SMTL ID : 8p4f.1

Structural insights into human co-transcriptional capping - structure 6

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-mer

Ligands

1 x MGT: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE(Covalent)

MGT.1: 15 residues within 4Å: Chain A: G.1 Chain R: K.203, S.204, F.206, D.207, M.214, R.218, E.373, N.374, Q.376, F.406, R.436, A.438, N.439, S.440 10 PLIP interactions: 10 interactions with chain R Hydrogen bonds: R:N.374, R:N.374, R:Q.376, R:N.439, R:S.440, R:Q.507 Salt bridges: R:D.207, R:R.218, R:R.218, R:E.373

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain B: C.71, T.73, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.71, B:C.74, B:C.81, B:H.84 ZN.3: 5 residues within 4Å: Chain B: C.111, C.114, C.154, G.183, C.184 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.111, B:C.114, B:C.184 ZN.5: 4 residues within 4Å: Chain C: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.1119, C:C.1122, C:C.1137, C:C.1140 ZN.6: 4 residues within 4Å: Chain H: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.17, H:C.20, H:C.39, H:C.42 ZN.7: 5 residues within 4Å: Chain H: C.86, C.89, H.91, C.114, C.119 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.86, H:C.89, H:C.114, H:C.119 ZN.8: 4 residues within 4Å: Chain I: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.7, I:C.10, I:C.44, I:C.45 ZN.9: 6 residues within 4Å: Chain K: C.19, C.22, T.24, C.36, R.37, C.39 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.19, K:C.22, K:C.36, K:C.39 ZN.10: 4 residues within 4Å: Chain N: C.16, C.19, C.33, C.36 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.16, N:C.19, N:C.33, N:C.36

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: C.29 Chain B: D.495, D.497, D.499 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.495, B:D.497

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.11: 23 residues within 4Å: Chain A: G.1, A.2 Chain R: N.234, A.236, C.277, A.278, G.279, P.280, G.281, G.282, F.283, T.301, L.302, N.306, G.334, D.335, I.336, T.337, D.364, G.365, G.366, L.383, K.404 15 PLIP interactions: 15 interactions with chain R Hydrophobic interactions: R:A.236, R:D.364 Hydrogen bonds: R:N.234, R:A.278, R:G.279, R:G.282, R:F.283, R:T.301, R:L.302, R:D.335, R:D.335, R:I.336, R:T.337, R:G.366 Salt bridges: R:D.364

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garg, G. et al., Structural insights into human co-transcriptional capping. Mol.Cell (2023)

Release Date

2023-07-19

Peptides

DNA-directed RNA polymerase II subunit RPB1: B
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase II subunit RPB3: D
DNA-directed RNA polymerase II subunit E: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2: F
DNA-directed RNA polymerases I, II, and III subunit RPABC3: G
DNA-directed RNA polymerase II subunit RPB9: H
DNA-directed RNA polymerases I, II, and III subunit RPABC5: I
DNA-directed RNA polymerase II subunit RPB11-a: J
RNA polymerase II subunit K: K
Transcription elongation factor SPT4: N
Transcription elongation factor SPT5: O
DNA-directed RNA polymerase II subunit RPB7: P
RNA polymerase II subunit D: Q
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
E

F
F

G
H

H
I

I
J

J
K

K
L

N
Y

O
Z

P
G

Q
D

R
O

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerases I, II, and III subunit RPABC2

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

RNA polymerase II subunit K

Transcription elongation factor SPT4

Transcription elongation factor SPT5

DNA-directed RNA polymerase II subunit RPB7

RNA polymerase II subunit D

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

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