6UMH | pdb_00006umh

Crystal structure of erenumab Fab-a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.224 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6UMH

This is version 1.2 of the entry. See complete history

Literature

Molecular Insight into Recognition of the CGRPR Complex by Migraine Prevention Therapy Aimovig (Erenumab).

Garces, F.Mohr, C.Zhang, L.Huang, C.S.Chen, Q.King, C.Xu, C.Wang, Z.

(2020) Cell Rep 30: 1714

  • DOI: https://doi.org/10.1016/j.celrep.2020.01.029
  • Primary Citation Related Structures: 
    6UMG, 6UMH, 6UMI, 6UMJ

  • PubMed Abstract: 

    Calcitonin-gene-related peptide (CGRP) plays a key role in migraine pathophysiology. Aimovig (erenumab; erenumab-aooe in the United States) is the only US Food and Drug Administration (FDA)-approved monoclonal antibody (mAb) therapy against the CGRP receptor (CGRPR) for the prevention of migraine. Aimovig is also the first FDA-approved mAb against a G-protein-coupled receptor (GPCR). Here, we report the architecture and functional attributes of erenumab critical for its potent antagonism against CGRPR. The crystal structure of erenumab in complex with CGRPR reveals a direct ligand-blocking mechanism, enabled by a remarkable 21-residue-long complementary determining region (CDR)-H3 loop, which adopts a tyrosine-rich helix-turn tip and projects into the deep interface of the calcitonin receptor-like receptor (CLR) and RAMP1 subunits of CGRPR. Furthermore, erenumab engages with residues specific to CLR and RAMP1, providing the molecular basis for its exquisite selectivity. Such structural insights reveal the drug action mechanism of erenumab and shed light on developing antibody therapeutics targeting GPCRs.


  • Organizational Affiliation
    • Department of Therapeutic Discovery, Amgen Research, Amgen, Thousand Oaks, CA 91320, USA.

Macromolecule Content 

  • Total Structure Weight: 98.26 kDa 
  • Atom Count: 7,055 
  • Modeled Residue Count: 891 
  • Deposited Residue Count: 906 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
erenumab Fab heavy chain, IgG1A [auth H],
C [auth h]
237Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
erenumab Fab light chain, IgG1B [auth L],
D [auth l]
216Homo sapiensMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD

Query on MPD



Download:Ideal Coordinates CCD File
I [auth L],
S [auth l]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
G [auth H]
H
K [auth L]
L
M [auth L]
G [auth H],
H,
K [auth L],
L,
M [auth L],
N [auth L],
Q [auth h],
R [auth h],
U [auth l],
V [auth l]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
PDO

Query on PDO



Download:Ideal Coordinates CCD File
E [auth H]
F [auth H]
J [auth L]
O [auth h]
P [auth h]
E [auth H],
F [auth H],
J [auth L],
O [auth h],
P [auth h],
T [auth l]
1,3-PROPANDIOL
C3 H8 O2
YPFDHNVEDLHUCE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.273α = 90
b = 55.913β = 110.93
c = 170.086γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHASERphasing
MOLREPphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2020-02-12 
  • Deposition Author(s): Mohr, C.

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Structure summary