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- PDB-5o35: Structure of complement proteins complex -

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Basic information

Entry
Database: PDB / ID: 5o35
TitleStructure of complement proteins complex
Components
  • (Complement C3) x 2
  • Complement factor H,Complement factor H
KeywordsIMMUNE SYSTEM / Complement / regulation / complex
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / symbiont cell surface / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / regulation of complement activation ...regulation of complement activation, alternative pathway / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / symbiont cell surface / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / regulation of complement activation / complement component C3b binding / complement-mediated synapse pruning / Alternative complement activation / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement receptor mediated signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / Regulation of Complement cascade / response to bacterium / Post-translational protein phosphorylation / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein phosphorylation / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / heparin binding / secretory granule lumen / G alpha (i) signalling events / blood microparticle / immune response / G protein-coupled receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / inflammatory response / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 ...: / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Anaphylatoxin domain signature. / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C3 / Complement factor H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.2 Å
AuthorsXue, X. / Wu, J. / Forneris, F. / Gros, P.
Funding support United States, Netherlands, 3items
OrganizationGrant numberCountry
National Institutes of HealthR01AI030040-16 United States
NWOSpinoza 01.80.104.00 Netherlands
European Research CouncilAdG 233229 Netherlands
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Regulator-dependent mechanisms of C3b processing by factor I allow differentiation of immune responses.
Authors: Xue, X. / Wu, J. / Ricklin, D. / Forneris, F. / Di Crescenzio, P. / Schmidt, C.Q. / Granneman, J. / Sharp, T.H. / Lambris, J.D. / Gros, P.
History
DepositionMay 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3
B: Complement C3
C: Complement factor H,Complement factor H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,6864
Polymers218,2623
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16150 Å2
ΔGint-52 kcal/mol
Surface area87690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.900, 142.900, 312.721
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 71393.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#2: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 104073.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#3: Protein Complement factor H,Complement factor H / H factor 1


Mass: 42795.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1, HF2 / Cell line (production host): HEK293E / Production host: Homo sapiens (human) / References: UniProt: P08603
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.25 Å3/Da / Density % sol: 71.04 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 60mM Ammonium sulfate, 6% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 4.2→61.88 Å / Num. obs: 27699 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.089 / Net I/σ(I): 7.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 4.2→61.878 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.79
RfactorNum. reflection% reflection
Rfree0.2461 1393 5.03 %
Rwork0.2164 --
obs0.2175 27698 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.2→61.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15181 0 0 0 15181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415525
X-RAY DIFFRACTIONf_angle_d0.89121074
X-RAY DIFFRACTIONf_dihedral_angle_d12.1239487
X-RAY DIFFRACTIONf_chiral_restr0.0522352
X-RAY DIFFRACTIONf_plane_restr0.0052729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2009-4.35080.25691300.27882555X-RAY DIFFRACTION95
4.3508-4.52470.27881210.26072581X-RAY DIFFRACTION95
4.5247-4.73030.26311560.22732567X-RAY DIFFRACTION94
4.7303-4.97910.25791360.22032618X-RAY DIFFRACTION95
4.9791-5.29030.25721470.21532590X-RAY DIFFRACTION95
5.2903-5.69740.27741430.22742605X-RAY DIFFRACTION95
5.6974-6.26830.26381360.23412605X-RAY DIFFRACTION95
6.2683-7.16980.26071310.22092673X-RAY DIFFRACTION95
7.1698-9.0120.19831560.17592658X-RAY DIFFRACTION94
9.012-37.27630.2211360.17932803X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7799-0.0974-0.11245.5434-0.27842.3772-0.1035-1.91390.58980.81980.2181.22560.2185-0.3649-0.27781.225-0.1872-0.04991.20460.12371.5319.14940.747229.8372
20.69451.0575-0.74476.3122-0.66292.8582-0.1091-0.6988-0.29450.29880.3561-0.91970.49320.3378-0.14551.0495-0.0358-0.21821.04720.1631.004634.38242.003727.8804
30.94751.03980.10172.3068-1.1253.89760.41590.0760.08570.20620.2110.54370.2015-0.0998-0.62231.0395-0.16060.13350.9697-0.1311.132851.496727.160711.8029
45.96543.4283-1.27163.0033-0.99551.51030.00950.25750.0954-0.13960.30120.13260.2186-0.0045-0.39941.3555-0.1047-0.17011.2387-0.10331.179540.991722.9244-11.1751
52.0651-0.316-1.52880.6394-1.0465.022-0.01030.09710.2448-0.14030.4810.12720.1433-0.3979-0.60041.33-0.2033-0.42241.04410.24831.648615.30037.99194.4042
63.05593.35610.16854.1281-0.59121.2964-0.22450.70561.0967-0.5510.87121.2171-0.0681-0.1419-0.26961.2149-0.09470.16430.99580.04341.848729.038129.308413.4561
72.66173.4819-0.0285.0937-0.37790.10020.22680.01880.3397-0.32050.1310.68360.0187-0.3711-0.20921.1909-0.16810.14890.9098-0.00231.133533.768115.533814.4905
81.36062.0147-0.40172.3623-0.84630.48030.2188-0.40480.20010.1249-0.1839-0.0706-0.15880.1534-0.01081.3163-0.28540.24760.9325-0.13311.046461.700537.51317.1712
92.51271.2978-0.02422.76-1.07811.5827-0.0487-0.08120.0930.0108-0.1364-0.352-0.33450.47530.23530.8151-0.27560.08580.90610.01680.485549.0825-25.436738.7536
101.59471.36450.54111.1140.86820.3066-0.04580.1756-0.4673-0.18550.2372-0.2307-0.29890.1929-0.1411.3056-0.27480.24431.1532-0.12290.975889.365253.95287.3989
112.56253.09681.79553.80122.28041.5059-0.20030.07330.62981.1793-0.77970.4626-0.6747-1.2777-0.03122.60210.04380.18981.1835-0.23291.786559.957986.953927.084
121.3297-0.06110.68157.1148-1.80211.05680.4312-0.53460.2970.3584-0.6768-0.29010.01610.05160.0761.8668-0.27470.33891.2523-0.32151.194553.212735.61138.6464
132.0396-0.43911.16037.9461-2.61144.7138-0.358-1.00320.54850.92470.35040.636-1.0317-0.1479-0.08541.3524-0.16470.12151.4107-0.02310.839635.3142-23.394559.2718
145.0433-5.93193.29319.7923-2.00563.31580.2704-1.7744-1.75450.840.7045-0.01460.62320.6296-1.30351.21540.11470.20792.09280.00481.662759.9205-55.034465.7145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 277 )
4X-RAY DIFFRACTION4chain 'A' and (resid 278 through 412 )
5X-RAY DIFFRACTION5chain 'A' and (resid 413 through 539 )
6X-RAY DIFFRACTION6chain 'A' and (resid 540 through 582 )
7X-RAY DIFFRACTION7chain 'A' and (resid 583 through 664 )
8X-RAY DIFFRACTION8chain 'B' and (resid 752 through 1012 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1013 through 1319 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1320 through 1663 )
11X-RAY DIFFRACTION11chain 'C' and (resid 21 through 73 )
12X-RAY DIFFRACTION12chain 'C' and (resid 74 through 207 )
13X-RAY DIFFRACTION13chain 'C' and (resid 208 through 1176 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1177 through 1231 )

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