7LEZ

Trimeric human Arginase 1 in complex with mAb1 - 2 hArg:2 mAb1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structures of inhibitory antibodies complexed with arginase 1 provide insight into mechanism of action.

Palte, R.L.Juan, V.Gomez-Llorente, Y.Bailly, M.A.Chakravarthy, K.Chen, X.Cipriano, D.Fayadat-Dilman, L.Gathiaka, S.Greb, H.Hall, B.Handa, M.Hsieh, M.Kofman, E.Lin, H.Miller, J.R.Nguyen, N.O'Neil, J.Shaheen, H.Sterner, E.Strickland, C.Sun, A.Taremi, S.Scapin, G.

(2021) Commun Biol 4: 927-927

  • DOI: https://doi.org/10.1038/s42003-021-02444-z
  • Primary Citation of Related Structures:  
    7LEX, 7LEY, 7LEZ, 7LF0, 7LF1, 7LF2

  • PubMed Abstract: 

    Human Arginase 1 (hArg1) is a metalloenzyme that catalyzes the hydrolysis of L-arginine to L-ornithine and urea, and modulates T-cell-mediated immune response. Arginase-targeted therapies have been pursued across several disease areas including immunology, oncology, nervous system dysfunction, and cardiovascular dysfunction and diseases. Currently, all published hArg1 inhibitors are small molecules usually less than 350 Da in size. Here we report the cryo-electron microscopy structures of potent and inhibitory anti-hArg antibodies bound to hArg1 which form distinct macromolecular complexes that are greater than 650 kDa. With local resolutions of 3.5 Å or better we unambiguously mapped epitopes and paratopes for all five antibodies and determined that the antibodies act through orthosteric and allosteric mechanisms. These hArg1:antibody complexes present an alternative mechanism to inhibit hArg1 activity and highlight the ability to utilize antibodies as probes in the discovery and development of peptide and small molecule inhibitors for enzymes in general.


  • Organizational Affiliation

    Department of Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA. rachel.kubiak@merck.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mAb1 heavy chainA [auth D],
L [auth G],
M [auth R],
N [auth Q]
455Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mAb1 light chainB [auth E],
C [auth I],
G [auth P],
H [auth O]
214Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Arginase-1322Homo sapiensMutation(s): 0 
Gene Names: ARG1
EC: 3.5.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P05089 (Homo sapiens)
Explore P05089 
Go to UniProtKB:  P05089
GTEx:  ENSG00000118520 
Entity Groups  
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UniProt GroupP05089
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
O [auth A]
P [auth A]
Q [auth B]
R [auth B]
S [auth C]
O [auth A],
P [auth A],
Q [auth B],
R [auth B],
S [auth C],
T [auth C],
U [auth M],
V [auth M],
W [auth N],
X [auth N],
Y [auth J],
Z [auth J]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC2.0.23

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release