3DDR

Structure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex.

Krieg, S.Huche, F.Diederichs, K.Izadi-Pruneyre, N.Lecroisey, A.Wandersman, C.Delepelaire, P.Welte, W.

(2009) Proc Natl Acad Sci U S A 106: 1045-1050

  • DOI: https://doi.org/10.1073/pnas.0809406106
  • Primary Citation of Related Structures:  
    3CSL, 3CSN, 3DDR

  • PubMed Abstract: 

    Gram-negative bacteria use specific heme uptake systems, relying on outer membrane receptors and excreted heme-binding proteins (hemophores) to scavenge and actively transport heme. To unravel the unknown molecular details involved, we present 3 structures of the Serratia marcescens receptor HasR in complex with its hemophore HasA. The transfer of heme over a distance of 9 A from its high-affinity site in HasA into a site of lower affinity in HasR is coupled with the exergonic complex formation of the 2 proteins. Upon docking to the receptor, 1 of the 2 axial heme coordinations of the hemophore is initially broken, but the position and orientation of the heme is preserved. Subsequently, steric displacement of heme by a receptor residue ruptures the other axial coordination, leading to heme transfer into the receptor.


  • Organizational Affiliation

    Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HasR protein
A, B
865Serratia marcescensMutation(s): 1 
Gene Names: hasR
Membrane Entity: Yes 
UniProt
Find proteins for Q79AD2 (Serratia marcescens)
Explore Q79AD2 
Go to UniProtKB:  Q79AD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79AD2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemophore HasA
C, D
206Serratia marcescensMutation(s): 0 
Gene Names: hasA
UniProt
Find proteins for Q54450 (Serratia marcescens)
Explore Q54450 
Go to UniProtKB:  Q54450
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54450
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
M [auth C],
N [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
H [auth B]
I [auth B]
J [auth B]
K [auth B]
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.41α = 90
b = 162.72β = 90
c = 597.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Atomic model
  • Version 1.3: 2012-03-21
    Changes: Database references
  • Version 1.4: 2017-10-25
    Changes: Refinement description
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary