (P20436) DNA-directed RNA polymerase II subunit RPB9 × 1 (P27999) DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 (P22139) DNA-directed RNA polymerase II subunit RPB11 × 1 (P38902) DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 (P40422) Chromatin elongation factor SPT4 × 1 (A0A6A5PX04) Transcription elongation factor SPT5 × 1 (A0A6L0ZFJ2) DNA-directed RNA polymerase II subunit RPB4 × 1 (P20433) DNA-directed RNA polymerase II subunit RPB7 × 1 (P34087) FACT complex subunit POB3 × 1 (A0A6A5PUM6) FACT complex subunit SPT16 × 1 (P32558) Histone H3.2 × 2 (P84233) Histone H4 × 2 (P62799) Histone H2A type 1 × 2 (P06897) ZINC ION × 9 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name H2B11_XENLA
Isoform —
PDB entities 23
Chains and sequence ranges Author chain d; PDBConstruct 2–123; UniProt 5–126 Author chain h; PDBConstruct 2–123; UniProt 5–126

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id7nky
Deposition date deposition_date2021-02-19
Structure title titleRNA Polymerase II-Spt4/5-nucleosome-FACT structure
Keywords keywordsChromatin, nucleosome, elongation, histone chaperone, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7nky__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7nky__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

7nky__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)76.47 Å
Rg (electron density)77.05 Å
Total Rg76.76 Å
Atom count51842
Residues6036
Excluded volume904790 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7nky__assembly_1__model_1 27-meric (27) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (25)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id7nkyA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily100 — RNA polymerase Rpb1, domain 3
Domain ID domain_id7nkyA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily140 —
Domain ID domain_id7nkyO01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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7. Citations (1)