7O7N

(h-alpha2M)4 semiactivated I state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures show the mechanistic basis of pan-peptidase inhibition by human alpha 2 -macroglobulin.

Luque, D.Goulas, T.Mata, C.P.Mendes, S.R.Gomis-Ruth, F.X.Caston, J.R.

(2022) Proc Natl Acad Sci U S A 119: e2200102119-e2200102119

  • DOI: https://doi.org/10.1073/pnas.2200102119
  • Primary Citation of Related Structures:  
    7O7L, 7O7M, 7O7N, 7O7O, 7O7P, 7O7Q, 7O7R, 7O7S

  • PubMed Abstract: 

    Human α2-macroglobulin (hα2M) is a multidomain protein with a plethora of essential functions, including transport of signaling molecules and endopeptidase inhibition in innate immunity. Here, we dissected the molecular mechanism of the inhibitory function of the ∼720-kDa hα2M tetramer through eight cryo–electron microscopy (cryo-EM) structures of complexes from human plasma. In the native complex, the hα2M subunits are organized in two flexible modules in expanded conformation, which enclose a highly porous cavity in which the proteolytic activity of circulating plasma proteins is tested. Cleavage of bait regions exposed inside the cavity triggers rearrangement to a compact conformation, which closes openings and entraps the prey proteinase. After the expanded-to-compact transition, which occurs independently in the four subunits, the reactive thioester bond triggers covalent linking of the proteinase, and the receptor-binding domain is exposed on the tetramer surface for receptor-mediated clearance from circulation. These results depict the molecular mechanism of a unique suicidal inhibitory trap.


  • Organizational Affiliation

    Spanish National Microbiology Centre, Institute of Health Carlos III, 28220 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-2-macroglobulin
A, B, C, D
1,474Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01023 (Homo sapiens)
Explore P01023 
Go to UniProtKB:  P01023
GTEx:  ENSG00000175899 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01023
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P01023-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.15
RECONSTRUCTIONRELION2.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2017-88736-R
Spanish Ministry of Economy and CompetitivenessSpainBFU2019-107725-RB-I00
Spanish Ministry of Economy and CompetitivenessSpainJCI-2012-13573
Spanish Ministry of Science, Innovation, and UniversitiesSpainBES2016-076877

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references