SMTL ID : 8waw.1

De novo transcribing complex 13 (TC13), the early elongation complex with Pol II positioned 13nt downstream of TSS

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ILX- TRX- GLY- ILE- GLY- CSX- ASN- HYP: Alpha-amanitin(Non-covalent)

ILX-TRX-GLY-ILE-GLY-CSX-ASN-HYP.1: 23 residues within 4Å: Chain F: N.742, N.746, R.749, I.779, S.782, Q.783, V.787, V.788, G.789, Q.790, Q.791, N.792, G.795, K.796, R.797, H.839, G.842, G.843, E.845, G.846, D.849, H.1108 Chain G: Q.718 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:R.749, F:I.779, F:I.779, F:Q.783, F:N.792 Hydrogen bonds: F:N.746, F:R.749, F:S.782, F:Q.783, F:Q.790, F:Q.791, F:N.792, F:N.792, F:D.849, F:H.1108 pi-Cation interactions: F:R.749, F:R.749

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain F: C.71, T.73, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.71, F:C.74, F:C.81, F:H.84 ZN.3: 5 residues within 4Å: Chain F: C.111, C.114, C.154, G.183, C.184 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.111, F:C.114, F:C.184 ZN.6: 4 residues within 4Å: Chain G: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.1119, G:C.1122, G:C.1137, G:C.1140 ZN.7: 4 residues within 4Å: Chain H: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.88, H:C.90, H:C.94, H:C.97 ZN.8: 4 residues within 4Å: Chain N: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.17, N:C.20, N:C.39, N:C.42 ZN.9: 4 residues within 4Å: Chain N: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.86, N:C.89, N:C.114, N:C.119 ZN.10: 4 residues within 4Å: Chain O: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.7, O:C.10, O:C.44, O:C.45 ZN.11: 5 residues within 4Å: Chain Q: C.19, C.22, T.24, C.36, C.39 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.19, Q:C.22, Q:C.36, Q:C.39

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain E: G.13 Chain F: D.495, D.497, D.499 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.495, F:D.497, F:D.497, F:D.499

1 x W0F: [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

W0F.5: 11 residues within 4Å: Chain D: C.46 Chain E: G.13 Chain F: R.460, N.493, D.497, T.854 Chain G: R.721, Y.724, D.792, K.942, R.975 8 PLIP interactions: 3 interactions with chain F, 5 interactions with chain G Hydrogen bonds: F:R.460, F:N.493, F:D.497, G:Y.724 Salt bridges: G:R.721, G:R.721, G:K.942, G:R.975

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Structural visualization of transcription initiation in action. Science (2023)

Release Date

2023-12-06

Peptides

General transcription factor IIF subunit 1: A
General transcription factor IIF subunit 2: B
DNA-directed RNA polymerase subunit: F
DNA-directed RNA polymerase subunit beta: G
DNA-directed RNA polymerase II subunit RPB3: H
DNA-directed RNA polymerase II subunit RPB4: I
DNA-directed RNA polymerase II subunit E: J
DNA-directed RNA polymerase II subunit F: K
DNA-directed RNA polymerase II subunit RPB7: L
DNA-directed RNA polymerases I, II, and III subunit RPABC3: M
DNA-directed RNA polymerase II subunit RPB9: N
DNA-directed RNA polymerases I, II, and III subunit RPABC5: O
DNA-directed RNA polymerase II subunit RPB11-a: P
RPB12: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
T

F
o

G
p

H
q

I
r

J
s

K
t

L
u

M
v

N
w

O
x

P
y

Q
z

General transcription factor IIF subunit 1

General transcription factor IIF subunit 2

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

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