5O32

The structure of complement complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.21 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Regulator-dependent mechanisms of C3b processing by factor I allow differentiation of immune responses.

Xue, X.Wu, J.Ricklin, D.Forneris, F.Di Crescenzio, P.Schmidt, C.Q.Granneman, J.Sharp, T.H.Lambris, J.D.Gros, P.

(2017) Nat Struct Mol Biol 24: 643-651

  • DOI: https://doi.org/10.1038/nsmb.3427
  • Primary Citation of Related Structures:  
    5O32, 5O35

  • PubMed Abstract: 

    The complement system labels microbes and host debris for clearance. Degradation of surface-bound C3b is pivotal to direct immune responses and protect host cells. How the serine protease factor I (FI), assisted by regulators, cleaves either two or three distant peptide bonds in the CUB domain of C3b remains unclear. We present a crystal structure of C3b in complex with FI and regulator factor H (FH; domains 1-4 with 19-20). FI binds C3b-FH between FH domains 2 and 3 and a reoriented C3b C-terminal domain and docks onto the first scissile bond, while stabilizing its catalytic domain for proteolytic activity. One cleavage in C3b does not affect its overall structure, whereas two cleavages unfold CUB and dislodge the thioester-containing domain (TED), affecting binding of regulators and thereby determining the number of cleavages. These data explain how FI generates late-stage opsonins iC3b or C3dg in a context-dependent manner, to react to foreign, danger or healthy self signals.


  • Organizational Affiliation

    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C3A,
F [auth E]
645Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01024-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C3B,
G [auth F]
915Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01024-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement factor H,Complement factor HC,
H [auth G]
383Homo sapiensMutation(s): 0 
Gene Names: CFHHFHF1HF2
UniProt & NIH Common Fund Data Resources
Find proteins for P08603 (Homo sapiens)
Explore P08603 
Go to UniProtKB:  P08603
PHAROS:  P08603
GTEx:  ENSG00000000971 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08603
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Complement factor ID,
I [auth H]
321Homo sapiensMutation(s): 0 
Gene Names: CFIIF
EC: 3.4.21.45
UniProt & NIH Common Fund Data Resources
Find proteins for P05156 (Homo sapiens)
Explore P05156 
Go to UniProtKB:  P05156
PHAROS:  P05156
GTEx:  ENSG00000205403 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05156
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P05156-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Complement factor IE [auth I],
J
244Homo sapiensMutation(s): 0 
Gene Names: CFIIF
EC: 3.4.21.45
UniProt & NIH Common Fund Data Resources
Find proteins for P05156 (Homo sapiens)
Explore P05156 
Go to UniProtKB:  P05156
PHAROS:  P05156
GTEx:  ENSG00000205403 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05156
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P05156-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, M
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G89225LT
GlyCosmos:  G89225LT
GlyGen:  G89225LT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L, N
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth H]
BA [auth H]
CA [auth H]
DA [auth J]
EA [auth J]
AA [auth H],
BA [auth H],
CA [auth H],
DA [auth J],
EA [auth J],
FA [auth J],
R [auth D],
S [auth D],
T [auth D],
U [auth I],
V [auth I],
W [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
GA [auth J]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
O [auth A]
P [auth D]
Q [auth D]
X [auth E]
Y [auth H]
O [auth A],
P [auth D],
Q [auth D],
X [auth E],
Y [auth H],
Z [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.21 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.37α = 69.764
b = 122.79β = 76.101
c = 157.2γ = 70.13
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ERC Advanced grantNetherlands233229
NWO SpinozaNetherlands01.80.104.00
NIH R01United StatesAI030040-16

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary