SMTL ID : 7znj.1

Structure of an ALYREF-exon junction complex hexamer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-6-mer

Ligands

6 x U- U- U- U- U- U: RNA(Non-covalent)

U-U-U-U-U-U.1: 23 residues within 4Å: Chain A: P.92, T.93, R.94, G.120, G.121, V.124, T.141, G.143, R.144, D.147, R.150, F.175, Q.178, N.263, T.264, K.265, H.286, G.287, R.294, T.312, D.313, V.314, N.334 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.2: 23 residues within 4Å: Chain E: P.92, T.93, R.94, G.120, G.121, V.124, T.141, G.143, R.144, D.147, R.150, F.175, Q.178, N.263, T.264, K.265, H.286, G.287, R.294, T.312, D.313, V.314, N.334 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.3: 22 residues within 4Å: Chain I: P.92, T.93, R.94, G.120, G.121, T.141, G.143, R.144, D.147, R.150, F.175, Q.178, N.263, T.264, K.265, H.286, G.287, R.294, T.312, D.313, V.314, N.334 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.4: 22 residues within 4Å: Chain M: P.92, R.94, G.120, G.121, V.124, T.141, G.143, R.144, D.147, R.150, F.175, Q.178, N.263, T.264, K.265, H.286, G.287, R.294, T.312, D.313, V.314, N.334 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.5: 22 residues within 4Å: Chain Q: P.92, T.93, R.94, G.120, G.121, T.141, G.143, R.144, D.147, R.150, F.175, Q.178, N.263, T.264, K.265, H.286, G.287, R.294, T.312, D.313, V.314, N.334 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.6: 23 residues within 4Å: Chain U: P.92, T.93, R.94, G.120, G.121, V.124, T.141, G.143, R.144, D.147, R.150, F.175, Q.178, N.263, T.264, K.265, H.286, G.287, R.294, T.312, D.313, V.314, N.334 Protein-ligand interaction information (PLIP) not available

6 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: T.67, D.165 Ligands: ANP.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.67 MG.9: 3 residues within 4Å: Chain E: T.67, D.165 Ligands: ANP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.67 MG.11: 3 residues within 4Å: Chain I: T.67, D.165 Ligands: ANP.12 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.67 MG.13: 3 residues within 4Å: Chain M: T.67, D.165 Ligands: ANP.14 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.67 MG.15: 3 residues within 4Å: Chain Q: T.67, D.165 Ligands: ANP.16 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.67 MG.17: 3 residues within 4Å: Chain U: T.67, D.165 Ligands: ANP.18 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:T.67

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.8: 18 residues within 4Å: Chain A: F.36, K.38, Q.43, Q.61, S.62, G.63, T.64, G.65, K.66, T.67, A.68, E.166, G.318, D.320, R.345, R.348, Y.349 Ligands: MG.7 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:K.38, A:Q.43, A:G.63, A:T.64, A:T.64, A:G.65, A:K.66, A:K.66, A:T.67, A:T.67, A:T.67, A:A.68, A:G.318, A:D.320, A:D.320, A:R.345, A:R.345, A:R.348, A:R.348, A:Y.349 Salt bridges: A:R.348 pi-Stacking: A:F.36, A:F.36, A:Y.349, A:Y.349 ANP.10: 18 residues within 4Å: Chain E: F.36, K.38, Q.43, Q.61, S.62, G.63, T.64, G.65, K.66, T.67, A.68, E.166, G.318, D.320, R.345, R.348, Y.349 Ligands: MG.9 22 PLIP interactions: 22 interactions with chain E Hydrogen bonds: E:K.38, E:Q.43, E:G.63, E:T.64, E:G.65, E:K.66, E:K.66, E:T.67, E:T.67, E:T.67, E:A.68, E:G.318, E:D.320, E:R.345, E:R.345, E:R.348, E:R.348 Salt bridges: E:R.348 pi-Stacking: E:F.36, E:F.36, E:Y.349, E:Y.349 ANP.12: 18 residues within 4Å: Chain I: F.36, K.38, Q.43, Q.61, S.62, G.63, T.64, G.65, K.66, T.67, A.68, E.166, G.318, D.320, R.345, R.348, Y.349 Ligands: MG.11 23 PLIP interactions: 23 interactions with chain I Hydrogen bonds: I:K.38, I:Q.43, I:G.63, I:T.64, I:T.64, I:G.65, I:K.66, I:K.66, I:T.67, I:T.67, I:T.67, I:A.68, I:G.318, I:D.320, I:R.345, I:R.345, I:R.348, I:R.348 Salt bridges: I:R.348 pi-Stacking: I:F.36, I:F.36, I:Y.349, I:Y.349 ANP.14: 18 residues within 4Å: Chain M: F.36, K.38, Q.43, Q.61, S.62, G.63, T.64, G.65, K.66, T.67, A.68, E.166, G.318, D.320, R.345, R.348, Y.349 Ligands: MG.13 22 PLIP interactions: 22 interactions with chain M Hydrogen bonds: M:K.38, M:Q.43, M:G.63, M:T.64, M:G.65, M:K.66, M:K.66, M:T.67, M:T.67, M:T.67, M:A.68, M:G.318, M:D.320, M:R.345, M:R.345, M:R.348, M:R.348 Salt bridges: M:R.348 pi-Stacking: M:F.36, M:F.36, M:Y.349, M:Y.349 ANP.16: 18 residues within 4Å: Chain Q: F.36, K.38, Q.43, Q.61, S.62, G.63, T.64, G.65, K.66, T.67, A.68, E.166, G.318, D.320, R.345, R.348, Y.349 Ligands: MG.15 24 PLIP interactions: 24 interactions with chain Q Hydrogen bonds: Q:K.38, Q:Q.43, Q:G.63, Q:T.64, Q:T.64, Q:G.65, Q:K.66, Q:K.66, Q:T.67, Q:T.67, Q:T.67, Q:A.68, Q:G.318, Q:D.320, Q:R.345, Q:R.345, Q:R.348, Q:R.348, Q:Y.349 Salt bridges: Q:R.348 pi-Stacking: Q:F.36, Q:F.36, Q:Y.349, Q:Y.349 ANP.18: 18 residues within 4Å: Chain U: F.36, K.38, Q.43, Q.61, S.62, G.63, T.64, G.65, K.66, T.67, A.68, E.166, G.318, D.320, R.345, R.348, Y.349 Ligands: MG.17 22 PLIP interactions: 22 interactions with chain U Hydrogen bonds: U:K.38, U:Q.43, U:G.63, U:T.64, U:G.65, U:K.66, U:K.66, U:T.67, U:T.67, U:T.67, U:A.68, U:G.318, U:D.320, U:R.345, U:R.345, U:R.348, U:R.348 Salt bridges: U:R.348 pi-Stacking: U:F.36, U:F.36, U:Y.349, U:Y.349

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pacheco-Fiallos, B. et al., mRNA recognition and packaging by the human transcription-export complex. Nature (2023)

Release Date

2023-04-12

Peptides

Eukaryotic initiation factor 4A-III, N-terminally processed: AEIMQU
Protein mago nashi homolog: BFJNRV
RNA-binding protein 8A: CGKOSW
Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
a

I
F

M
f

Q
K

U
k

B
B

F
b

J
G

N
g

R
L

V
l

C
C

G
c

K
H

O
h

S
M

W
m

D
D

H
d

L
I

P
i

T
N

X
n

Eukaryotic initiation factor 4A-III, N-terminally processed

Protein mago nashi homolog

RNA-binding protein 8A

Maltose/maltodextrin-binding periplasmic protein,THO complex subunit 4

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