SMTL ID : 8w8f.1

human co-transcriptional RNA capping enzyme RNGTT-CMTR1

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-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain C: D.495, D.497, D.499 Chain P: U.17 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.495, C:D.497, C:D.499, C:D.499

8 x ZN: ZINC ION(Non-covalent)

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

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

GTP.9: 1 residues within 4Å: Chain P: A.2 No protein-ligand interaction detected (PLIP)

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

mRNA-capping enzyme: A
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1: B
DNA-directed RNA polymerase subunit: C
DNA-directed RNA polymerase subunit beta: D
DNA-directed RNA polymerase II subunit RPB3: E
DNA-directed RNA polymerase II subunit RPB4: F
DNA-directed RNA polymerase II subunit E: G
DNA-directed RNA polymerase II subunit F: H
DNA-directed RNA polymerase II subunit RPB7: I
DNA-directed RNA polymerases I, II, and III subunit RPABC3: J
DNA-directed RNA polymerase II subunit RPB9: K
DNA-directed RNA polymerases I, II, and III subunit RPABC5: L
DNA-directed RNA polymerase II subunit RPB11-a: M
RPB12: N
Transcription elongation factor SPT4: R
Transcription elongation factor SPT5: S

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
b

C
A

D
B

E
C

F
D

G
E

H
F

I
G

J
H

K
I

L
J

M
K

N
L

R
Y

S
Z

mRNA-capping enzyme

Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1

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

Transcription elongation factor SPT4

Transcription elongation factor SPT5

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