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GeezerVison is showing www.rcsb.org — RCSB PDB - 3KLS: Structure of complement C5 in complex with SSL7

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 Data API 

 3KLS | pdb_00003kls

Structure of complement C5 in complex with SSL7

  • PDB DOI: https://doi.org/10.2210/pdb3KLS/pdb
  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens, Staphylococcus aureus subsp. aureus MRSA252
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2009-11-09 Released: 2009-11-24 
  • 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.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.263 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3KLS

Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history. 

Literature

  • Download Mendeley

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 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1073/pnas.0910565107
  • Primary Citation 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.


  • Organizational Affiliation: 
    • Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus, Denmark.
Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (NAG)

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (NAG)


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


Find Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (NAG)


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


Find Similar Assemblies

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

  • Total Structure Weight: 431.38 kDa 
  • Atom Count: 27,683 
  • Modeled Residue Count: 3,482 
  • Deposited Residue Count: 3,814 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Complement C5A,
C [auth B]
1,676Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens)
Explore P01031 
Go to UniProtKB:  P01031
GTEx:  ENSG00000106804 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01031
Glycosylation
Glycosylation Sites: 2
Glycosylation
  • Focus chain A
  • Focus chain C [auth B]
Go to GlyGen: P01031-1
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Exotoxin 1B [auth X],
D [auth Y]
231Staphylococcus aureus subsp. aureus MRSA252Mutation(s): 1 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C],
F [auth D]
2N-Glycosylation
Interactions
  • Focus chain E [auth C]
  • Focus chain F [auth D]
Interactions & Density
  • Focus chain E [auth C]
  • Focus chain F [auth D]
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
  • SDF format, chain L [auth A]
  • SDF format, chain Q [auth B]
  • MOL2 format, chain L [auth A]
  • MOL2 format, chain Q [auth B]
  • mmCIF format, chain L [auth A]
  • mmCIF format, chain Q [auth B]
L [auth A],
Q [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Interactions
  • Focus chain L [auth A]
  • Focus chain Q [auth B]
Interactions & Density
  • Focus chain L [auth A]
  • Focus chain Q [auth B]
CD

Query on CD



Download:Ideal Coordinates CCD File
  • SDF format, chain G [auth A]
  • SDF format, chain H [auth A]
  • SDF format, chain I [auth A]
  • SDF format, chain J [auth A]
  • SDF format, chain K [auth A]
  • SDF format, chain M [auth B]
  • SDF format, chain N [auth B]
  • SDF format, chain O [auth B]
  • SDF format, chain P [auth B]
  • MOL2 format, chain G [auth A]
  • MOL2 format, chain H [auth A]
  • MOL2 format, chain I [auth A]
  • MOL2 format, chain J [auth A]
  • MOL2 format, chain K [auth A]
  • MOL2 format, chain M [auth B]
  • MOL2 format, chain N [auth B]
  • MOL2 format, chain O [auth B]
  • MOL2 format, chain P [auth B]
  • mmCIF format, chain G [auth A]
  • mmCIF format, chain H [auth A]
  • mmCIF format, chain I [auth A]
  • mmCIF format, chain J [auth A]
  • mmCIF format, chain K [auth A]
  • mmCIF format, chain M [auth B]
  • mmCIF format, chain N [auth B]
  • mmCIF format, chain O [auth B]
  • mmCIF format, chain P [auth B]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Interactions
  • Focus chain G [auth A]
  • Focus chain H [auth A]
  • Focus chain I [auth A]
  • Focus chain J [auth A]
  • Focus chain K [auth A]
  • Focus chain M [auth B]
  • Focus chain N [auth B]
  • Focus chain O [auth B]
  • Focus chain P [auth B]
Interactions & Density
  • Focus chain G [auth A]
  • Focus chain H [auth A]
  • Focus chain I [auth A]
  • Focus chain J [auth A]
  • Focus chain K [auth A]
  • Focus chain M [auth B]
  • Focus chain N [auth B]
  • Focus chain O [auth B]
  • Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.263 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.875α = 90
b = 143.875β = 90
c = 241.24γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Released Date: 2009-11-24 
  • 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  (Full details and data files)

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2018-05-30
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-11-10
    Changes: Database references, Structure summary
  • Version 2.2: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-06
    Changes: Structure summary
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