SMTL ID : 8oki.1

Cryo-EM structure of Pyrococcus furiosus transcription elongation complex bound to Spt4/5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x G- A- C- C- A- G- G- C- G: RNA(Non-covalent)

G-A-C-C-A-G-G-C-G.1: 25 residues within 4Å: Chain A: I.229, R.426, Q.427, P.428, D.461, D.463, D.465 Chain B: T.418, G.419, P.469, Q.672, K.875, K.883, Q.1008 Chain L: C.13, G.14, C.15, C.16, T.17, G.18, G.19, T.20, C.21, A.22 Ligands: MG.4 Protein-ligand interaction information (PLIP) not available

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.60, C.63, C.70, H.73 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.60, A:C.63, A:C.70, A:H.73 ZN.3: 4 residues within 4Å: Chain A: C.100, C.103, C.147, C.150 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.100, A:C.103, A:C.147, A:C.150 ZN.5: 4 residues within 4Å: Chain B: C.1059, C.1062, C.1077, C.1080 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1059, B:C.1062, B:C.1077, B:C.1080 ZN.6: 4 residues within 4Å: Chain G: C.6, C.9, C.18, C.21 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.6, G:C.9, G:C.18, G:C.21 ZN.7: 4 residues within 4Å: Chain J: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.44, J:C.45 ZN.8: 4 residues within 4Å: Chain K: C.8, C.11, C.27, C.30 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.8, K:C.11, K:C.27, K:C.30

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.461, D.463, D.465 Ligands: G-A-C-C-A-G-G-C-G.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.461, A:D.461, A:D.463, A:D.465

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tarau, D.M. et al., Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment. Nucleic Acids Res. (2024)

Release Date

2024-04-24

Peptides

DNA-directed RNA polymerase subunit Rpo1N: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase subunit Rpo1C: C
DNA-directed RNA polymerase subunit Rpo3: D
Transcription elongation factor Spt5: E
DNA-directed RNA polymerase subunit Rpo5: F
Transcription elongation factor Spt4: G
DNA-directed RNA polymerase subunit Rpo6: H
DNA-directed RNA polymerase subunit Rpo11: I
DNA-directed RNA polymerase subunit Rpo10: J
DNA-directed RNA polymerase subunit Rpo12: K
DNA-directed RNA polymerase subunit Rpo7: N
DNA-directed RNA polymerase subunit Rpo4: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
G

F
H

G
I

H
K

I
L

J
N

K
P

N
E

O
F

DNA-directed RNA polymerase subunit Rpo1N

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit Rpo1C

DNA-directed RNA polymerase subunit Rpo3

Transcription elongation factor Spt5

DNA-directed RNA polymerase subunit Rpo5

Transcription elongation factor Spt4

DNA-directed RNA polymerase subunit Rpo6

DNA-directed RNA polymerase subunit Rpo11

DNA-directed RNA polymerase subunit Rpo10

DNA-directed RNA polymerase subunit Rpo12

DNA-directed RNA polymerase subunit Rpo7

DNA-directed RNA polymerase subunit Rpo4

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