3OXU | pdb_00003oxu

Complement components factor H CCP19-20 and C3d in complex

PDB DOI: https://doi.org/10.2210/pdb3OXU/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Komagataella pastoris, Escherichia coli
Mutation(s): Yes

Deposited: 2010-09-22 Released: 2011-02-16
Deposition Author(s): Morgan, H.P., Schmidt, C.Q., Guariento, M., Gillespie, D., Herbert, A.P., Mertens, H., Blaum, B.S., Svergun, D., Johansson, C.M., Uhrin, D., Barlow, P.N., Hannan, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.206 (Depositor), 0.202 (DCC)
R-Value Work:
0.171 (Depositor), 0.168 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural basis for engagement by complement factor H of C3b on a self surface.

Morgan, H.P., Schmidt, C.Q., Guariento, M., Blaum, B.S., Gillespie, D., Herbert, A.P., Kavanagh, D., Mertens, H.D., Svergun, D.I., Johansson, C.M., Uhrin, D., Barlow, P.N., Hannan, J.P.

(2011) Nat Struct Mol Biol 18: 463-470

PubMed: 21317894 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.2018
Primary Citation Related Structures:
3OXU

PubMed Abstract:
Complement factor H (FH) attenuates C3b molecules tethered by their thioester domains to self surfaces and thereby protects host tissues. Factor H is a cofactor for initial C3b proteolysis that ultimately yields a surface-attached fragment (C3d) corresponding to the thioester domain. We used NMR and X-ray crystallography to study the C3d-FH19-20 complex in atomic detail and identify glycosaminoglycan-binding residues in factor H module 20 of the C3d-FH19-20 complex. Mutagenesis justified the merging of the C3d-FH19-20 structure with an existing C3b-FH1-4 crystal structure. We concatenated the merged structure with the available FH6-8 crystal structure and new SAXS-derived FH1-4, FH8-15 and FH15-19 envelopes. The combined data are consistent with a bent-back factor H molecule that binds through its termini to two sites on one C3b molecule and simultaneously to adjacent polyanionic host-surface markers.

Organizational Affiliation

Institute of Structural and Molecular Biology, School of Biological Sciences, King's Buildings, University of Edinburgh, Edinburgh, UK.

Macromolecule Content

Total Structure Weight: 151.39 kDa
Atom Count: 10,982
Modeled Residue Count: 1,252
Deposited Residue Count: 1,338
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	A, B, C	317	Homo sapiens	Mutation(s): 1 Gene Names: C3, complement H factor, CPAMD1
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
HF protein	D, E, F	129	Homo sapiens	Mutation(s): 0 Gene Names: complement component C3
UniProt & NIH Common Fund Data Resources
Find proteins for P08603 (Homo sapiens) Explore P08603 Go to UniProtKB: P08603
PHAROS: P08603 GTEx: ENSG00000000971
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08603
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth B] J [auth C] K [auth C] G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D], N [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.206 (Depositor), 0.202 (DCC)
R-Value Work: 0.171 (Depositor), 0.168 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.675	α = 112.75
b = 82.99	β = 110.14
c = 85.605	γ = 99.96

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-02-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-02-20
Changes: Database references
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary