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 2.0 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 ...

    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
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C3A,
F [auth E]		645Homo sapiensMutation(s): 0 
Gene Names: C3, CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C3B,
G [auth F]		915Homo sapiensMutation(s): 0 
Gene Names: C3, CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Complement factor H,Complement factor HC,
H [auth G]		383Homo sapiensMutation(s): 0 
Gene Names: CFH, HF, HF1, HF2
UniProt & NIH Common Fund Data Resources
Find proteins for P08603 (Homo sapiens)
Explore P08603 
Go to UniProtKB:  P08603
PHAROS:  P08603
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08603
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Complement factor ID,
I [auth H]		321Homo sapiensMutation(s): 0 
Gene Names: CFI, IF
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05156
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Complement factor IE [auth I],
J		244Homo sapiensMutation(s): 0 
Gene Names: CFI, IF
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05156
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G89225LT
GlyCosmos:  G89225LT
GlyGen:  G89225LT
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L, N
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / 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		 Ligand Interaction
MLI
Query on MLI
Download Ideal Coordinates CCD File 
GA [auth J]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L		 Ligand Interaction
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		 Ligand Interaction
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

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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