2XWJ | pdb_00002xwj

Crystal Structure of Complement C3b in Complex with Factor B

PDB DOI: https://doi.org/10.2210/pdb2XWJ/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2010-11-04 Released: 2011-01-12
Deposition Author(s): Forneris, F., Ricklin, D., Wu, J., Tzekou, A., Wallace, R.S., Lambris, J.D., Gros, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free:
0.281 (Depositor), 0.281 (DCC)
R-Value Work:
0.228 (Depositor), 0.229 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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Literature

Structures of C3B in Complex with Factors B and D Give Insight Into Complement Convertase Formation.

Forneris, F., Ricklin, D., Wu, J., Tzekou, A., Wallace, R.S., Lambris, J.D., Gros, P.

(2010) Science 330: 1816

PubMed: 21205667 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1195821
Primary Citation Related Structures:
2XW9, 2XWA, 2XWB, 2XWJ

PubMed Abstract:
Activation of the complement cascade induces inflammatory responses and marks cells for immune clearance. In the central complement-amplification step, a complex consisting of surface-bound C3b and factor B is cleaved by factor D to generate active convertases on targeted surfaces. We present crystal structures of the pro-convertase C3bB at 4 angstrom resolution and its complex with factor D at 3.5 angstrom resolution. Our data show how factor B binding to C3b forms an open "activation" state of C3bB. Factor D specifically binds the open conformation of factor B through a site distant from the catalytic center and is activated by the substrate, which displaces factor D's self-inhibitory loop. This concerted proteolytic mechanism, which is cofactor-dependent and substrate-induced, restricts complement amplification to C3b-tagged target cells.

Organizational Affiliation

Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.

Macromolecule Content

Total Structure Weight: 1,036.65 kDa
Atom Count: 71,260
Modeled Residue Count: 9,013
Deposited Residue Count: 9,204
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT C3 BETA CHAIN	A, C, E, G	645	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024 Go to UniProtKB: P01024
PHAROS: P01024 GTEx: ENSG00000125730
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01024
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT C3 ALPHA CHAIN	B, D, F, H	915	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024 Go to UniProtKB: P01024
PHAROS: P01024 GTEx: ENSG00000125730
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01024
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain F Focus chain H	Go to GlyGen: P01024-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT FACTOR B	I, J, K, L	741	Homo sapiens	Mutation(s): 2 EC: 3.4.21.47
UniProt & NIH Common Fund Data Resources
Find proteins for P00751 (Homo sapiens) Explore P00751 Go to UniProtKB: P00751
PHAROS: P00751 GTEx: ENSG00000243649
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00751
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain I Focus chain J Focus chain K Focus chain L	Go to GlyGen: P00751-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth D] SDF format, chain O [auth F] SDF format, chain P [auth H] SDF format, chain Q [auth I] SDF format, chain S [auth J] SDF format, chain U [auth K] SDF format, chain W [auth L] MOL2 format, chain M [auth B] MOL2 format, chain N [auth D] MOL2 format, chain O [auth F] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth I] MOL2 format, chain S [auth J] MOL2 format, chain U [auth K] MOL2 format, chain W [auth L] mmCIF format, chain M [auth B] mmCIF format, chain N [auth D] mmCIF format, chain O [auth F] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth I] mmCIF format, chain S [auth J] mmCIF format, chain U [auth K] mmCIF format, chain W [auth L]	M [auth B] N [auth D] O [auth F] P [auth H] Q [auth I] M [auth B], N [auth D], O [auth F], P [auth H], Q [auth I], S [auth J], U [auth K], W [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth B] Focus chain N [auth D] Focus chain O [auth F] Focus chain P [auth H] Focus chain Q [auth I] Focus chain S [auth J] Focus chain U [auth K] Focus chain W [auth L] Interactions & Density Focus chain M [auth B] Focus chain N [auth D] Focus chain O [auth F] Focus chain P [auth H] Focus chain Q [auth I] Focus chain S [auth J] Focus chain U [auth K] Focus chain W [auth L]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain R [auth I] SDF format, chain V [auth K] SDF format, chain X [auth L] SDF format, chain T [auth J] MOL2 format, chain R [auth I] MOL2 format, chain V [auth K] MOL2 format, chain X [auth L] MOL2 format, chain T [auth J] mmCIF format, chain R [auth I] mmCIF format, chain V [auth K] mmCIF format, chain X [auth L] mmCIF format, chain T [auth J]	R [auth I], T [auth J], V [auth K], X [auth L]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain R [auth I] Focus chain T [auth J] Focus chain V [auth K] Focus chain X [auth L] Interactions & Density Focus chain R [auth I] Focus chain T [auth J] Focus chain V [auth K] Focus chain X [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.281 (Depositor), 0.281 (DCC)
R-Value Work: 0.228 (Depositor), 0.229 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 262.16	α = 90
b = 297.87	β = 90
c = 341.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-01-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-12
Type: Initial release
Version 1.1: 2012-04-11
Changes: Database references, Other, Refinement description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-11-06
Changes: Structure summary