1r9t

RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE

Method: X-RAY DIFFRACTION

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

DNA-directed RNA polymerase II largest subunit

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 10 DNA 2 RNA 1	RNA strand × 1 DNA template strand × 1 DNA nontemplate strand × 1 DNA-directed RNA polymerase II 140 kDa polypeptide × 1 （P08518） DNA-directed RNA polymerase II 45 kDa polypeptide × 1 （P16370） DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide × 1 （P20434） DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide × 1 （P20435） DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide × 1 （P20436） DNA-directed RNA polymerase II 14.2 kDa polypeptide × 1 （P27999） DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide × 1 （P22139） DNA-directed RNA polymerase II 13.6 kDa polypeptide × 1 （P38902） DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide × 1 （P40422） ZINC ION × 8 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 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 140 kDa polypeptide

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 10 DNA 2 RNA 1	RNA strand × 1 DNA template strand × 1 DNA nontemplate strand × 1 DNA-directed RNA polymerase II largest subunit × 1 （P04050） DNA-directed RNA polymerase II 45 kDa polypeptide × 1 （P16370） DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide × 1 （P20434） DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide × 1 （P20435） DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide × 1 （P20436） DNA-directed RNA polymerase II 14.2 kDa polypeptide × 1 （P27999） DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide × 1 （P22139） DNA-directed RNA polymerase II 13.6 kDa polypeptide × 1 （P38902） DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide × 1 （P40422） ZINC ION × 8 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 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 45 kDa polypeptide

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 10 DNA 2 RNA 1	RNA strand × 1 DNA template strand × 1 DNA nontemplate strand × 1 DNA-directed RNA polymerase II largest subunit × 1 （P04050） DNA-directed RNA polymerase II 140 kDa polypeptide × 1 （P08518） DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide × 1 （P20434） DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide × 1 （P20435） DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide × 1 （P20436） DNA-directed RNA polymerase II 14.2 kDa polypeptide × 1 （P27999） DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide × 1 （P22139） DNA-directed RNA polymerase II 13.6 kDa polypeptide × 1 （P38902） DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide × 1 （P40422） ZINC ION × 8 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 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 27 kDa polypeptide

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 10 DNA 2 RNA 1	RNA strand × 1 DNA template strand × 1 DNA nontemplate strand × 1 DNA-directed RNA polymerase II largest subunit × 1 （P04050） DNA-directed RNA polymerase II 140 kDa polypeptide × 1 （P08518） DNA-directed RNA polymerase II 45 kDa polypeptide × 1 （P16370） DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide × 1 （P20435） DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide × 1 （P20436） DNA-directed RNA polymerase II 14.2 kDa polypeptide × 1 （P27999） DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide × 1 （P22139） DNA-directed RNA polymerase II 13.6 kDa polypeptide × 1 （P38902） DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide × 1 （P40422） ZINC ION × 8 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB5_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 23 kDa polypeptide

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 10 DNA 2 RNA 1	RNA strand × 1 DNA template strand × 1 DNA nontemplate strand × 1 DNA-directed RNA polymerase II largest subunit × 1 （P04050） DNA-directed RNA polymerase II 140 kDa polypeptide × 1 （P08518） DNA-directed RNA polymerase II 45 kDa polypeptide × 1 （P16370） DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide × 1 （P20434） DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide × 1 （P20436） DNA-directed RNA polymerase II 14.2 kDa polypeptide × 1 （P27999） DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide × 1 （P22139） DNA-directed RNA polymerase II 13.6 kDa polypeptide × 1 （P38902） DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide × 1 （P40422） ZINC ION × 8 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB6_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 14.5 kDa polypeptide

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 10 DNA 2 RNA 1	RNA strand × 1 DNA template strand × 1 DNA nontemplate strand × 1 DNA-directed RNA polymerase II largest subunit × 1 （P04050） DNA-directed RNA polymerase II 140 kDa polypeptide × 1 （P08518） DNA-directed RNA polymerase II 45 kDa polypeptide × 1 （P16370） DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide × 1 （P20434） DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide × 1 （P20435） DNA-directed RNA polymerase II 14.2 kDa polypeptide × 1 （P27999） DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide × 1 （P22139） DNA-directed RNA polymerase II 13.6 kDa polypeptide × 1 （P38902） DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide × 1 （P40422） ZINC ION × 8 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB8_YEAST
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain H； PDBConstruct 1–146； UniProt 1–146

DNA-directed RNA polymerase II 14.2 kDa polypeptide

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 10 DNA 2 RNA 1	RNA strand × 1 DNA template strand × 1 DNA nontemplate strand × 1 DNA-directed RNA polymerase II largest subunit × 1 （P04050） DNA-directed RNA polymerase II 140 kDa polypeptide × 1 （P08518） DNA-directed RNA polymerase II 45 kDa polypeptide × 1 （P16370） DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide × 1 （P20434） DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide × 1 （P20435） DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide × 1 （P20436） DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide × 1 （P22139） DNA-directed RNA polymerase II 13.6 kDa polypeptide × 1 （P38902） DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide × 1 （P40422） ZINC ION × 8 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 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 8.3 kDa polypeptide

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 10 DNA 2 RNA 1	RNA strand × 1 DNA template strand × 1 DNA nontemplate strand × 1 DNA-directed RNA polymerase II largest subunit × 1 （P04050） DNA-directed RNA polymerase II 140 kDa polypeptide × 1 （P08518） DNA-directed RNA polymerase II 45 kDa polypeptide × 1 （P16370） DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide × 1 （P20434） DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide × 1 （P20435） DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide × 1 （P20436） DNA-directed RNA polymerase II 14.2 kDa polypeptide × 1 （P27999） DNA-directed RNA polymerase II 13.6 kDa polypeptide × 1 （P38902） DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide × 1 （P40422） ZINC ION × 8 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB10_YEAST
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain J； PDBConstruct 1–70； UniProt 1–70

DNA-directed RNA polymerase II 13.6 kDa polypeptide

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 10 DNA 2 RNA 1	RNA strand × 1 DNA template strand × 1 DNA nontemplate strand × 1 DNA-directed RNA polymerase II largest subunit × 1 （P04050） DNA-directed RNA polymerase II 140 kDa polypeptide × 1 （P08518） DNA-directed RNA polymerase II 45 kDa polypeptide × 1 （P16370） DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide × 1 （P20434） DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide × 1 （P20435） DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide × 1 （P20436） DNA-directed RNA polymerase II 14.2 kDa polypeptide × 1 （P27999） DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide × 1 （P22139） DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide × 1 （P40422） ZINC ION × 8 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 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 7.7 kDa polypeptide

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 10 DNA 2 RNA 1	RNA strand × 1 DNA template strand × 1 DNA nontemplate strand × 1 DNA-directed RNA polymerase II largest subunit × 1 （P04050） DNA-directed RNA polymerase II 140 kDa polypeptide × 1 （P08518） DNA-directed RNA polymerase II 45 kDa polypeptide × 1 （P16370） DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide × 1 （P20434） DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide × 1 （P20435） DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide × 1 （P20436） DNA-directed RNA polymerase II 14.2 kDa polypeptide × 1 （P27999） DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide × 1 （P22139） DNA-directed RNA polymerase II 13.6 kDa polypeptide × 1 （P38902） ZINC ION × 8 MAGNESIUM ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPC10_YEAST
Isoform	—
PDB entities	13
Chains and sequence ranges	Author chain L； PDBConstruct 1–70； UniProt 1–70

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_id	1r9t
Deposition date deposition_date	2003-10-30
Structure title title	RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE
Keywords keywords	;TRANSCRIPTION, MRNA, MULTIPROTEIN COMPLEX, MOLECULAR MACHINE, DNA, TRANSCRIPTION-DNA-RNA COMPLEX, TRANSCRIPTION-DNA-RNA HYBRID complex ;; TRANSCRIPTION/DNA-RNA HYBRID
Experimental Method method	X-RAY DIFFRACTION

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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.

1r9t__assembly_1__model_1

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

Download this curve (.dat)

1r9t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1r9t__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	47.53 Å
Rg (electron density)	47.01 Å
Total Rg	47.32 Å
Atom count	29248
Residues	3594
Excluded volume	518280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1r9t__assembly_1__model_1`	tridecameric （13）	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 (16)

Entity 1 Entity 1 polymer

Description description	RNA strand
Molecular weight formula_weight	3264.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R
Atom count atom_count	29248

AUCGAGAGGA

Entity 2 Entity 2 polymer

Description description	DNA template strand
Molecular weight formula_weight	8534.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

CTACCGATAAGCAGACGATCCTCTCGAT

Entity 3 Entity 3 polymer

Description description	DNA nontemplate strand
Molecular weight formula_weight	4286.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

CTGCTTATCGGTAG

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase II largest subunit
Molecular weight formula_weight	191821.6 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

MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR

Entity 5 Entity 5 polymer

Description description	DNA-directed RNA polymerase II 140 kDa polypeptide
Molecular weight formula_weight	138937.3 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

MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF

Entity 6 Entity 6 polymer

Description description	DNA-directed RNA polymerase II 45 kDa polypeptide
Molecular weight formula_weight	35330.5 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

MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW

Entity 7 Entity 7 polymer

Description description	DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
Molecular weight formula_weight	25117.1 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	E

MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Entity 8 Entity 8 polymer

Description description	DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
Molecular weight formula_weight	17931.8 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	F

MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Entity 9 Entity 9 polymer

Description description	DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
Molecular weight formula_weight	16525.4 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	H

MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR

Entity 10 Entity 10 polymer

Description description	DNA-directed RNA polymerase II 14.2 kDa polypeptide
Molecular weight formula_weight	14308.2 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	I

MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS

Entity 11 Entity 11 polymer

Description description	DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide
Molecular weight formula_weight	8290.7 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	J

MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD

Entity 12 Entity 12 polymer

Description description	DNA-directed RNA polymerase II 13.6 kDa polypeptide
Molecular weight formula_weight	13633.5 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	K

MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Entity 13 Entity 13 polymer

Description description	DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
Molecular weight formula_weight	7730.0 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	L

MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR

Entity 14 Entity 14 non-polymer

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

Entity 15 Entity 15 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 16 Entity 16 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

▼

6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1r9ta_
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

Domain ID domain_id	d1r9tb_
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

Domain ID domain_id	d1r9tc_
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

Domain ID domain_id	d1r9te_
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

Domain ID domain_id	d1r9tf_
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

Domain ID domain_id	d1r9th_
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

Domain ID domain_id	d1r9ti_
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

Domain ID domain_id	d1r9tj_
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

Domain ID domain_id	d1r9tk_
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

Domain ID domain_id	d1r9tl_
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

CATH v4.4 (21 domains)

Domain ID domain_id	1r9tA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1r9tA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	180 — RNA polymerase ii

Domain ID domain_id	1r9tA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily	100 — RNA polymerase Rpb1, domain 3

Domain ID domain_id	1r9tA06
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily	30 — RNA polymerase Rpb1 funnel domain

Domain ID domain_id	1r9tA09
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	1r9tB04
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
Homologous superfamily homologous superfamily	10 — RNA polymerase Rpb2, domain 2

Domain ID domain_id	1r9tB05
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1070 — Hypothetical Protein Ta0175; Chain: A, domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1r9tB06
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
Homologous superfamily homologous superfamily	10 — DNA-directed RNA polymerase, subunit 2, domain 6

Domain ID domain_id	1r9tB07
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	1r9tB08
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1800 — DCoH-like
Homologous superfamily homologous superfamily	10 — RNA polymerase alpha subunit dimerisation domain

Domain ID domain_id	1r9tC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	1r9tC02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

Domain ID domain_id	1r9tE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1340 — Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
Homologous superfamily homologous superfamily	10 — RNA polymerase, Rpb5, N-terminal domain

Domain ID domain_id	1r9tE02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily	20 — RPB5-like RNA polymerase subunit

Domain ID domain_id	1r9tF00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily	10 — RNA polymerase subunit, RPB6/omega

Domain ID domain_id	1r9tH00
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	1r9tI01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1r9tI02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1r9tJ00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1r9tK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	1r9tL00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	30 — RNA polymerase ii, chain L

▶

Unit-cell length a length_a	168.846 Å
Unit-cell length b length_b	222.958 Å
Unit-cell length c length_c	193.602 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2390
R_work r_work	0.2300
R_free r_free	0.3170

RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE

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

DNA-directed RNA polymerase II largest subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerase II 140 kDa polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerase II 45 kDa polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerase II 14.2 kDa polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerase II 13.6 kDa polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer