Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 402.45 kDa 
• Atom Count: 24809 
• Modelled Residue Count: 3122 
• Deposited Residue Count: 3558 
• Unique protein chains: 2

3KM9

Structure of complement C5 in complex with the C-terminal beta-grasp domain of SSL7

• PDB DOI: 10.2210/pdb3KM9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Staphylococcus aureus subsp. aureus str. Newman
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-10 Released: 2009-12-01 
• Deposition Author(s): Laursen, N.S., Gordon, N., Hermans, S., Lorenz, N., Jackson, N., Wines, B., Spillner, E., Christensen, J.B., Jensen, M., Fredslund, F., Bjerre, M., Sottrup-Jensen, L., Fraser, J.D., Andersen, G.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.297 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 

Literature

Structural basis for inhibition of complement C5 by the SSL7 protein from Staphylococcus aureus

Laursen, N.S., Gordon, N., Hermans, S., Lorenz, N., Jackson, N., Wines, B., Spillner, E., Christensen, J.B., Jensen, M., Fredslund, F., Bjerre, M., Sottrup-Jensen, L., Fraser, J.D., Andersen, G.R.

(2010) Proc Natl Acad Sci U S A 107: 3681-3686

• PubMed: 20133685 
• DOI: 10.1073/pnas.0910565107
• Primary Citation of Related Structures:  
  3KLS, 3KM9


• PubMed Abstract: 
  

Staphylococcus aureus secretes the SSL7 protein as part of its immune evasion strategy. The protein binds both complement C5 and IgA, yet it is unclear whether SSL7 cross-links these two proteins and, if so, what purpose this serves the pathogen. We have isolated a stable IgA-SSL7-C5 complex, and our crystal structure of the C5-SSL7 complex confirms that binding to C5 occurs exclusively through the C-terminal beta-grasp domain of SSL7 leaving the OB domain free to interact with IgA. SSL7 interacts with C5 >70 A from the C5a cleavage site without inducing significant conformational changes in C5, and efficient inhibition of convertase cleavage of C5 is shown to be IgA dependent. Inhibition of C5a production and bacteriolysis are all shown to require C5 and IgA binding while inhibition of hemolysis is achieved by the C5 binding SSL7 beta-grasp domain alone. These results provide a conceptual and structural basis for the development of a highly specific complement inhibitor preventing only the formation of the lytic membrane attack complex without affecting the important signaling functions of C5a.

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Organizational Affiliation: 

Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C5	A, C [auth B]	1676	Homo sapiens	Mutation(s): 0  Gene Names: C5, CPAMD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens) Explore P01031  Go to UniProtKB:  P01031
PHAROS:  P01031

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal enterotoxin-like toxin	B [auth X], D [auth Y]	103	Staphylococcus aureus subsp. aureus str. Newman	Mutation(s): 0  Gene Names: ssl7, NWMN_0394
UniProt
Find proteins for A0A0H3K6Z8 (Staphylococcus aureus (strain Newman)) Explore A0A0H3K6Z8  Go to UniProtKB:  A0A0H3K6Z8

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], F [auth D]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CD	G [auth A], H [auth A], I [auth A], K [auth B], L [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.297 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.79	α = 90
b = 144.79	β = 90
c = 245.28	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-10 
• Released Date: 2009-12-01 
Deposition Author(s): Laursen, N.S., Gordon, N., Hermans, S., Lorenz, N., Jackson, N., Wines, B., Spillner, E., Christensen, J.B., Jensen, M., Fredslund, F., Bjerre, M., Sottrup-Jensen, L., Fraser, J.D., Andersen, G.R.

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary