6ZHO

Crystal structure of a CGRP receptor ectodomain heterodimer with bound high affinity inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6ZHO/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-06-23 Released: 2020-07-15 
• Deposition Author(s): Southall, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.214 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 67.85 kDa 
• Atom Count: 5,282 
• Modelled Residue Count: 577 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor	A	594	Escherichia coli K-12, Homo sapiens	Mutation(s): 0  Gene Names: malE, b4034, JW3994, 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

Oligosaccharides

Help

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QLQ (Subject of Investigation/LOI)	C [auth A]	~{N}-[(2~{R})-3-(7-methyl-2~{H}-indazol-5-yl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-piperidin-4-yl-1-(4-pyridin-4-ylpiperazin-1-yl)propan-2-yl]amino]propan-2-yl]-2-oxidanylidene-spiro[1~{H}-pyrido[2,3-d][1,3]oxazine-4,4'-piperidine]-1'-carboxamide C40 H49 N11 O5 LIPVCPUZWNTQHV-SAIUNTKASA-N
PG4	D [auth A], E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.214 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.725	α = 90
b = 76.961	β = 90
c = 97.028	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Southall, S.M.

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2020-07-22
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2020-08-05
  Changes: Database references, Structure summary
• Version 3.0: 2021-08-18
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.1: 2021-08-25
  Changes: Advisory, Database references, Structure summary
• Version 3.2: 2024-01-24
  Changes: Data collection, Refinement description