3cqz

Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin

Method: X-RAY DIFFRACTION

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

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	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） ALPHA-AMANITIN × 1 （P85421） ZINC ION × 8 water × 4	Consistent with protein count

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

OrganismNot specified

UniProt P08518

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	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） ALPHA-AMANITIN × 1 （P85421） ZINC ION × 8 water × 4	Consistent with protein count

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 1–1223； 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	Protein heterocomplex	Heteromer	Protein 11	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） ALPHA-AMANITIN × 1 （P85421） ZINC ION × 8 water × 4	Consistent with protein count

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

OrganismNot specified

UniProt P20434

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	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） ALPHA-AMANITIN × 1 （P85421） ZINC ION × 8 water × 4	Consistent with protein count

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

OrganismNot specified

UniProt P20435

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	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） ALPHA-AMANITIN × 1 （P85421） ZINC ION × 8 water × 4	Consistent with protein count

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

OrganismNot specified

UniProt P20436

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	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） ALPHA-AMANITIN × 1 （P85421） ZINC ION × 8 water × 4	Consistent with protein count

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

OrganismNot specified

UniProt P27999

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	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） ALPHA-AMANITIN × 1 （P85421） ZINC ION × 8 water × 4	Consistent with protein count

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

OrganismNot specified

UniProt P22139

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	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） ALPHA-AMANITIN × 1 （P85421） ZINC ION × 8 water × 4	Consistent with protein count

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

OrganismNot specified

UniProt P38902

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	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） ALPHA-AMANITIN × 1 （P85421） ZINC ION × 8 water × 4	Consistent with protein count

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

OrganismNot specified

UniProt P40422

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	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） ALPHA-AMANITIN × 1 （P85421） ZINC ION × 8 water × 4	Consistent with protein count

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

ALPHA-AMANITIN

OrganismNot specified

UniProt P85421

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	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） ZINC ION × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMATX_AMAPH
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain M； PDBConstruct 1–8； UniProt 1–8

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	3cqz
Deposition date deposition_date	2008-04-03
Structure title title	Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin
Keywords keywords	;TRANSCRIPTION-TOXIN COMPLEX, ALPHA AMANITIN, TOXIN, INHIBITOR, POLYMERASE, TRANSFERASE, DNA BINDING, ZINC-FINGER, PHOSPHOPROTEIN, TRANSCRIPTION ;; TRANSCRIPTION/TOXIN
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.

3cqz__assembly_1__model_1

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

Download this curve (.dat)

3cqz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cqz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.81 Å
Rg (electron density)	48.01 Å
Total Rg	48.35 Å
Atom count	27323
Residues	3434
Excluded volume	487890 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cqz__assembly_1__model_1`	undecameric （11）	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 (13)

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	27340

MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

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	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR

Entity 11 Entity 11 polymer

Description description	ALPHA-AMANITIN
Molecular weight formula_weight	939.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

IWGIGCNP

Entity 12 Entity 12 non-polymer

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

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

▼

6. Fold Classification (SCOP + CATH) 29 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d3cqza1
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	d3cqzb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family family	e.29.1.1 — RNA-polymerase beta

Domain ID domain_id	d3cqzf1
Class class	a — All alpha proteins
Fold Fold fold	a.143 — RPB6/omega subunit-like
Superfamily Superfamily superfamily	a.143.1 — RPB6/omega subunit-like
Family Family family	a.143.1.2 — RPB6

Domain ID domain_id	d3cqzh_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.8 — RNA polymerase subunit RBP8

Domain ID domain_id	d3cqzj_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.11 — RNA polymerase subunit RPB10
Family Family family	a.4.11.1 — RNA polymerase subunit RPB10

Domain ID domain_id	d3cqzk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
Family Family family	d.74.3.2 — RBP11/RpoL

Domain ID domain_id	d3cqzl1
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.9 — RNA polymerase subunits
Family Family family	g.41.9.2 — RBP12 subunit of RNA polymerase II

CATH v4.4 (22 domains)

Domain ID domain_id	3cqzA01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	860 — DNA Excision Repair, Uvrb; Chain A
Homologous superfamily homologous superfamily	120 — RNA polymerase II, clamp domain

Domain ID domain_id	3cqzA03
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	3cqzA04
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	3cqzA05
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	3cqzA06
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	3cqzA09
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	3cqzB04
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	3cqzB05
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	3cqzB06
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	3cqzB07
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	3cqzB08
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	3cqzC01
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	3cqzC02
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	3cqzE01
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	3cqzE02
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	3cqzF00
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	3cqzH00
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	3cqzI01
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	3cqzI02
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	3cqzJ00
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	3cqzK00
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	3cqzL00
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	122.510 Å
Unit-cell length b length_b	222.480 Å
Unit-cell length c length_c	374.230 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2020
R_work r_work	0.2000
R_free r_free	0.2730

Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin

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