6RQJ

Structure of human complement C5 complexed with tick inhibitors OmCI, RaCI1 and CirpT1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

An inhibitor of complement C5 provides structural insights into activation.

Reichhardt, M.P.Johnson, S.Tang, T.Morgan, T.Tebeka, N.Popitsch, N.Deme, J.C.Jore, M.M.Lea, S.M.

(2020) Proc Natl Acad Sci U S A 117: 362-370

  • DOI: https://doi.org/10.1073/pnas.1909973116
  • Primary Citation of Related Structures:  
    6RPT, 6RQJ

  • PubMed Abstract: 

    The complement system is a crucial part of innate immune defenses against invading pathogens. The blood-meal of the tick Rhipicephalus pulchellus lasts for days, and the tick must therefore rely on inhibitors to counter complement activation. We have identified a class of inhibitors from tick saliva, the CirpT family, and generated detailed structural data revealing their mechanism of action. We show direct binding of a CirpT to complement C5 and have determined the structure of the C5-CirpT complex by cryoelectron microscopy. This reveals an interaction with the peripheral macro globulin domain 4 (C5_MG4) of C5. To achieve higher resolution detail, the structure of the C5_MG4-CirpT complex was solved by X-ray crystallography (at 2.7 Å). We thus present the fold of the CirpT protein family, and provide detailed mechanistic insights into its inhibitory function. Analysis of the binding interface reveals a mechanism of C5 inhibition, and provides information to expand our biological understanding of the activation of C5, and thus the terminal complement pathway.


  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C5999Homo sapiensMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement inhibitorB [auth C]165Rhipicephalus pulchellusMutation(s): 2 
UniProt
Find proteins for Q5YD59 (Ornithodoros moubata)
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Go to UniProtKB:  Q5YD59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YD59
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Rhipicephalus appendiculatus RaCI1C [auth D]81Rhipicephalus pulchellusMutation(s): 0 
UniProt
Find proteins for A0A141SFN4 (Rhipicephalus appendiculatus)
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Go to UniProtKB:  A0A141SFN4
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UniProt GroupA0A141SFN4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C5D [auth B]655Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens)
Explore P01031 
Go to UniProtKB:  P01031
PHAROS:  P01031
GTEx:  ENSG00000106804 
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UniProt GroupP01031
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 8.9 kDa family member112Rhipicephalus pulchellusMutation(s): 0 
UniProt
Find proteins for L7MB58 (Rhipicephalus pulchellus)
Explore L7MB58 
Go to UniProtKB:  L7MB58
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UniProt GroupL7MB58
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Finnish Cultural FoundationFinland--
Wellcome TrustUnited Kingdom100298
Wellcome TrustUnited Kingdom201536
Wolfson FoundationUnited KingdomWL160052

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Source and taxonomy
  • Version 1.2: 2020-01-22
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary