Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.95 kDa 
• Atom Count: 1790 
• Modelled Residue Count: 216 
• Deposited Residue Count: 218 
• Unique protein chains: 1

1QB2

CRYSTAL STRUCTURE OF THE CONSERVED SUBDOMAIN OF HUMAN PROTEIN SRP54M AT 2.1A RESOLUTION: EVIDENCE FOR THE MECHANISM OF SIGNAL PEPTIDE BINDING

• DOI: 10.2210/pdb1QB2/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-04-29 Released: 1999-10-20 
• Deposition Author(s): Clemons Jr., W.M., Gowda, K., Black, S.D., Zwieb, C., Ramakrishnan, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.318 
• R-Value Work: 0.245 

Literature

Crystal structure of the conserved subdomain of human protein SRP54M at 2.1 A resolution: evidence for the mechanism of signal peptide binding.

Clemons Jr., W.M., Gowda, K., Black, S.D., Zwieb, C., Ramakrishnan, V.

(1999) J Mol Biol 292: 697-705

• PubMed: 10497032 
• DOI: 10.1006/jmbi.1999.3090
• Primary Citation of Related Structures:  
  1QB2


• PubMed Abstract: 
  

Protein SRP54 is an integral part of the mammalian signal recognition particle (SRP), a cytosolic ribonucleoprotein complex which associates with ribosomes and serves to recognize, bind, and transport proteins destined for the membrane or secretion. The methionine-rich M-domain of protein SRP54 (SRP54M) binds the SRP RNA and the signal peptide as the nascent protein emerges from the ribosome. A focal point of this critical cellular function is the detailed understanding of how different hydrophobic signal peptides are recognized efficiently and transported specifically, despite considerable variation in sequence. We have solved the crystal structure of a conserved functional subdomain of the human SRP54 protein (hSRP54m) at 2.1 A resolution showing a predominantly alpha helical protein with a large fraction of the structure available for binding. RNA binding is predicted to occur in the vicinity of helices 4 to 6. The N-terminal helix extends significantly from the core of the structure into a large but constricted hydrophobic groove of an adjacent molecule, thus revealing molecular details of possible interactions between alpha helical signal peptides and human SRP54.

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Organizational Affiliation: 

Department of Biochemistry, The University of Utah, School of Medicine, 50 North Medical Drive, Salt Lake City, UT 84132, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN SIGNAL RECOGNITION PARTICLE 54 KD PROTEIN	A, B	109	Homo sapiens	Mutation(s): 0  Gene Names: SRP54 EC: 3.6.5
Find proteins for P61011 (Homo sapiens) Explore P61011  Go to UniProtKB:  P61011
NIH Common Fund Data Resources
PHAROS:  P61011 GTEx:  ENSG00000100883

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.318 
• R-Value Work: 0.245 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.91	α = 90
b = 61.34	β = 90
c = 129.22	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
X-PLOR	refinement
MADNESS	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-04-29 
• Released Date: 1999-10-20 
Deposition Author(s): Clemons Jr., W.M., Gowda, K., Black, S.D., Zwieb, C., Ramakrishnan, V.

Revision History  

• Version 1.0: 1999-10-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description