Crystal structure of alpha-1-microglobulin at 2.3 A resolution

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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The crystal structure of human alpha(1)-microglobulin reveals a potential haem-binding site.

Meining, W.Skerra, A.

(2012) Biochem J 445: 175-182

  • DOI: https://doi.org/10.1042/BJ20120448
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We describe the 2.3 Å (1 Å=0.1 nm) X-ray structure of α1m (α1-microglobulin), an abundant protein in human blood plasma, which reveals the β-barrel fold typical for lipocalins with a deep pocket lined by four loops at its open rim. Loop #1 harbours the residue Cys34 which is responsible for covalent cross-linking with plasma IgA. A single disulfide bond between Cys72 and Cys169 connects the C-terminal segment to the β-barrel, as in many other lipocalins. The exposed imidazole side chains of His122 and His123 in loop #4 give rise to a double Ni2+-binding site together with a crystallographic neighbour. The closest structural relatives of α1m are the complement protein component C8γ, the L-prostaglandin D synthase and lipocalin 15, three other structurally characterized members of the lipocalin family in humans that have only distant sequence similarity. In contrast with these, α1m is initially expressed as a bifunctional fusion protein with the protease inhibitor bikunin. Neither the electron density nor ESI-MS (electrospray ionization MS) provide evidence for a chromophore bound to the recombinant α1m, also known as 'yellow/brown lipocalin'. However, the three side chains of Lys92, Lys118 and Lys130 that were reported to be involved in covalent chromophore binding appear to be freely accessible to ligands accommodated in the hydrophobic pocket. A structural feature similar to the well-known Cys-Pro haem-binding motif indicates the presence of a haem-binding site within the loop region of α1m, which explains previous biochemical findings and supports a physiological role in haem scavenging, as well as redox-mediated detoxification.

  • Organizational Affiliation

    Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Freising-Weihenstephan 85350, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein AMBP193Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P02760 (Homo sapiens)
Explore P02760 
Go to UniProtKB:  P02760
PHAROS:  P02760
GTEx:  ENSG00000106927 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02760
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.721α = 90
b = 66.721β = 90
c = 80.255γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-06-20
    Changes: Database references
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description