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3PRX | pdb_00003prx

Structure of Complement C5 in Complex with CVF and SSL7

PDB DOI: https://doi.org/10.2210/pdb3PRX/pdb

Classification: IMMUNE SYSTEM/TOXIN
Organism(s): Homo sapiens, Naja kaouthia, Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-30 Released: 2011-01-19
Deposition Author(s): Laursen, N.S., Andersen, G.R., Sottrup-Jensen, L., Andersen, K.R., Spillner, E., Braren, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.30 Å
R-Value Free:
0.261 (Depositor), 0.246 (DCC)
R-Value Work:
0.208 (Depositor), 0.195 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

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Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex.

Laursen, N.S., Andersen, K.R., Braren, I., Spillner, E., Sottrup-Jensen, L., Andersen, G.R.

(2011) EMBO J 30: 606-616

PubMed: 21217642 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/emboj.2010.341
Primary Citation Related Structures:
3PRX, 9TDL

PubMed Abstract:
Complement acts as a danger-sensing system in the innate immune system, and its activation initiates a strong inflammatory response and cleavage of the proteins C3 and C5 by proteolytic enzymes, the convertases. These contain a non-catalytic substrate contacting subunit (C3b or C4b) in complex with a protease subunit (Bb or C2a). We determined the crystal structures of the C3b homologue cobra venom factor (CVF) in complex with C5, and in complex with C5 and the inhibitor SSL7 at 4.3 Å resolution. The structures reveal a parallel two-point attachment between C5 and CVF, where the presence of SSL7 only slightly affects the C5-CVF interface, explaining the IgA dependence for SSL7-mediated inhibition of C5 cleavage. CVF functions as a relatively rigid binding scaffold inducing a conformational change in C5, which positions its cleavage site in proximity to the serine protease Bb. A general model for substrate recognition by the convertases is presented based on the C5-CVF and C3b-Bb-SCIN structures. Prior knowledge concerning interactions between the endogenous convertases and their substrates is rationalized by this model.

Organizational Affiliation

Department of Molecular Biology, Aarhus University, Aarhus, Denmark.

Asymmetric Unit

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Biological Assembly 1

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Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 3-mer - A1B1C1

Find Similar Assemblies

Biological assembly 1 assigned by authors.

Biological Assembly 2

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Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 3-mer - A1B1C1

Find Similar Assemblies

Biological assembly 2 assigned by authors.

Macromolecule Content

Total Structure Weight: 800.65 kDa
Atom Count: 48,236
Modeled Residue Count: 6,064
Deposited Residue Count: 7,098
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C5	A, C	1,676	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01031
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C	Go to GlyGen: P01031-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobra venom factor	B, D	1,642	Naja kaouthia	Mutation(s): 0
UniProt
Find proteins for Q91132 (Naja kaouthia) Explore Q91132 Go to UniProtKB: Q91132
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q91132
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B Focus chain D
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Superantigen-like protein 7	E [auth X], F [auth Y]	231	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for D3JIB2 (Staphylococcus aureus) Explore D3JIB2 Go to UniProtKB: D3JIB2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3JIB2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth E], H [auth F], I [auth G], J [auth H]	2		N-Glycosylation	Interactions Focus chain G [auth E] Focus chain H [auth F] Focus chain I [auth G] Focus chain J [auth H] Interactions & Density Focus chain G [auth E] Focus chain H [auth F] Focus chain I [auth G] Focus chain J [auth H]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain K [auth A] MOL2 format, chain L [auth C] MOL2 format, chain K [auth A] mmCIF format, chain L [auth C] mmCIF format, chain K [auth A]	K [auth A], L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth C] Interactions & Density Focus chain K [auth A] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.30 Å
R-Value Free: 0.261 (Depositor), 0.246 (DCC)
R-Value Work: 0.208 (Depositor), 0.195 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.65	α = 90
b = 181.96	β = 90
c = 392.78	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-01-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary

GeezerVison

3PRX | pdb_00003prx

Structure of Complement C5 in Complex with CVF and SSL7

Literature

Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Expand

Oligosaccharides

Entity ID: 4

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)