2YX8

Crystal structure of the extracellular domain of human RAMP1

• PDB DOI: https://doi.org/10.2210/pdb2YX8/pdb

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


• Deposited: 2007-04-24 Released: 2008-04-29 
• Deposition Author(s): Kusano, S., Kukimoto-Niino, M., Shirouzu, M., Shindo, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.281 
• R-Value Work: 0.221 

Literature

Crystal structure of the human receptor activity-modifying protein 1 extracellular domain.

Kusano, S., Kukimoto-Niino, M., Akasaka, R., Toyama, M., Terada, T., Shirouzu, M., Shindo, T., Yokoyama, S.

(2008) Protein Sci 17: 1907-1914

• PubMed: 18725456 
• DOI: https://doi.org/10.1110/ps.036012.108
• Primary Citation of Related Structures:  
  2YX8


• PubMed Abstract: 
  

  Receptor activity-modifying protein (RAMP) 1 forms a heterodimer with calcitonin receptor-like receptor (CRLR) and regulates its transport to the cell surface. The CRLR.RAMP1 heterodimer functions as a specific receptor for calcitonin gene-related peptide (CGRP). Here, we report the crystal structure of the human RAMP1 extracellular domain. The RAMP1 structure is a three-helix bundle that is stabilized by three disulfide bonds. The RAMP1 residues important for cell-surface expression of the CRLR.RAMP1 heterodimer are clustered to form a hydrophobic patch on the molecular surface. The hydrophobic patch is located near the tryptophan residue essential for binding of the CGRP antagonist, BIBN4096BS. These results suggest that the hydrophobic patch participates in the interaction with CRLR and the formation of the ligand-binding pocket when it forms the CRLR.RAMP1 heterodimer.

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Organizational Affiliation: 

RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.78 kDa 
• Atom Count: 683 
• Modelled Residue Count: 81 
• Deposited Residue Count: 93 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor activity-modifying protein 1	A	93	Homo sapiens	Mutation(s): 0  Gene Names: RAMP1
UniProt & NIH Common Fund Data Resources
Find proteins for O60894 (Homo sapiens) Explore O60894  Go to UniProtKB:  O60894
PHAROS:  O60894 GTEx:  ENSG00000132329

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.281 
• R-Value Work: 0.221 
• Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.097	α = 90
b = 43.097	β = 90
c = 82.992	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Kusano, S., Kukimoto-Niino, M., Shirouzu, M., Shindo, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance