5flm

Structure of transcribing mammalian RNA polymerase II

Method: ELECTRON MICROSCOPY

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

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 × 1 （Q3T0Q3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 × 1 （Q1JQ91） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 × 1 （Q2T9T3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 × 1 （Q5E9B8） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 × 1 （F2Z4H3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 × 1 （Q32P73） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 × 1 （Q32P78） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 × 1 （Q32P79） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 × 1 （Q3ZBC0） DNA, DNA-RNA ELONGATION SCAFFOLD × 1 RNA, DNA-RNA ELONGATION SCAFFOLD × 1 DNA, DNA-RNA ELONGATION SCAFFOLD × 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	A5PJW8_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1174； UniProt 1–1174

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3

OrganismNot specified

UniProt Q3T0Q3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 × 1 （A5PJW8） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 × 1 （Q1JQ91） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 × 1 （Q2T9T3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 × 1 （Q5E9B8） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 × 1 （F2Z4H3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 × 1 （Q32P73） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 × 1 （Q32P78） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 × 1 （Q32P79） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 × 1 （Q3ZBC0） DNA, DNA-RNA ELONGATION SCAFFOLD × 1 RNA, DNA-RNA ELONGATION SCAFFOLD × 1 DNA, DNA-RNA ELONGATION SCAFFOLD × 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_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–275； UniProt 1–275

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4

OrganismNot specified

UniProt Q1JQ91

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 × 1 （A5PJW8） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 × 1 （Q3T0Q3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 × 1 （Q2T9T3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 × 1 （Q5E9B8） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 × 1 （F2Z4H3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 × 1 （Q32P73） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 × 1 （Q32P78） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 × 1 （Q32P79） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 × 1 （Q3ZBC0） DNA, DNA-RNA ELONGATION SCAFFOLD × 1 RNA, DNA-RNA ELONGATION SCAFFOLD × 1 DNA, DNA-RNA ELONGATION SCAFFOLD × 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	Q1JQ91_BOVIN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–142； UniProt 1–142

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1

OrganismNot specified

UniProt Q2T9T3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 × 1 （A5PJW8） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 × 1 （Q3T0Q3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 × 1 （Q1JQ91） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 × 1 （Q5E9B8） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 × 1 （F2Z4H3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 × 1 （Q32P73） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 × 1 （Q32P78） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 × 1 （Q32P79） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 × 1 （Q3ZBC0） DNA, DNA-RNA ELONGATION SCAFFOLD × 1 RNA, DNA-RNA ELONGATION SCAFFOLD × 1 DNA, DNA-RNA ELONGATION SCAFFOLD × 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_BOVIN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–210； UniProt 1–210

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7

OrganismNot specified

UniProt Q5E9B8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 × 1 （A5PJW8） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 × 1 （Q3T0Q3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 × 1 （Q1JQ91） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 × 1 （Q2T9T3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 × 1 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 × 1 （F2Z4H3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 × 1 （Q32P73） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 × 1 （Q32P78） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 × 1 （Q32P79） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 × 1 （Q3ZBC0） DNA, DNA-RNA ELONGATION SCAFFOLD × 1 RNA, DNA-RNA ELONGATION SCAFFOLD × 1 DNA, DNA-RNA ELONGATION SCAFFOLD × 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	RPB7_BOVIN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–172； UniProt 1–172

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3

OrganismNot specified

UniProt F2Z4H3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 × 1 （A5PJW8） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 × 1 （Q3T0Q3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 × 1 （Q1JQ91） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 × 1 （Q2T9T3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 × 1 （Q5E9B8） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 × 1 （Q32P73） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 × 1 （Q32P78） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 × 1 （Q32P79） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 × 1 （Q3ZBC0） DNA, DNA-RNA ELONGATION SCAFFOLD × 1 RNA, DNA-RNA ELONGATION SCAFFOLD × 1 DNA, DNA-RNA ELONGATION SCAFFOLD × 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	F2Z4H3_BOVIN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–150； UniProt 1–150

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

OrganismNot specified

UniProt Q32P73

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 × 1 （A5PJW8） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 × 1 （Q3T0Q3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 × 1 （Q1JQ91） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 × 1 （Q2T9T3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 × 1 （Q5E9B8） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 × 1 （F2Z4H3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 × 1 （Q32P78） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 × 1 （Q32P79） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 × 1 （Q3ZBC0） DNA, DNA-RNA ELONGATION SCAFFOLD × 1 RNA, DNA-RNA ELONGATION SCAFFOLD × 1 DNA, DNA-RNA ELONGATION SCAFFOLD × 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_BOVIN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain I； PDBConstruct 1–125； UniProt 1–125

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5

OrganismNot specified

UniProt Q32P78

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 × 1 （A5PJW8） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 × 1 （Q3T0Q3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 × 1 （Q1JQ91） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 × 1 （Q2T9T3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 × 1 （Q5E9B8） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 × 1 （F2Z4H3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 × 1 （Q32P73） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 × 1 （Q32P79） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 × 1 （Q3ZBC0） DNA, DNA-RNA ELONGATION SCAFFOLD × 1 RNA, DNA-RNA ELONGATION SCAFFOLD × 1 DNA, DNA-RNA ELONGATION SCAFFOLD × 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_BOVIN
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain J； PDBConstruct 1–67； UniProt 1–67

DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11

OrganismNot specified

UniProt Q32P79

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 × 1 （A5PJW8） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 × 1 （Q3T0Q3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 × 1 （Q1JQ91） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 × 1 （Q2T9T3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 × 1 （Q5E9B8） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 × 1 （F2Z4H3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 × 1 （Q32P73） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 × 1 （Q32P78） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 × 1 （Q3ZBC0） DNA, DNA-RNA ELONGATION SCAFFOLD × 1 RNA, DNA-RNA ELONGATION SCAFFOLD × 1 DNA, DNA-RNA ELONGATION SCAFFOLD × 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_BOVIN
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain K； PDBConstruct 1–117； UniProt 1–117

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4

OrganismNot specified

UniProt Q3ZBC0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 × 1 （A5PJW8） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 × 1 （Q3T0Q3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 × 1 （Q1JQ91） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 × 1 （Q2T9T3） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 × 1 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 × 1 （Q5E9B8） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 × 1 （F2Z4H3） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 × 1 （Q32P73） DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 × 1 （Q32P78） DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 × 1 （Q32P79） DNA, DNA-RNA ELONGATION SCAFFOLD × 1 RNA, DNA-RNA ELONGATION SCAFFOLD × 1 DNA, DNA-RNA ELONGATION SCAFFOLD × 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_BOVIN
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain L； PDBConstruct 1–58； UniProt 1–58

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	5flm
Deposition date deposition_date	2015-10-26
Structure title title	Structure of transcribing mammalian RNA polymerase II
Keywords keywords	TRANSCRIPTION, ELONGATION; TRANSCRIPTION
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

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

5flm__assembly_1__model_1

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

Download this curve (.dat)

5flm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5flm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.95 Å
Rg (electron density)	50.61 Å
Total Rg	50.78 Å
Atom count	32712
Residues	3976
Excluded volume	578190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5flm__assembly_1__model_1`	pentadecameric （15）	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 (17)

Entity 1 Entity 1 polymer

Description description	DNA-DIRECTED RNA POLYMERASE
Molecular weight formula_weight	217436.1 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	A
Atom count atom_count	32712

MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTGMFFGSAPSPMGGISPAMTPWNQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAYEPRSPGGYTPQSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTSPSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPKYTPTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDDEN

Entity 2 Entity 2 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
Molecular weight formula_weight	134041.4 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	B

MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSMLARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV

Entity 3 Entity 3 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
Molecular weight formula_weight	31466.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLRPETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN

Entity 4 Entity 4 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
Molecular weight formula_weight	16347.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MAAGGSDPRSGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY

Entity 5 Entity 5 polymer

Description description	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1
Molecular weight formula_weight	24514.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDGLDQTLEEFKAQFGGKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLVQ

Entity 6 Entity 6 polymer

Description description	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2
Molecular weight formula_weight	14491.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD

Entity 7 Entity 7 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
Molecular weight formula_weight	19314.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS

Entity 8 Entity 8 polymer

Description description	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
Molecular weight formula_weight	17162.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKKLAF

Entity 9 Entity 9 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
Molecular weight formula_weight	14507.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MEPDGTYEPGIVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE

Entity 10 Entity 10 polymer

Description description	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5
Molecular weight formula_weight	7655.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLLNYAPLEK

Entity 11 Entity 11 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
Molecular weight formula_weight	13310.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE

Entity 12 Entity 12 polymer

Description description	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
Molecular weight formula_weight	7018.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Entity 13 Entity 13 polymer

Description description	DNA, DNA-RNA ELONGATION SCAFFOLD
Molecular weight formula_weight	12085.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

GGCAGTACTAGTAAACTAGTATTGAAAGTACTTGAGCTT

Entity 14 Entity 14 polymer

Description description	RNA, DNA-RNA ELONGATION SCAFFOLD
Molecular weight formula_weight	6414.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	P

UAUAUGCAUAAAGACCAGGC

Entity 15 Entity 15 polymer

Description description	DNA, DNA-RNA ELONGATION SCAFFOLD
Molecular weight formula_weight	11942.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

AAGCTCAAGTACTTAAGCCTGGTCATTACTAGTACTGCC

Entity 16 Entity 16 non-polymer

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

Entity 17 Entity 17 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) 17 domains

CATH v4.4 (17 domains)

Domain ID domain_id	5flmA01
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	5flmA02
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	5flmB01
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	5flmC01
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	5flmC02
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	5flmD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	40 — RNA Polymerase II, Rpb4 subunit

Domain ID domain_id	5flmE01
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	5flmE02
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	5flmF00
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	5flmG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

Domain ID domain_id	5flmG02
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	5flmH01
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	5flmI01
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	5flmI02
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	5flmJ00
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	5flmK00
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	5flmL00
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	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	264134

Structure of transcribing mammalian RNA polymerase II

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

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 POLYMERASE II SUBUNIT RPB4

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 POLYMERASE II SUBUNIT RPB7

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