SMTL ID : 8w8e.1

human co-transcriptional RNA capping enzyme RNGTT

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain N: U.16 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.499, A:D.499

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: C.111, C.114, G.183 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.111, A:C.114 ZN.3: 4 residues within 4Å: Chain A: C.71, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.71, A:C.74, A:C.81, A:H.84 ZN.4: 4 residues within 4Å: Chain B: C.1119, C.1122, C.1137, C.1140 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1119, B:C.1122, B:C.1137 ZN.5: 4 residues within 4Å: Chain C: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.88, C:C.90, C:C.94, C:C.97 ZN.6: 4 residues within 4Å: Chain I: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39, I:C.42 ZN.7: 5 residues within 4Å: Chain I: C.86, C.89, C.114, C.119, H.121 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.119 ZN.8: 5 residues within 4Å: Chain L: C.19, C.22, T.24, C.36, E.38 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:C.22, L:C.36 ZN.10: 3 residues within 4Å: Chain T: C.20, C.23, C.37 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:C.20, T:C.23, T:C.37

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.9: 4 residues within 4Å: Chain N: A.1 Chain V: N.69, T.70, R.72 4 PLIP interactions: 4 interactions with chain V Hydrogen bonds: V:N.69, V:T.70, V:R.72 Salt bridges: V:R.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structures of co-transcriptional RNA capping enzymes on paused transcription complex. Nat Commun (2024)

Release Date

2024-04-10

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerase II subunit RPB4: D
DNA-directed RNA polymerase II subunit E: E
DNA-directed RNA polymerase II subunit F: F
DNA-directed RNA polymerase II subunit RPB7: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase II subunit RPB9: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5: J
DNA-directed RNA polymerase II subunit RPB11-a: K
RPB12: L
Negative elongation factor A: P
Negative elongation factor B: Q
Negative elongation factor C/D: R
Negative elongation factor E: S
Transcription elongation factor SPT4: T
Transcription elongation factor SPT5: U
mRNA-capping enzyme: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

P
U

Q
V

R
W

S
X

T
Y

U
Z

V
a

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerase II subunit RPB4

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerase II subunit F

DNA-directed RNA polymerase II subunit RPB7

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11-a

RPB12

Negative elongation factor A

Negative elongation factor B

Negative elongation factor C/D

Negative elongation factor E

Transcription elongation factor SPT4

Transcription elongation factor SPT5

mRNA-capping enzyme

Related Entries With Identical Sequence