1DUL | pdb_00001dul

STRUCTURE OF THE RIBONUCLEOPROTEIN CORE OF THE E. COLI SIGNAL RECOGNITION PARTICLE

PDB DOI: https://doi.org/10.2210/pdb1DUL/pdb
NAKB: 1DUL

Classification: SIGNALING PROTEIN/RNA
Organism(s): synthetic construct, Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2000-01-17 Released: 2000-02-28
Deposition Author(s): Batey, R.T., Rambo, R.P., Lucast, L., Rha, B., Doudna, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.221 (Depositor)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of the ribonucleoprotein core of the signal recognition particle.

Batey, R.T., Rambo, R.P., Lucast, L., Rha, B., Doudna, J.A.

(2000) Science 287: 1232-1239

PubMed: 10678824 Search on PubMed
DOI: https://doi.org/10.1126/science.287.5456.1232
Primary Citation Related Structures:
1DUL

PubMed Abstract:
The signal recognition particle (SRP), a protein-RNA complex conserved in all three kingdoms of life, recognizes and transports specific proteins to cellular membranes for insertion or secretion. We describe here the 1.8 angstrom crystal structure of the universal core of the SRP, revealing protein recognition of a distorted RNA minor groove. Nucleotide analog interference mapping demonstrates the biological importance of observed interactions, and genetic results show that this core is functional in vivo. The structure explains why the conserved residues in the protein and RNA are required for SRP assembly and defines a signal sequence recognition surface composed of both protein and RNA.

Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA.

Macromolecule Content

Total Structure Weight: 28.84 kDa
Atom Count: 1,892
Modeled Residue Count: 118
Deposited Residue Count: 154
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal recognition particle protein	B [auth A]	105	Escherichia coli	Mutation(s): 1 Gene Names: ffh EC: 3.6.5.4
UniProt
Find proteins for P0AGD7 (Escherichia coli (strain K12)) Explore P0AGD7 Go to UniProtKB: P0AGD7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AGD7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
4.5 S RNA DOMAIN IV	A [auth B]	49	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	C [auth B], D [auth B], E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	F [auth B], G [auth B], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	B [auth A]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.221 (Depositor)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.199 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.567	α = 90
b = 78.291	β = 96.14
c = 32.849	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-02-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-02-28
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2019-11-06
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2020-10-14
Changes: Derived calculations, Structure summary
Version 2.2: 2024-11-20
Changes: Data collection, Database references, Structure summary