7NYD

cryoEM structure of 2C9-sMAC

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  mpstruc

  • Deposited: 2021-03-22 Released: 2021-10-06 
  • Deposition Author(s): Menny, A., Couves, E.C., Bubeck, D.
  • Funding Organization(s): European Research Council (ERC), Cancer Research UK, Engineering and Physical Sciences Research Council

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis of soluble membrane attack complex packaging for clearance.

Menny, A.Lukassen, M.V.Couves, E.C.Franc, V.Heck, A.J.R.Bubeck, D.

(2021) Nat Commun 12: 6086-6086

  • DOI: https://doi.org/10.1038/s41467-021-26366-w
  • Primary Citation of Related Structures:  
    7NYC, 7NYD

  • PubMed Abstract: 

    Unregulated complement activation causes inflammatory and immunological pathologies with consequences for human disease. To prevent bystander damage during an immune response, extracellular chaperones (clusterin and vitronectin) capture and clear soluble precursors to the membrane attack complex (sMAC). However, how these chaperones block further polymerization of MAC and prevent the complex from binding target membranes remains unclear. Here, we address that question by combining cryo electron microscopy (cryoEM) and cross-linking mass spectrometry (XL-MS) to solve the structure of sMAC. Together our data reveal how clusterin recognizes and inhibits polymerizing complement proteins by binding a negatively charged surface of sMAC. Furthermore, we show that the pore-forming C9 protein is trapped in an intermediate conformation whereby only one of its two transmembrane β-hairpins has unfurled. This structure provides molecular details for immune pore formation and helps explain a complement control mechanism that has potential implications for how cell clearance pathways mediate immune homeostasis.


  • Organizational Affiliation

    Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C8 beta chainA [auth D]537Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07358 (Homo sapiens)
Explore P07358 
Go to UniProtKB:  P07358
PHAROS:  P07358
GTEx:  ENSG00000021852 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07358
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P07358-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C8 alpha chainB [auth E]554Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07357 (Homo sapiens)
Explore P07357 
Go to UniProtKB:  P07357
PHAROS:  P07357
GTEx:  ENSG00000157131 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07357
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P07357-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C9C [auth G],
F [auth H]
538Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P02748 (Homo sapiens)
Explore P02748 
Go to UniProtKB:  P02748
PHAROS:  P02748
GTEx:  ENSG00000113600 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02748
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P02748-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C7D [auth C]821Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P10643 (Homo sapiens)
Explore P10643 
Go to UniProtKB:  P10643
PHAROS:  P10643
GTEx:  ENSG00000112936 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10643
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P10643-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C6E [auth B]913Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P13671 (Homo sapiens)
Explore P13671 
Go to UniProtKB:  P13671
PHAROS:  P13671
GTEx:  ENSG00000039537 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13671
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P13671-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component C8 gamma chainG [auth F]182Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07360 (Homo sapiens)
Explore P07360 
Go to UniProtKB:  P07360
PHAROS:  P07360
GTEx:  ENSG00000176919 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07360
Sequence Annotations
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  • Reference Sequence
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C5H [auth A]1,658Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens)
Explore P01031 
Go to UniProtKB:  P01031
PHAROS:  P01031
GTEx:  ENSG00000106804 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01031
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01031-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42227JK
GlyCosmos:  G42227JK
GlyGen:  G42227JK
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
R [auth G],
V [auth B],
X [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
L [auth D]
M [auth D]
O [auth E]
P [auth E]
S [auth G]
L [auth D],
M [auth D],
O [auth E],
P [auth E],
S [auth G],
U [auth C]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
W [auth B]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
N [auth D],
Q [auth E],
T [auth G],
Y [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTISOLDE
MODEL REFINEMENTCoot9.1
MODEL REFINEMENTREFMAC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionNo. 864751
Cancer Research UKUnited KingdomC24523/A26234
Engineering and Physical Sciences Research CouncilUnited KingdomEP/L015498/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other
  • Version 2.0: 2024-07-24
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary