Structural Basis of Initial RNA Polymerase II Transcription

Cheung, A.C.M; Sainsbury, S; Cramer, P.

4A3C

RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid

Macromolecule Annotations for the Entities in PDB 4A3C

Domain Annotation: CATH CATH Database (version 4.0.0) Homepage

Chains	Domain	Class	Architecture	Topology	Homology
C1	4a3cC01	Alpha Beta	2-Layer Sandwich	Gyrase A; domain 2
C2	4a3cC02	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit; Chain A, domain 2	RNA Polymerase Alpha Subunit; Chain A, domain 2
E1	4a3cE01	Alpha Beta	3-Layer(aba) Sandwich	Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
E2	4a3cE02	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit
F	4a3cF00	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit
G1	4a3cG01	Alpha Beta	2-Layer Sandwich	Dna Ligase; domain 1	DNA-directed RNA polymerase ii subunit; domain 1
G2	4a3cG02	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins
H	4a3cH00	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins
I1	4a3cI01	Mainly Beta	Single Sheet	N-terminal domain of TfIIb
I2	4a3cI02	Mainly Beta	Single Sheet	N-terminal domain of TfIIb
J	4a3cJ00	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like
K	4a3cK00	Alpha Beta	2-Layer Sandwich	Gyrase A; domain 2
L	4a3cL00	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	RNA polymerase ii, chain L

Protein Family Annotation Pfam Database Homepage

Chains	Pfam Accession	Pfam Identifier	Pfam Description	Type	Source

Gene Product Annotation Gene Ontology Consortium Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 (4A3C:A)	RNA Polymerase Ii Activity DNA Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding Transferase Activity Nucleotidyltransferase Activity Metal Ion Binding	Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase Ii Translesion Synthesis	Nucleus DNA Directed RNA Polymerase Ii Core Complex Cytoplasmic Stress Granule
B	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 (4A3C:B)	RNA Polymerase Ii Activity DNA Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding Transferase Activity Nucleotidyltransferase Activity Ribonucleoside Binding Metal Ion Binding	Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase Ii	Nucleus DNA Directed RNA Polymerase Ii Core Complex Cytoplasmic Stress Granule
C	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 (4A3C:C)	RNA Polymerase Ii Activity DNA Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding Metal Ion Binding Protein Dimerization Activity	Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase Ii Termination of RNA Polymerase Ii Transcription	Nucleus Nucleoplasm DNA Directed RNA Polymerase Ii Core Complex
D	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 (4A3C:D)	Nucleotide Binding Single Stranded DNA Binding Single Stranded RNA Binding Catalytic Activity DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding Translation Initiation Factor Binding	Nuclear Transcribed MRNA Catabolic Process Deadenylation Dependent Decay Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase Ii Transcription Initiation From RNA Polymerase Ii Promoter MRNA Processing MRNA Export From Nucleus in Response to Heat Stress Recruitment of 3' End Processing Factors to RNA Polymerase Ii Holoenzyme Complex Cellular Metabolic Process Positive Regulation of Translational Initiation	P Body Nucleus DNA Directed RNA Polymerase Ii Core Complex Cytoplasm
E	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 (4A3C:E)	RNA Polymerase I Activity RNA Polymerase Ii Activity RNA Polymerase Iii Activity DNA Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding	Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase I Transcription by RNA Polymerase Ii Transcription by RNA Polymerase Iii Termination of RNA Polymerase Iii Transcription Ribosome Biogenesis TRNA Transcription by RNA Polymerase Iii	Nucleus Nucleoplasm DNA Directed RNA Polymerase Ii Core Complex DNA Directed RNA Polymerase Iii Complex DNA Directed RNA Polymerase I Complex
F	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 (4A3C:F)	RNA Polymerase I Activity RNA Polymerase Ii Activity RNA Polymerase Iii Activity DNA Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding	Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase I Transcription by RNA Polymerase Ii Transcription by RNA Polymerase Iii Termination of RNA Polymerase Iii Transcription Ribosome Biogenesis TRNA Transcription by RNA Polymerase Iii	Nucleus Nucleoplasm DNA Directed RNA Polymerase Ii Core Complex DNA Directed RNA Polymerase Iii Complex DNA Directed RNA Polymerase I Complex Cytoplasm
G	RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 (4A3C:G)	Nucleic Acid Binding Single Stranded DNA Binding Single Stranded RNA Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding Translation Initiation Factor Binding	Nuclear Transcribed MRNA Catabolic Process Exonucleolytic Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase Ii Transcription Initiation From RNA Polymerase Ii Promoter Positive Regulation of Translational Initiation Positive Regulation of Nuclear Transcribed MRNA Poly(a) Tail Shortening	P Body Nucleus DNA Directed RNA Polymerase Ii Core Complex Cytoplasm
H	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 (4A3C:H)	RNA Polymerase I Activity RNA Polymerase Ii Activity RNA Polymerase Iii Activity DNA Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding	Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase I Transcription by RNA Polymerase Ii Transcription by RNA Polymerase Iii Termination of RNA Polymerase Iii Transcription Ribosome Biogenesis TRNA Transcription by RNA Polymerase Iii	Nucleus Nucleoplasm DNA Directed RNA Polymerase Ii Core Complex DNA Directed RNA Polymerase Iii Complex DNA Directed RNA Polymerase I Complex
I	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 (4A3C:I)	Nucleic Acid Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding Zinc Ion Binding Metal Ion Binding	Transcription RNA Templated Maintenance of Transcriptional Fidelity During DNA Templated Transcription Elongation From RNA Polymerase Ii Promoter DNA Repair Transcription Coupled Nucleotide Excision Repair Transcription DNA Templated Transcription by RNA Polymerase Ii Transcription Initiation From RNA Polymerase Ii Promoter MRNA Cleavage Cellular Response to DNA Damage Stimulus	Nucleus DNA Directed RNA Polymerase Ii Core Complex Nucleolus
J	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 (4A3C:J)	RNA Polymerase I Activity RNA Polymerase Ii Activity RNA Polymerase Iii Activity DNA Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding Zinc Ion Binding Metal Ion Binding	Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase I Transcription by RNA Polymerase Ii Transcription by RNA Polymerase Iii Termination of RNA Polymerase Iii Transcription Ribosome Biogenesis TRNA Transcription by RNA Polymerase Iii	Nucleus Nucleoplasm DNA Directed RNA Polymerase Ii Core Complex DNA Directed RNA Polymerase Iii Complex Nucleolus DNA Directed RNA Polymerase I Complex
K	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 (4A3C:K)	RNA Polymerase Ii Activity DNA Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding Protein Dimerization Activity	Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase Ii Termination of RNA Polymerase Ii Transcription	Nucleus DNA Directed RNA Polymerase Ii Core Complex
L	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 (4A3C:L)	RNA Polymerase I Activity RNA Polymerase Ii Activity RNA Polymerase Iii Activity DNA Binding DNA Directed 5' 3' RNA Polymerase Activity RNA Directed 5' 3' RNA Polymerase Activity Protein Binding Zinc Ion Binding Metal Ion Binding	Transcription RNA Templated Transcription DNA Templated Transcription by RNA Polymerase I Transcription by RNA Polymerase Ii Transcription by RNA Polymerase Iii Termination of RNA Polymerase Iii Transcription Ribosome Biogenesis TRNA Transcription by RNA Polymerase Iii	Nucleus Nucleoplasm DNA Directed RNA Polymerase Ii Core Complex DNA Directed RNA Polymerase Iii Complex Nucleolus DNA Directed RNA Polymerase I Complex
N	NON TEMPLATE DNA (4A3C:N)	none	none	none
P	TRANSCRIPT RNA, 5'-R(CPAPGPGP*AP)-3' (4A3C:P)	none	none	none
T	TEMPLATE DNA (4A3C:T)	none	none	none

Protein Modification Annotation

Type	PDB Residue Nr.	Description

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139555 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

4A3C

RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid

Macromolecule Annotations for the Entities in PDB 4A3C

Domain Annotation: CATH CATH Database (version 4.0.0) Homepage

Protein Family Annotation Pfam Database Homepage

Gene Product Annotation Gene Ontology Consortium Homepage

Protein Modification Annotation