2C37 | pdb_00002c37

RNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH U8 RNA

PDB DOI: https://doi.org/10.2210/pdb2C37/pdb

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

Deposited: 2005-10-04 Released: 2005-11-23
Deposition Author(s): Lorentzen, E., Conti, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.282 (Depositor), 0.285 (DCC)
R-Value Work:
0.266 (Depositor), 0.272 (DCC)
R-Value Observed:
0.267 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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: 702.87 kDa
Atom Count: 46,570
Modeled Residue Count: 6,044
Deposited Residue Count: 6,276
Unique protein chains: 2

Macromolecules

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| 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

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| 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P Query on U5P Download:Ideal Coordinates CCD File SDF format, chain AB [auth U] SDF format, chain BB [auth U] SDF format, chain CB [auth U] SDF format, chain FA [auth E] SDF format, chain IA [auth F] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain QA [auth J] SDF format, chain SA [auth M] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain VA [auth N] SDF format, chain TA [auth M] SDF format, chain OA [auth I] SDF format, chain NA [auth I] SDF format, chain MA [auth H] SDF format, chain KB [auth X] SDF format, chain IB [auth W] SDF format, chain HB [auth W] SDF format, chain GB [auth W] SDF format, chain GA [auth E] SDF format, chain EB [auth V] SDF format, chain EA [auth E] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain AB [auth U] MOL2 format, chain BB [auth U] MOL2 format, chain CB [auth U] MOL2 format, chain FA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain QA [auth J] MOL2 format, chain SA [auth M] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain VA [auth N] MOL2 format, chain TA [auth M] MOL2 format, chain OA [auth I] MOL2 format, chain NA [auth I] MOL2 format, chain MA [auth H] MOL2 format, chain KB [auth X] MOL2 format, chain IB [auth W] MOL2 format, chain HB [auth W] MOL2 format, chain GB [auth W] MOL2 format, chain GA [auth E] MOL2 format, chain EB [auth V] MOL2 format, chain EA [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain AB [auth U] mmCIF format, chain BB [auth U] mmCIF format, chain CB [auth U] mmCIF format, chain FA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain QA [auth J] mmCIF format, chain SA [auth M] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain VA [auth N] mmCIF format, chain TA [auth M] mmCIF format, chain OA [auth I] mmCIF format, chain NA [auth I] mmCIF format, chain MA [auth H] mmCIF format, chain KB [auth X] mmCIF format, chain IB [auth W] mmCIF format, chain HB [auth W] mmCIF format, chain GB [auth W] mmCIF format, chain GA [auth E] mmCIF format, chain EB [auth V] mmCIF format, chain EA [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	AB [auth U] BA [auth B] BB [auth U] CA [auth B] CB [auth U] AB [auth U], BA [auth B], BB [auth U], CA [auth B], CB [auth U], EA [auth E], EB [auth V], FA [auth E], GA [auth E], GB [auth W], HB [auth W], IA [auth F], IB [auth W], JA [auth G], KA [auth G], KB [auth X], MA [auth H], NA [auth I], OA [auth I], QA [auth J], SA [auth M], TA [auth M], VA [auth N], Y [auth A], Z [auth A]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain AB [auth U] Focus chain BA [auth B] Focus chain BB [auth U] Focus chain CA [auth B] Focus chain CB [auth U] Focus chain EA [auth E] Focus chain EB [auth V] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain GB [auth W] Focus chain HB [auth W] Focus chain IA [auth F] Focus chain IB [auth W] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain KB [auth X] Focus chain MA [auth H] Focus chain NA [auth I] Focus chain OA [auth I] Focus chain QA [auth J] Focus chain SA [auth M] Focus chain TA [auth M] Focus chain VA [auth N] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AB [auth U] Focus chain BA [auth B] Focus chain BB [auth U] Focus chain CA [auth B] Focus chain CB [auth U] Focus chain EA [auth E] Focus chain EB [auth V] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain GB [auth W] Focus chain HB [auth W] Focus chain IA [auth F] Focus chain IB [auth W] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain KB [auth X] Focus chain MA [auth H] Focus chain NA [auth I] Focus chain OA [auth I] Focus chain QA [auth J] Focus chain SA [auth M] Focus chain TA [auth M] Focus chain VA [auth N] Focus chain Y [auth A] Focus chain Z [auth A]
RP5 Query on RP5 Download:Ideal Coordinates CCD File SDF format, chain WA [auth N] MOL2 format, chain WA [auth N] mmCIF format, chain WA [auth N]	WA [auth N]	5-O-phosphono-beta-D-ribofuranose C₅ H₁₁ O₈ P KTVPXOYAKDPRHY-TXICZTDVSA-N		Interactions Focus chain WA [auth N] Interactions & Density Focus chain WA [auth N]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain PA [auth J] SDF format, chain UA [auth N] SDF format, chain ZA [auth T] SDF format, chain YA [auth R] SDF format, chain XA [auth P] SDF format, chain RA [auth L] SDF format, chain LA [auth H] SDF format, chain JB [auth X] SDF format, chain HA [auth F] SDF format, chain DB [auth V] SDF format, chain DA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain UA [auth N] MOL2 format, chain ZA [auth T] MOL2 format, chain YA [auth R] MOL2 format, chain XA [auth P] MOL2 format, chain RA [auth L] MOL2 format, chain LA [auth H] MOL2 format, chain JB [auth X] MOL2 format, chain HA [auth F] MOL2 format, chain DB [auth V] MOL2 format, chain DA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain PA [auth J] mmCIF format, chain UA [auth N] mmCIF format, chain ZA [auth T] mmCIF format, chain YA [auth R] mmCIF format, chain XA [auth P] mmCIF format, chain RA [auth L] mmCIF format, chain LA [auth H] mmCIF format, chain JB [auth X] mmCIF format, chain HA [auth F] mmCIF format, chain DB [auth V] mmCIF format, chain DA [auth D]	AA [auth B] DA [auth D] DB [auth V] HA [auth F] JB [auth X] AA [auth B], DA [auth D], DB [auth V], HA [auth F], JB [auth X], LA [auth H], PA [auth J], RA [auth L], UA [auth N], XA [auth P], YA [auth R], ZA [auth T]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain DA [auth D] Focus chain DB [auth V] Focus chain HA [auth F] Focus chain JB [auth X] Focus chain LA [auth H] Focus chain PA [auth J] Focus chain RA [auth L] Focus chain UA [auth N] Focus chain XA [auth P] Focus chain YA [auth R] Focus chain ZA [auth T] Interactions & Density Focus chain AA [auth B] Focus chain DA [auth D] Focus chain DB [auth V] Focus chain HA [auth F] Focus chain JB [auth X] Focus chain LA [auth H] Focus chain PA [auth J] Focus chain RA [auth L] Focus chain UA [auth N] Focus chain XA [auth P] Focus chain YA [auth R] Focus chain ZA [auth T]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain FB [auth V] MOL2 format, chain FB [auth V] mmCIF format, chain FB [auth V]	FB [auth V]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FB [auth V] Interactions & Density Focus chain FB [auth V]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.282 (Depositor), 0.285 (DCC)
R-Value Work: 0.266 (Depositor), 0.272 (DCC)
R-Value Observed: 0.267 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.02	α = 90
b = 212.94	β = 90
c = 433.09	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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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 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary