SMTL ID : 4c3i.1

Structure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

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

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: K.1100, K.1103, Y.1104, Y.1120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.1120 Salt bridges: A:K.1100, A:K.1103 SO4.2: 2 residues within 4Å: Chain A: P.499, P.609 No protein-ligand interaction detected (PLIP) SO4.11: 3 residues within 4Å: Chain K: E.67, D.69, N.99 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.99

7 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.102, C.105, C.233, C.236 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.102, A:C.105, A:C.233, A:C.236 ZN.4: 4 residues within 4Å: Chain A: C.62, C.65, C.72, H.75 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.62, A:C.65, A:C.72, A:H.75 ZN.6: 4 residues within 4Å: Chain B: C.1104, C.1107, C.1128, C.1131 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1104, B:C.1107, B:C.1128, B:C.1131 ZN.8: 4 residues within 4Å: Chain I: C.10, C.13, C.30, C.33 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.13, I:C.30 ZN.9: 4 residues within 4Å: Chain I: C.86, Q.88, C.89, C.114 No protein-ligand interaction detected (PLIP) ZN.10: 4 residues within 4Å: Chain J: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.45, J:C.46 ZN.12: 5 residues within 4Å: Chain L: C.31, C.34, S.36, C.48, C.51 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:C.34, L:C.48, L:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.627 Chain B: D.784, D.785 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.784

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 8 residues within 4Å: Chain A: V.7, G.8, S.9, E.10 Chain G: Y.46, K.106, T.108, F.115 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: G:Y.46, G:T.108, G:F.115, A:E.10 Hydrogen bonds: G:Y.46, G:Y.46, G:K.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez-Tornero, C. et al., Crystal Structure of the 14-Subunit RNA Polymerase I. Nature (2013)

Release Date

2013-10-23

Peptides

DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190: A
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135: B
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1: C
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14: D
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1: E
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2: F
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43: G
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3: H
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12: I
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5: J
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2: K
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4: L
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49: M
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34: N

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

M
M

N
N

DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190

DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135

DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1

DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2

DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3

DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5

DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2

DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4

DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49

DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34

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