Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - ABCDEFGHIJKL Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer -A6BCDEFG 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 639178.81 
• Atom Count: 31639 
• Residue Count: 5578 
• Unique protein chains: 13
• Unique nucleic acid chains: 1
• Unique hybrid chains: 1

6D6R

Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction

• DOI: 10.2210/pdb6D6R/pdb
• EMDataResource: EMD-7809

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2018-04-22 Released: 2018-06-20 
• Deposition Author(s): Weick, E.-M., Lima, C.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; Howard Hughes Medical Institute 

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Experimental Data Snapshot

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

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

• PubMed: 29906447 
• Primary Citation of Related Structures:  
  6D6Q

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Exosome complex component RRP45	A	473	Homo sapiens	Mutation(s): 0  Gene Names: EXOSC9 (PMSCL1)
Find proteins for Q06265 (Homo sapiens) Go to Gene View: EXOSC9 Go to UniProtKB:  Q06265

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Exosome complex component RRP41	B	249	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Exosome complex component RRP43	C	278	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Exosome complex component RRP46	D	237	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Exosome complex component RRP42	E	293	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Exosome complex component MTR3	F	272	Homo sapiens	Mutation(s): 0  Gene Names: EXOSC6 (MTR3)
Find proteins for Q5RKV6 (Homo sapiens) Go to Gene View: EXOSC6 Go to UniProtKB:  Q5RKV6

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Exosome complex component RRP40	G	277	Homo sapiens	Mutation(s): 0  Gene Names: EXOSC3 (RRP40)
Find proteins for Q9NQT5 (Homo sapiens) Go to Gene View: EXOSC3 Go to UniProtKB:  Q9NQT5

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
Exosome complex component RRP4	H	296	Homo sapiens	Mutation(s): 0  Gene Names: EXOSC2 (RRP4)
Find proteins for Q13868 (Homo sapiens) Go to Gene View: EXOSC2 Go to UniProtKB:  Q13868

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
Exosome complex component CSL4	I	197	Homo sapiens	Mutation(s): 0  Gene Names: EXOSC1 (CSL4)
Find proteins for Q9Y3B2 (Homo sapiens) Go to Gene View: EXOSC1 Go to UniProtKB:  Q9Y3B2

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
Exosome component 10	J	761	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Exosome complex exonuclease RRP44	K	960	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
M-phase phosphoprotein 6	L	162	Homo sapiens	Mutation(s): 0  Gene Names: MPHOSPH6 (MPP6)
Find proteins for Q99547 (Homo sapiens) Go to Gene View: MPHOSPH6 Go to UniProtKB:  Q99547

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
Exosome RNA helicase MTR4	M	1045	Homo sapiens	Mutation(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
Molecule	Chains	Length	Organism
RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')	N	16	synthetic construct

Entity ID: 15
Molecule	Chains	Length	Organism
DNA/RNA (62-MER)	O	62	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	K	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ANP	M	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	K	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-04-22 
• Released Date: 2018-06-20 
• Deposition Author(s): Weick, E.-M., Lima, C.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	GM118080
Howard Hughes Medical Institute	United States	--

Revision History 

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