4E0S

Crystal Structure of C5b-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.21 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of c5b-6 suggests structural basis for priming assembly of the membrane attack complex.

Aleshin, A.E.Discipio, R.G.Stec, B.Liddington, R.C.

(2012) J.Biol.Chem. 287: 19642-19652

  • DOI: 10.1074/jbc.M112.361121

  • PubMed Abstract: 
  • The complement membrane attack complex (MAC) forms transmembrane pores in pathogen membranes. The first step in MAC assembly is cleavage of C5 to generate metastable C5b, which forms a stable complex with C6, termed C5b-6. C5b-6 initiates pore format ...

    The complement membrane attack complex (MAC) forms transmembrane pores in pathogen membranes. The first step in MAC assembly is cleavage of C5 to generate metastable C5b, which forms a stable complex with C6, termed C5b-6. C5b-6 initiates pore formation via the sequential recruitment of homologous proteins: C7, C8, and 12-18 copies of C9, each of which comprises a central MAC-perforin domain flanked by auxiliary domains. We recently proposed a model of pore assembly, in which the auxiliary domains play key roles, both in stabilizing the closed conformation of the protomers and in driving the sequential opening of the MAC-perforin β-sheet of each new recruit to the growing pore. Here, we describe an atomic model of C5b-6 at 4.2 Å resolution. We show that C5b provides four interfaces for the auxiliary domains of C6. The largest interface is created by the insertion of an interdomain linker from C6 into a hydrophobic groove created by a major reorganization of the α-helical domain of C5b. In combination with the rigid body docking of N-terminal elements of both proteins, C5b becomes locked into a stable conformation. Both C6 auxiliary domains flanking the linker pack tightly against C5b. The net effect is to induce the clockwise rigid body rotation of four auxiliary domains, as well as the opening/twisting of the central β-sheet of C6, in the directions predicted by our model to activate or prime C6 for the subsequent steps in MAC assembly. The complex also suggests novel small molecule strategies for modulating pathological MAC assembly.


    Organizational Affiliation

    Program on Infectious Diseases, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement C5
A
1676Homo sapiensMutation(s): 0 
Gene Names: C5 (CPAMD4)
Find proteins for P01031 (Homo sapiens)
Go to Gene View: C5
Go to UniProtKB:  P01031
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Complement component C6
B
913Homo sapiensMutation(s): 0 
Gene Names: C6
Find proteins for P13671 (Homo sapiens)
Go to Gene View: C6
Go to UniProtKB:  P13671
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BGC
Query on BGC

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B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC
Query on FUC

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B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

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A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.21 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.218 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 158.949α = 90.00
b = 227.529β = 90.00
c = 278.157γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
Blu-Icedata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-04-25
    Type: Database references
  • Version 1.2: 2012-06-20
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description