2C5Q

Crystal structure of yeast YER010Cp

PDB DOI: https://doi.org/10.2210/pdb2C5Q/pdb

Classification: STRUCTURAL GENOMICS,UNKNOWN FUNCTION
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-10-31 Released: 2005-11-14
Deposition Author(s): Leulliot, N., Quevillon-Cheruel, S., Graille, M., Schiltz, M., Blondeau, K., Janin, J., van Tilbeurgh, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.183
R-Value Work: 0.155
R-Value Observed: 0.156

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Yeast Yer010Cp, a Knotable Member of the Rraa Protein Family.

Leulliot, N., Quevillon-Cheruel, S., Graille, M., Schiltz, M., Blondeau, K., Janin, J., Van Tilbeurgh, H.

(2005) Protein Sci 14: 2751

PubMed: 16195557 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1110/ps.051684005
Primary Citation of Related Structures:
2C5Q

PubMed Abstract:
We present here the structure of Yer010c protein of unknown function, solved by Multiple Anomalous Diffraction and revealing a common fold and oligomerization state with proteins of the regulator of ribonuclease activity A (RraA) family. In Escherichia coli, RraA has been shown to regulate the activity of ribonuclease E by direct interaction. The absence of ribonuclease E in yeast suggests a different function for this family member in this organism. Yer010cp has a few supplementary secondary structure elements and a deep pseudo-knot at the heart of the protein core. A tunnel at the interface between two monomers, lined with conserved charged residues, has unassigned residual electron density and may constitute an active site for a yet unknown activity.

Organizational Affiliation

Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Bâtiment 430, 91405 Orsay, France. Nicolas.leulliot@ibbmc.u-psud.fr

Macromolecule Content

Total Structure Weight: 159.77 kDa
Atom Count: 12,424
Modelled Residue Count: 1,396
Deposited Residue Count: 1,440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RRAA-LIKE PROTEIN YER010C	A, B, C, D, E A, B, C, D, E, F	240	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40011 Go to UniProtKB: P40011
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40011
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth F] SDF format, chain P [auth F] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain S [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F]	G [auth A] H [auth B] I [auth B] J [auth C] K [auth D] G [auth A], H [auth B], I [auth B], J [auth C], K [auth D], L [auth D], M [auth D], N [auth D], O [auth F], P [auth F], Q [auth F], R [auth F], S [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F]