2QKI

Human C3c in complex with the inhibitor compstatin

• PDB DOI:  https://doi.org/10.2210/pdb2QKI/pdb

• Classification: Immune system/hydrolase inhibitor
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-07-11 Released: 2007-08-14 
• Deposition Author(s): Janssen, B.J.C., Halff, E.F., Lambris, J.D., Gros, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.281 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

Structure of compstatin in complex with complement component C3c reveals a new mechanism of complement inhibition.

Janssen, B.J., Halff, E.F., Lambris, J.D., Gros, P.

(2007) J Biol Chem 282: 29241-29247

• PubMed: 17684013 
• DOI: https://doi.org/10.1074/jbc.M704587200
• Primary Citation of Related Structures:  
  2QKI


• PubMed Abstract: 
  

Undesired complement activation is a major cause of tissue injury in various pathological conditions and contributes to several immune complex diseases. Compstatin, a 13-residue peptide, is an effective inhibitor of the activation of complement component C3 and thus blocks a central and crucial step in the complement cascade. The precise binding site on C3, the structure in the bound form, and the exact mode of action of compstatin are unknown. Here we present the crystal structure of compstatin in complex with C3c, a major proteolytic fragment of C3. The structure reveals that the compstatin-binding site is formed by the macroglobulin (MG) domains 4 and 5. This binding site is part of the structurally stable MG-ring formed by domains MG 1-6 and is far away from any other known binding site on C3. Compstatin does not alter the conformation of C3c, whereas compstatin itself undergoes a large conformational change upon binding. We propose a model in which compstatin sterically hinders the access of the substrate C3 to the convertase complexes, thus blocking complement activation and amplification. These insights are instrumental for further development of compstatin as a potential therapeutic.

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Organizational Affiliation: 

Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 273.11 kDa 
• Atom Count: 18,480 
• Modelled Residue Count: 2,250 
• Deposited Residue Count: 2,378 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	A, D	643	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	B, E	188	Homo sapiens	Mutation(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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	C, F	343	Homo sapiens	Mutation(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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
compstatin	G, H	15	N/A	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	AB [auth D], BA [auth B], BB [auth D], CB [auth D], EA [auth C], GB [auth E], HB [auth E], LB [auth F], MB [auth H], T [auth A], U [auth A], V [auth A], W [auth A], WA [auth D], X [auth A], XA [auth D], YA [auth D], ZA [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR	AA [auth B], DA [auth C], DB [auth E], EB [auth E], FB [auth E], HA [auth D], IA [auth D], JA [auth D], JB [auth F], KA [auth D], KB [auth F], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], RA [auth D], S [auth A], SA [auth D], TA [auth D], UA [auth D], VA [auth D], Y [auth B], Z [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
K	CA [auth C], FA [auth D], GA [auth D], IB [auth F], K [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.281 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.809	α = 90
b = 124.754	β = 95.08
c = 127.367	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Janssen, B.J.C., Halff, E.F., Lambris, J.D., Gros, P.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary