4IFD | pdb_00004ifd

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

PDB DOI: https://doi.org/10.2210/pdb4IFD/pdb
NAKB: 4IFD

Classification: HYDROLASE/RNA
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-12-14 Released: 2013-02-06
Deposition Author(s): Makino, D.L., Conti, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.224 (Depositor), 0.225 (DCC)
R-Value Work:
0.182 (Depositor), 0.186 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.

Makino, D.L., Baumgartner, M., Conti, E.

(2013) Nature 495: 70-75

PubMed: 23376952 Search on PubMed
DOI: https://doi.org/10.1038/nature11870
Primary Citation Related Structures:
4IFD

PubMed Abstract:
The exosome is the major 3'-5' RNA-degradation complex in eukaryotes. The ubiquitous core of the yeast exosome (Exo-10) is formed by nine catalytically inert subunits (Exo-9) and a single active RNase, Rrp44. In the nucleus, the Exo-10 core recruits another nuclease, Rrp6. Here we crystallized an approximately 440-kilodalton complex of Saccharomyces cerevisiae Exo-10 bound to a carboxy-terminal region of Rrp6 and to an RNA duplex with a 3'-overhang of 31 ribonucleotides. The 2.8 Å resolution structure shows how RNA is funnelled into the Exo-9 channel in a single-stranded conformation by an unwinding pore. Rrp44 adopts a closed conformation and captures the RNA 3'-end that exits from the side of Exo-9. Exo-9 subunits bind RNA with sequence-unspecific interactions reminiscent of archaeal exosomes. The substrate binding and channelling mechanisms of 3'-5' RNA degradation complexes are conserved in all kingdoms of life.

Organizational Affiliation

Department of Structural Cell Biology, MPI for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Macromolecule Content

Total Structure Weight: 438.16 kDa
Atom Count: 26,848
Modeled Residue Count: 3,403
Deposited Residue Count: 3,838
Unique protein chains: 11
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP45	A	304	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: D9954.1, RRP45, YDR280W
UniProt
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05636 Go to UniProtKB: Q05636
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05636
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component SKI6	B	248	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ECM20, G7587, RRP41, SKI6, YGR195W
UniProt
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P46948 Go to UniProtKB: P46948
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46948
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP43	C	393	Saccharomyces cerevisiae S288C	Mutation(s): 2 Gene Names: RRP43, YCR035C, YCR35C, YCR522
UniProt
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25359 Go to UniProtKB: P25359
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25359
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP46	D	245	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RRP46, YGR095C
UniProt
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53256 Go to UniProtKB: P53256
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53256
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP42	E	267	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: RRP42, YDL111C
UniProt
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12277 Go to UniProtKB: Q12277
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12277
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component MTR3	F	250	Saccharomyces cerevisiae S288C	Mutation(s): 2 Gene Names: G6676, MTR3, YGR158C
UniProt
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P48240 Go to UniProtKB: P48240
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48240
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP40	G	242	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RRP40, YOL142W
UniProt
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08285 Go to UniProtKB: Q08285
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08285
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP4	H	361	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RRP4, YHR069C
UniProt
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38792 Go to UniProtKB: P38792
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38792
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component CSL4	I	301	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: CSL4, N1154, SKI4, YNL232W
UniProt
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53859 Go to UniProtKB: P53859
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53859
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex exonuclease DIS3	J	1,003	Saccharomyces cerevisiae S288C	Mutation(s): 2 Gene Names: DIS3, O2197, RRP44, YOL021C EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
UniProt
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08162 Go to UniProtKB: Q08162
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08162
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex exonuclease RRP6	K	179	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RRP6, UNC733, YOR001W EC: 3.1.13
UniProt
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12149 Go to UniProtKB: Q12149
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12149
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 12
RNA (45-MER)	L [auth R]	45	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain S [auth G] MOL2 format, chain S [auth G] mmCIF format, chain S [auth G]	S [auth G]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain S [auth G] Interactions & Density Focus chain S [auth G]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain R [auth G] SDF format, chain U [auth H] SDF format, chain V [auth H] SDF format, chain W [auth H] MOL2 format, chain O [auth C] MOL2 format, chain R [auth G] MOL2 format, chain U [auth H] MOL2 format, chain V [auth H] MOL2 format, chain W [auth H] mmCIF format, chain O [auth C] mmCIF format, chain R [auth G] mmCIF format, chain U [auth H] mmCIF format, chain V [auth H] mmCIF format, chain W [auth H]	O [auth C], R [auth G], U [auth H], V [auth H], W [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain R [auth G] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H] Interactions & Density Focus chain O [auth C] Focus chain R [auth G] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain BA [auth J] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain T [auth H] SDF format, chain X [auth I] SDF format, chain Y [auth J] SDF format, chain Z [auth J] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain T [auth H] MOL2 format, chain X [auth I] MOL2 format, chain Y [auth J] MOL2 format, chain Z [auth J] mmCIF format, chain AA [auth J] mmCIF format, chain BA [auth J] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain T [auth H] mmCIF format, chain X [auth I] mmCIF format, chain Y [auth J] mmCIF format, chain Z [auth J]	AA [auth J] BA [auth J] M [auth A] N [auth A] P [auth E] AA [auth J], BA [auth J], M [auth A], N [auth A], P [auth E], Q [auth F], T [auth H], X [auth I], Y [auth J], Z [auth J]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain AA [auth J] Focus chain BA [auth J] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth E] Focus chain Q [auth F] Focus chain T [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth J] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth E] Focus chain Q [auth F] Focus chain T [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth J]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain DA [auth J] MOL2 format, chain DA [auth J] mmCIF format, chain DA [auth J]	DA [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth J] Interactions & Density Focus chain DA [auth J]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth J] MOL2 format, chain CA [auth J] mmCIF format, chain CA [auth J]	CA [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth J] Interactions & Density Focus chain CA [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.224 (Depositor), 0.225 (DCC)
R-Value Work: 0.182 (Depositor), 0.186 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.09	α = 90
b = 107.44	β = 110.63
c = 150.46	γ = 90

Software Package:

Software Name	Purpose
RemDAq	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-02-06

Deposition Author(s):

Makino, D.L.

Conti, E.

Revision History (Full details and data files)

Version 1.0: 2013-02-06
Type: Initial release
Version 1.1: 2013-03-13
Changes: Database references
Version 1.2: 2013-11-13
Changes: Database references
Version 1.3: 2017-11-15
Changes: Refinement description
Version 1.4: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-30
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

4IFD | pdb_00004ifd

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

Literature

Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)