2XXA

The Crystal Structure of the Signal Recognition Particle (SRP) in Complex with its Receptor(SR)

PDB DOI: https://doi.org/10.2210/pdb2XXA/pdb
NAKB: 2XXA

Classification: PROTEIN TRANSPORT
Organism(s): Escherichia coli K-12, Deinococcus radiodurans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-11-09 Released: 2011-03-02
Deposition Author(s): Ataide, S.F., Schmitz, N., Shen, K., Ke, A., Shan, S., Doudna, J.A., Ban, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.94 Å
R-Value Free:
0.267 (Depositor), 0.290 (DCC)
R-Value Work:
0.232 (Depositor), 0.260 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of the Signal Recognition Particle in Complex with its Receptor.

Ataide, S.F., Schmitz, N., Shen, K., Ke, A., Shan, S., Doudna, J.A., Ban, N.

(2011) Science 331: 881

PubMed: 21330537 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.1196473
Primary Citation of Related Structures:
2XXA

PubMed Abstract:
Cotranslational targeting of membrane and secretory proteins is mediated by the universally conserved signal recognition particle (SRP). Together with its receptor (SR), SRP mediates the guanine triphosphate (GTP)-dependent delivery of translating ribosomes bearing signal sequences to translocons on the target membrane. Here, we present the crystal structure of the SRP:SR complex at 3.9 angstrom resolution and biochemical data revealing that the activated SRP:SR guanine triphosphatase (GTPase) complex binds the distal end of the SRP hairpin RNA where GTP hydrolysis is stimulated. Combined with previous findings, these results suggest that the SRP:SR GTPase complex initially assembles at the tetraloop end of the SRP RNA and then relocalizes to the opposite end of the RNA. This rearrangement provides a mechanism for coupling GTP hydrolysis to the handover of cargo to the translocon.

Organizational Affiliation

Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zurich (ETH Zurich), Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 232.07 kDa
Atom Count: 15,090
Modelled Residue Count: 1,594
Deposited Residue Count: 1,682
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIGNAL RECOGNITION PARTICLE PROTEIN	A, C	433	Escherichia coli K-12	Mutation(s): 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AGD7
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SRP RECEPTOR FTSY	B, D	302	Escherichia coli K-12	Mutation(s): 0 EC: 3.6.5.4
UniProt
Find proteins for P10121 (Escherichia coli (strain K12)) Explore P10121 Go to UniProtKB: P10121
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10121
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 3
Molecule	Chains	Length	Organism	Image
4.5S RNA	E [auth F], F [auth G]	106	Deinococcus radiodurans
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCP Query on GCP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	G [auth A], I [auth B], K [auth C], M [auth D]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ PHBDHXOBFUBCJD-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	H [auth A], J [auth B], L [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.94 Å
R-Value Free: 0.267 (Depositor), 0.290 (DCC)
R-Value Work: 0.232 (Depositor), 0.260 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.1	α = 90
b = 131.04	β = 90
c = 266.04	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-02
Type: Initial release
Version 1.1: 2015-05-20
Changes: Other, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2015-06-03
Changes: Derived calculations
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description