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Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2

Analyse Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7B7U
Type: protein
Length: 3,136 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta…
EC: 2.7.7.6, 3.1.3.16
UniProt: I3LJR4, A0A0B8RVL1, I3LCH3, I3LSI7, F1SKN8, A0A4X1ULF2, P60899, A0A4X1UK25, I3LN51, Q8IXW5
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 12 distinct chains · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit (EC 2.7.7.6)	protein	986	45% helix, 13% strand	I3LJR4
B	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	979	29% helix, 24% strand	A0A0B8RVL1
C	DNA-directed RNA polymerase II subunit RPB3	protein	257	25% helix, 28% strand	I3LCH3
E	DNA-directed RNA polymerase II subunit E	protein	209	38% helix, 19% strand	I3LSI7
F	DNA-directed RNA polymerase II subunit F	protein	78	37% helix, 8% strand	F1SKN8
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	148	5% helix, 45% strand	A0A4X1ULF2
I	DNA-directed RNA polymerase II subunit RPB9	protein	115	8% helix, 29% strand	P60899
J	Uncharacterized protein	protein	67	45% helix, 1% strand	—
K	RNA_POL_L_2 domain-containing protein	protein	115	40% helix, 25% strand	A0A4X1UK25
L	RNA polymerase II subunit K	protein	44	0% helix, 18% strand	I3LN51
M	Putative RNA polymerase II subunit B1 ctd phosphatase RPAP2 (EC 3.1.3.16)	protein	108	47% helix, 6% strand	Q8IXW5
N	Unknown	protein	30	0% helix, 7% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains C, I, J, L, M

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1199	0.87	0.88	134	empty
2	1120	0.82	0.83	115	empty
3	1134	0.79	0.81	87	empty
4	170	0.78	0.95	33	empty
5	797	0.78	0.82	85	empty

Interfaces

25 interfaces between chains.

A–B · 3601 Å² buried · 39 hydrogen bonds · protein-protein
C–K · 2337 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 2290 Å² buried · 34 hydrogen bonds · protein-protein
A–H · 2135 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 1599 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

7B7U · Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2 · the same entry in another collection · chain N against N, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt I3LJR4
Every structure of UniProt A0A0B8RVL1
Every structure of UniProt I3LCH3
Every structure of UniProt I3LSI7
Every structure of UniProt F1SKN8
Every structure of UniProt A0A4X1ULF2
Every structure of UniProt P60899
Every structure of UniProt A0A4X1UK25
Every structure of UniProt I3LN51
Every structure of UniProt Q8IXW5
Elsewhere: RCSB PDB 7B7U · PDBe 7B7U · UniProt I3LJR4 · UniProt A0A0B8RVL1 · UniProt I3LCH3 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt A0A4X1ULF2 · UniProt P60899 · UniProt A0A4X1UK25 · UniProt I3LN51 · UniProt Q8IXW5

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