6bm2

Pol II elongation complex with an abasic lesion at i-1 position

Method: X-RAY DIFFRACTION

▼

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

DNA-directed RNA polymerase II subunit RPB1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 10 DNA 1 RNA 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） ;DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ; × 1 ;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ; × 1 ZINC ION × 8 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1733； UniProt 1–1733

DNA-directed RNA polymerase II subunit RPB2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1 RNA 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） ;DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ; × 1 ;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ; × 1 ZINC ION × 8 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1224； UniProt 1–1224

DNA-directed RNA polymerase II subunit RPB3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1 RNA 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） ;DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ; × 1 ;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ; × 1 ZINC ION × 8 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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–318； UniProt 1–318

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

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1 RNA 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） ;DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ; × 1 ;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ; × 1 ZINC ION × 8 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	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–215； UniProt 1–215

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

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1 RNA 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） ;DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ; × 1 ;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ; × 1 ZINC ION × 8 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	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–155； UniProt 1–155

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

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1 RNA 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） ;DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ; × 1 ;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ; × 1 ZINC ION × 8 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	6
Chains and sequence ranges	Author chain H； PDBConstruct 1–146； UniProt 1–146

DNA-directed RNA polymerase II subunit RPB9

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1 RNA 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） ;DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ; × 1 ;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ; × 1 ZINC ION × 8 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	7
Chains and sequence ranges	Author chain I； PDBConstruct 1–122； UniProt 1–122

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

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1 RNA 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） ;DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ; × 1 ;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ; × 1 ZINC ION × 8 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	8
Chains and sequence ranges	Author chain J； PDBConstruct 1–70； UniProt 1–70

DNA-directed RNA polymerase II subunit RPB11

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1 RNA 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） ;DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ; × 1 ;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ; × 1 ZINC ION × 8 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	9
Chains and sequence ranges	Author chain K； PDBConstruct 1–120； UniProt 1–120

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

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1 RNA 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 (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ; × 1 ;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ; × 1 ZINC ION × 8 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	10
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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6bm2
Deposition date deposition_date	2017-11-13
Structure title title	Pol II elongation complex with an abasic lesion at i-1 position
Keywords keywords	Complex, DNA BINDING PROTEIN, DNA-RNA HYBRID, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6bm2__assembly_1__model_1

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

Download this curve (.dat)

6bm2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6bm2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.43 Å
Rg (electron density)	46.90 Å
Total Rg	47.20 Å
Atom count	28244
Residues	3520
Excluded volume	502680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6bm2__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (14)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase II subunit RPB1
Molecular weight formula_weight	191821.6 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	28244

MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase II subunit RPB2
Molecular weight formula_weight	138937.3 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 3 Entity 3 polymer

Description description	DNA-directed RNA polymerase II subunit RPB3
Molecular weight formula_weight	35330.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC1
Molecular weight formula_weight	25117.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 5 Entity 5 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC2
Molecular weight formula_weight	17931.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 6 Entity 6 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC3
Molecular weight formula_weight	16525.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 7 Entity 7 polymer

Description description	DNA-directed RNA polymerase II subunit RPB9
Molecular weight formula_weight	14308.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 8 Entity 8 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC5
Molecular weight formula_weight	8290.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 9 Entity 9 polymer

Description description	DNA-directed RNA polymerase II subunit RPB11
Molecular weight formula_weight	13633.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 10 Entity 10 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC4
Molecular weight formula_weight	7730.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 11 Entity 11 polymer

Description description	;DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3') ;
Molecular weight formula_weight	8779.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

CTACCGATAAGCAGAGGCANCTCTCGATG

Entity 12 Entity 12 polymer

Description description	;RNA (5'-R(APUPCPAPAPGPAPGP*A)-3') ;
Molecular weight formula_weight	2918.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R

AUCGAGAGA

Entity 13 Entity 13 non-polymer

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

Entity 14 Entity 14 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

▼

6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id	6bm2A01
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	6bm2A02
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	6bm2C01
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	6bm2C02
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	6bm2E01
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	6bm2E02
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	6bm2F00
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	6bm2H00
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	6bm2I01
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	6bm2I02
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	6bm2J00
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	6bm2K00
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	6bm2L00
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	169.110 Å
Unit-cell length b length_b	222.270 Å
Unit-cell length c length_c	193.710 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.28 °
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	3.403 Å
Low-resolution limit resolution_low	82.922 Å
R factor r_factor	0.2203
R_work r_work	0.2190
R_free r_free	0.2438

Pol II elongation complex with an abasic lesion at i-1 position

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerase II subunit RPB2

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 subunit RPB3

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 subunit RPABC1

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 subunit RPABC2

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 subunit RPABC3

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 subunit RPB9

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 subunit RPABC5

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 subunit RPB11

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 subunit RPABC4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer