6D6Q

Human nuclear exosome-MTR4 RNA complex - overall reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.

Weick, E.M.Puno, M.R.Januszyk, K.Zinder, J.C.DiMattia, M.A.Lima, C.D.

(2018) Cell 173: 1663


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP45
A
473Homo sapiensMutation(s): 0 
Gene Names: EXOSC9 (PMSCL1)
Find proteins for Q06265 (Homo sapiens)
Go to Gene View: EXOSC9
Go to UniProtKB:  Q06265
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP41
B
249Homo sapiensMutation(s): 0 
Gene Names: EXOSC4 (RRP41, SKI6)
Find proteins for Q9NPD3 (Homo sapiens)
Go to Gene View: EXOSC4
Go to UniProtKB:  Q9NPD3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP43
C
278Homo sapiensMutation(s): 0 
Gene Names: EXOSC8 (OIP2, RRP43)
Find proteins for Q96B26 (Homo sapiens)
Go to Gene View: EXOSC8
Go to UniProtKB:  Q96B26
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP46
D
237Homo sapiensMutation(s): 0 
Gene Names: EXOSC5 (CML28, RRP46)
Find proteins for Q9NQT4 (Homo sapiens)
Go to Gene View: EXOSC5
Go to UniProtKB:  Q9NQT4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP42
E
293Homo sapiensMutation(s): 0 
Gene Names: EXOSC7 (KIAA0116, RRP42)
Find proteins for Q15024 (Homo sapiens)
Go to Gene View: EXOSC7
Go to UniProtKB:  Q15024
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component MTR3
F
272Homo sapiensMutation(s): 0 
Gene Names: EXOSC6 (MTR3)
Find proteins for Q5RKV6 (Homo sapiens)
Go to Gene View: EXOSC6
Go to UniProtKB:  Q5RKV6
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP40
G
277Homo sapiensMutation(s): 0 
Gene Names: EXOSC3 (RRP40)
Find proteins for Q9NQT5 (Homo sapiens)
Go to Gene View: EXOSC3
Go to UniProtKB:  Q9NQT5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component RRP4
H
296Homo sapiensMutation(s): 0 
Gene Names: EXOSC2 (RRP4)
Find proteins for Q13868 (Homo sapiens)
Go to Gene View: EXOSC2
Go to UniProtKB:  Q13868
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Exosome complex component CSL4
I
197Homo sapiensMutation(s): 0 
Gene Names: EXOSC1 (CSL4)
Find proteins for Q9Y3B2 (Homo sapiens)
Go to Gene View: EXOSC1
Go to UniProtKB:  Q9Y3B2
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Exosome component 10
J
761Homo sapiensMutation(s): 1 
Gene Names: EXOSC10 (PMSCL, PMSCL2, RRP6)
EC: 3.1.13.-
Find proteins for Q01780 (Homo sapiens)
Go to Gene View: EXOSC10
Go to UniProtKB:  Q01780
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Exosome complex exonuclease RRP44
K
960Homo sapiensMutation(s): 2 
Gene Names: DIS3 (KIAA1008, RRP44)
EC: 3.1.13.-, 3.1.26.-
Find proteins for Q9Y2L1 (Homo sapiens)
Go to Gene View: DIS3
Go to UniProtKB:  Q9Y2L1
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
M-phase phosphoprotein 6
L
162Homo sapiensMutation(s): 0 
Gene Names: MPHOSPH6 (MPP6)
Find proteins for Q99547 (Homo sapiens)
Go to Gene View: MPHOSPH6
Go to UniProtKB:  Q99547
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Exosome RNA helicase MTR4
M
1045Homo sapiensMutation(s): 0 
Gene Names: MTREX (DOB1, KIAA0052, MTR4, SKIV2L2)
EC: 3.6.4.13
Find proteins for P42285 (Homo sapiens)
Go to UniProtKB:  P42285
Entity ID: 14
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')N16synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
DNA/RNA (62-MER)O62synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
M
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
K
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM118080
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references