5V6Y

Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer with bound high-affinity and altered selectivity adrenomedullin variant

• PDB DOI: https://doi.org/10.2210/pdb5V6Y/pdb

• Classification: TRANSPORT PROTEIN / MEMBRANE PROTEIN
• Organism(s): Escherichia coli O157:H7, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-03-17 Released: 2018-01-31 
• Deposition Author(s): Pioszak, A., Booe, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 274.19 kDa 
• Atom Count: 17,855 
• Modelled Residue Count: 2,257 
• Deposited Residue Count: 2,440 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor	A, B, C, D	593	Escherichia coli O157:H7, Homo sapiens	Mutation(s): 0  Gene Names: malE, Z5632, ECs5017, RAMP1, CALCRL, CGRPR
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for O60894 (Homo sapiens) Explore O60894  Go to UniProtKB:  O60894
PHAROS:  O60894 GTEx:  ENSG00000132329
Find proteins for Q16602 (Homo sapiens) Explore Q16602  Go to UniProtKB:  Q16602
PHAROS:  Q16602 GTEx:  ENSG00000064989
UniProt Groups	P0AEX9Q16602O60894

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADM	E, F, G, H	17	Homo sapiens	Mutation(s): 5
UniProt & NIH Common Fund Data Resources
Find proteins for P35318 (Homo sapiens) Explore P35318  Go to UniProtKB:  P35318
PHAROS:  P35318 GTEx:  ENSG00000148926

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	I, J, K, L	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	I, J, K, L	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.496	α = 90
b = 69.436	β = 99.43
c = 200	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Pioszak, A., Booe, J.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM104251

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2018-02-07
  Changes: Database references
• Version 1.2: 2018-03-14
  Changes: Database references
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 2.0: 2020-03-04
  Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary