2C35: PDB entry 2C35

Subunits Rpb4 and Rpb7 of human RNA polymerase II. Determined by X-ray diffraction at 2.7 Å resolution. Released 18 Nov 2005.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: HOMO SAPIENS
Chains: 8
Atoms: 9,290
Mol. weight: 146.53 kDa
Released: 18 Nov 2005

Explore 2C35 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2C35 contains 54 α-helices and 70 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
α-helix	17-19	3
β-strand	21	1	1
β-strand	30-31	2	2
α-helix	34-49	16
α-helix	55-58	4
α-helix	59-70	12
α-helix	77-88	12
α-helix	94-103	10
α-helix	108-114	7
α-helix	116-118	3
α-helix	124-137	14

Chain B: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-13	12	2
α-helix	15-17	3
α-helix	22-34	13
β-strand	38-39	2	2
β-strand	43-54	12	2
α-helix	55-57	3
β-strand	58	1	2
β-strand	66-77	12	2
β-strand	84-93	10	3
β-strand	96-101	6	3
β-strand	104-109	6	3
α-helix	110-112	3
β-strand	117-120	4	4
β-strand	127-130	4	4
β-strand	136-138	3	4
β-strand	142-153	12	3
β-strand	156-162	7	3
β-strand	169-170	2	3

Chain C: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	5
α-helix	17-19	3
β-strand	21	1	5
β-strand	30-31	2	6
α-helix	34-49	16
α-helix	55-58	4
α-helix	59-71	13
α-helix	77-88	12
α-helix	94-103	10
α-helix	108-114	7
α-helix	116-118	3
α-helix	124-137	14

Chain D: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-13	12	6
α-helix	15-17	3
α-helix	22-34	13
β-strand	38-39	2	6
β-strand	43-54	12	6
α-helix	55-57	3
β-strand	58	1	6
β-strand	61	1	7
β-strand	63	1	7
β-strand	66-77	12	6
β-strand	84-93	10	8
β-strand	96-101	6	8
β-strand	104-109	6	8
α-helix	110-112	3
β-strand	117-120	4	9
β-strand	127-130	4	9
β-strand	136-138	3	9
β-strand	142-153	12	8
β-strand	156-162	7	8
β-strand	169-170	2	8

Chains E and G: 11 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	10
α-helix	17-19	3
β-strand	21	1	10
α-helix	24-26	3
α-helix	29	1
β-strand	30-32	3	11
α-helix	34-49	16
α-helix	55-58	4
α-helix	59-71	13
α-helix	77-88	12
α-helix	94-103	10
α-helix	108-114	7
α-helix	116-118	3
α-helix	124-136	13

Chains F and H: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-13	12	11
α-helix	15-17	3
α-helix	22-34	13
β-strand	38-39	2	11
β-strand	43-54	12	11
β-strand	58-59	2	11
β-strand	66-77	12	11
β-strand	84-93	10	12
β-strand	96-101	6	12
β-strand	104-109	6	12
α-helix	110-112	3
β-strand	119-120	2	13
β-strand	127-129	3	13
β-strand	136-137	2	13
β-strand	142-153	12	12
β-strand	156-162	7	12
β-strand	169-170	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase II 16 kda polypeptide	A, C, E, G	protein	152	HOMO SAPIENS	O15514 (AlphaFold model)
DNA-directed RNA polymerase II 19 kda polypeptide	B, D, F, H	protein	172	HOMO SAPIENS	P62487 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>2C35_1 DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE (chains A, C, E, G)
GSRRASVGSQMAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNES
AEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEE
SKALIPSLEGRFEDEELQQILDDIQTKRSFQY

Sequence of entity 2 (B, D, F, H), FASTA

>2C35_2 DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE (chains B, D, F, H)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS

Primary citation

Crystal Structure and RNA Binding of the Rpb4/Rpb7 Subunits of Human RNA Polymerase II. Meka, H., Werner, F., Cordell, S.C. et al. Nucleic Acids Res (2005) 33:6435. DOI 10.1093/NAR/GKI945 · PubMed

Other PDB entries of the same protein (UniProt O15514 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EHZ 2.6 Å, Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate…
8XSO 2.7 Å, RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei
9T5H 2.7 Å, RNA polymerase II bound to Gdown1 and RPAP2
28JC 2.94 Å, RNA polymerase II bound to RPAP2 and Gdown1
8XRM 3.13 Å, RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA…
9EI1 3.2 Å, Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5…
9EI3 3.2 Å, Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5…
8XRJ 3.6 Å, RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei
9EI4 3.7 Å, Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5…
5IYB 3.9 Å, Human core-PIC in the open state
5IYC 3.9 Å, Human core-PIC in the initial transcribing state
5IYD 3.9 Å, Human core-PIC in the initial transcribing state (no IIS)

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