2C39 | pdb_00002c39

RNase PH core of the archaeal exosome in complex with ADP

PDB DOI: https://doi.org/10.2210/pdb2C39/pdb

Classification: HYDROLASE
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-10-05 Released: 2005-11-23
Deposition Author(s): Lorentzen, E., Conti, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.295 (Depositor), 0.283 (DCC)
R-Value Work:
0.274 (Depositor), 0.265 (DCC)
R-Value Observed:
0.275 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural Basis of 3' End RNA Recognition and Exoribonucleolytic Cleavage by an Exosome Rnase Ph Core.

Lorentzen, E., Conti, E.

(2005) Mol Cell 20: 473

PubMed: 16285928 Search on PubMed
DOI: https://doi.org/10.1016/j.molcel.2005.10.020
Primary Citation Related Structures:
2C37, 2C38, 2C39

PubMed Abstract:
The exosome is a macromolecular complex that plays fundamental roles in the biogenesis and turnover of a large number of RNA species. Here we report the crystal structures of the Rrp41-Rrp42 core complex of the S. solfataricus exosome bound to short single-stranded RNAs and to ADP. The RNA binding cleft recognizes four nucleotides in a sequence-unspecific manner, mainly by electrostatic interactions with the phosphate groups. Interactions at the 2' hydroxyls of the sugars provide specificity for RNA over DNA. The structures show both the bound substrate and the cleaved product of the reaction, suggesting a catalytic mechanism for the 3'-5' phosphorolytic activity of the exosome.

Organizational Affiliation

European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Macromolecule Content

Total Structure Weight: 699.21 kDa
Atom Count: 45,814
Modeled Residue Count: 6,022
Deposited Residue Count: 6,276
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE EXOSOME COMPLEX EXONUCLEASE 2	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	275	Saccharolobus solfataricus	Mutation(s): 0 EC: 3.1.13
UniProt
Find proteins for Q9UXC0 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q9UXC0 Go to UniProtKB: Q9UXC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UXC0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1	B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	248	Saccharolobus solfataricus	Mutation(s): 0 EC: 3.1.13
UniProt
Find proteins for Q9UXC2 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q9UXC2 Go to UniProtKB: Q9UXC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UXC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth B] SDF format, chain JA [auth X] SDF format, chain IA [auth V] SDF format, chain HA [auth T] SDF format, chain GA [auth R] SDF format, chain FA [auth P] SDF format, chain EA [auth N] SDF format, chain DA [auth L] SDF format, chain CA [auth J] SDF format, chain BA [auth H] SDF format, chain AA [auth F] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain JA [auth X] MOL2 format, chain IA [auth V] MOL2 format, chain HA [auth T] MOL2 format, chain GA [auth R] MOL2 format, chain FA [auth P] MOL2 format, chain EA [auth N] MOL2 format, chain DA [auth L] MOL2 format, chain CA [auth J] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain JA [auth X] mmCIF format, chain IA [auth V] mmCIF format, chain HA [auth T] mmCIF format, chain GA [auth R] mmCIF format, chain FA [auth P] mmCIF format, chain EA [auth N] mmCIF format, chain DA [auth L] mmCIF format, chain CA [auth J] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth H] CA [auth J] DA [auth L] EA [auth N] AA [auth F], BA [auth H], CA [auth J], DA [auth L], EA [auth N], FA [auth P], GA [auth R], HA [auth T], IA [auth V], JA [auth X], Y [auth B], Z [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth H] Focus chain CA [auth J] Focus chain DA [auth L] Focus chain EA [auth N] Focus chain FA [auth P] Focus chain GA [auth R] Focus chain HA [auth T] Focus chain IA [auth V] Focus chain JA [auth X] Focus chain Y [auth B] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth H] Focus chain CA [auth J] Focus chain DA [auth L] Focus chain EA [auth N] Focus chain FA [auth P] Focus chain GA [auth R] Focus chain HA [auth T] Focus chain IA [auth V] Focus chain JA [auth X] Focus chain Y [auth B] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.295 (Depositor), 0.283 (DCC)
R-Value Work: 0.274 (Depositor), 0.265 (DCC)
R-Value Observed: 0.275 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 206.2	α = 90
b = 214	β = 90
c = 432.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-11-23

Deposition Author(s):

Lorentzen, E.

Conti, E.

Revision History (Full details and data files)

Version 1.0: 2005-11-23
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2025-10-01
Changes: Advisory, Derived calculations, Structure summary