6TAV | pdb_00006tav

Crystal structure of endopeptidase-induced alpha2-macroglobulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 
    0.282 (Depositor), 0.329 (DCC) 
  • R-Value Work: 
    0.235 (Depositor) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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 Related Structures: 
    6TAV, 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.

Macromolecule Content 

  • Total Structure Weight: 666.2 kDa 
  • Atom Count: 41,633 
  • Modeled Residue Count: 5,234 
  • Deposited Residue Count: 5,896 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-2-macroglobulin
A, B, C, D
1,474Homo sapiensMutation(s): 0 
Gene Names: A2MCPAMD5FWP007
UniProt & NIH Common Fund Data Resources
Find proteins for P01023 (Homo sapiens)
Explore P01023 
Go to UniProtKB:  P01023
PHAROS:  P01023
GTEx:  ENSG00000175899 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01023
Glycosylation
Glycosylation Sites: 7Go to GlyGen: P01023-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G, J, O, V
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC
GlyCosmos: G22573RC
GlyGen: G22573RC
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, I, M, R
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, K, L, N, P
H, K, L, N, P, Q, S, T, U
2N-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 C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth D]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth D],
FA [auth D],
GA [auth D],
W [auth A],
X [auth A],
Y [auth A],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free:  0.282 (Depositor), 0.329 (DCC) 
  • R-Value Work:  0.235 (Depositor) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.8α = 90
b = 260.3β = 90
c = 281.8γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Advisory, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary
  • Version 1.4: 2025-09-17
    Changes: Database references