6H04

Closed conformation of the Membrane Attack Complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

CryoEM reveals how the complement membrane attack complex ruptures lipid bilayers.

Menny, A., Serna, M., Boyd, C.M., Gardner, S., Joseph, A.P., Morgan, B.P., Topf, M., Brooks, N.J., Bubeck, D.

(2018) Nat Commun 9: 5316-5316

  • DOI: 10.1038/s41467-018-07653-5
  • Primary Citation of Related Structures:  
    6H03, 6H04

  • PubMed Abstract: 

    • The membrane attack complex (MAC) is one of the immune system's first responders. Complement proteins assemble on target membranes to form pores that lyse pathogens and impact tissue homeostasis of self-cells. How MAC disrupts the membrane barrier remains unclear ...

    The membrane attack complex (MAC) is one of the immune system's first responders. Complement proteins assemble on target membranes to form pores that lyse pathogens and impact tissue homeostasis of self-cells. How MAC disrupts the membrane barrier remains unclear. Here we use electron cryo-microscopy and flicker spectroscopy to show that MAC interacts with lipid bilayers in two distinct ways. Whereas C6 and C7 associate with the outer leaflet and reduce the energy for membrane bending, C8 and C9 traverse the bilayer increasing membrane rigidity. CryoEM reconstructions reveal plasticity of the MAC pore and demonstrate how C5b6 acts as a platform, directing assembly of a giant β-barrel whose structure is supported by a glycan scaffold. Our work provides a structural basis for understanding how β-pore forming proteins breach the membrane and reveals a mechanism for how MAC kills pathogens and regulates cell functions.

    Organizational Affiliation: 

    Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK. d.bubeck@imperial.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement component C9538Homo sapiensMutation(s): 0 
Gene Names: C9
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P02748 (Homo sapiens)
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Go to UniProtKB:  P02748
PHAROS:  P02748
GTEx:  ENSG00000113600
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C5,Complement C5S [auth A]1580Homo sapiensMutation(s): 0 
Gene Names: C5
Membrane Entity: Yes 
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Find proteins for P01031 (Homo sapiens)
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PHAROS:  P01031
GTEx:  ENSG00000106804
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Complement component C8 beta chainT [auth C]537Homo sapiensMutation(s): 0 
Gene Names: C8B
Membrane Entity: Yes 
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Find proteins for P07358 (Homo sapiens)
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PHAROS:  P07358
GTEx:  ENSG00000021852
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Complement component C7U [auth D]821Homo sapiensMutation(s): 0 
Gene Names: C7
Membrane Entity: Yes 
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Find proteins for P10643 (Homo sapiens)
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PHAROS:  P10643
GTEx:  ENSG00000112936
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Complement component C8 gamma chainV [auth E]182Homo sapiensMutation(s): 0 
Gene Names: C8G
Membrane Entity: Yes 
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Find proteins for P07360 (Homo sapiens)
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PHAROS:  P07360
GTEx:  ENSG00000176919
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Complement component C8 alpha chainW [auth F]554Homo sapiensMutation(s): 0 
Gene Names: C8A
Membrane Entity: Yes 
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PHAROS:  P07357
GTEx:  ENSG00000157131
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Complement component C6X [auth B]913Homo sapiensMutation(s): 0 
Gene Names: C6
Membrane Entity: Yes 
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Find proteins for P13671 (Homo sapiens)
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PHAROS:  P13671
GTEx:  ENSG00000039537
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Oligosaccharides

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Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h]
AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], Y, Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG
Download Ideal Coordinates CCD File 
AB [auth Q] , AC [auth G] , BB [auth R] , BC [auth D] , CB [auth R] , CC [auth B] , DB [auth S] , EB [auth S] , 
AB [auth Q], AC [auth G], BB [auth R], BC [auth D], CB [auth R], CC [auth B], DB [auth S], EB [auth S], FB [auth T], GB [auth T], HB [auth U], IB [auth U], JB [auth V], KB [auth V], LB [auth W], MB [auth W], NB [auth X], OB [auth X], PB [auth P], QB [auth P], RA [auth L], RB [auth H], SA [auth L], SB [auth H], TA [auth M], TB [auth I], UA [auth M], UB [auth I], VA [auth N], VB [auth J], WA [auth N], WB [auth J], XA [auth O], XB [auth K], YA [auth O], YB [auth K], ZA [auth Q], ZB [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC26409/A16099
Medical Research Council (United Kingdom)United KingdomMR/M019292/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary