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- PDB-5fo7: Crystal Structure of Human Complement C3b at 2.8 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5fo7
TitleCrystal Structure of Human Complement C3b at 2.8 Angstrom resolution
Components
  • COMPLEMENT C3 BETA CHAIN
  • COMPLEMENT C3B ALPHA' CHAIN
KeywordsLIPID BINDING / COMPLEMENT SYSTEM / IMMUNE SYSTEM / PLASMA PROTEIN
Function / homology
Function and homology information


oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / N-terminal domain of TfIIb / : ...Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / N-terminal domain of TfIIb / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / 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 / Glycosyltransferase - #20 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / 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 / Other non-globular / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Single Sheet / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Jelly Rolls / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsForneris, F. / Wu, J. / Xue, X. / Gros, P.
CitationJournal: Embo J. / Year: 2016
Title: Regulators of Complement Activity Mediate Inhibitory Mechanisms Through a Common C3B-Binding Mode.
Authors: Forneris, F. / Wu, J. / Xue, X. / Ricklin, D. / Lin, Z. / Sfyroera, G. / Tzekou, A. / Volokhina, E. / Granneman, J.C. / Hauhart, R. / Bertram, P. / Liszewski, M.K. / Atkinson, J.P. / Lambris, J.D. / Gros, P.
History
DepositionNov 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 BETA CHAIN
B: COMPLEMENT C3B ALPHA' CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,9104
Polymers175,4672
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-44.8 kcal/mol
Surface area68690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.580, 136.510, 140.930
Angle α, β, γ (deg.)90.00, 96.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein COMPLEMENT C3 BETA CHAIN / C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 1


Mass: 71393.320 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-667 / Source method: isolated from a natural source / Details: PURIFIED FROM HUMAN PLASMA / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P01024
#2: Protein COMPLEMENT C3B ALPHA' CHAIN / C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 1


Mass: 104074.148 Da / Num. of mol.: 1 / Fragment: RESIDUES 749-1663 / Source method: isolated from a natural source / Details: PURIFIED FROM HUMAN PLASMA / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P01024
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Sequence detailsRESIDUE 1013 HAS BEEN CONVERTED FROM GLN TO GLU IN CONVERSION OF C3 PROTEIN TO C3B

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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: 3.44 Å3/Da / Density % sol: 64.3 % / Description: NONE
Crystal growDetails: 8% PEG 3350 35MM BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.8→70.07 Å / Num. obs: 109359 / % possible obs: 96.8 % / Observed criterion σ(I): 1.5 / Redundancy: 2.1 % / Biso Wilson estimate: 70.34 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I07

2i07


Resolution: 2.8→36.808 Å / SU ML: 0.48 / σ(F): 1.34 / Phase error: 33.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 2600 5.1 %
Rwork0.2292 --
obs0.2312 51243 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12122 0 28 0 12150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312402
X-RAY DIFFRACTIONf_angle_d0.6716810
X-RAY DIFFRACTIONf_dihedral_angle_d11.8194636
X-RAY DIFFRACTIONf_chiral_restr0.0241920
X-RAY DIFFRACTIONf_plane_restr0.0032169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.85090.44541370.38382630X-RAY DIFFRACTION98
2.8509-2.90570.35071430.35942615X-RAY DIFFRACTION98
2.9057-2.9650.37391470.33082553X-RAY DIFFRACTION98
2.965-3.02950.33131650.32232646X-RAY DIFFRACTION98
3.0295-3.09990.36591270.30372571X-RAY DIFFRACTION99
3.0999-3.17740.35981360.29142636X-RAY DIFFRACTION98
3.1774-3.26320.31061220.28562613X-RAY DIFFRACTION98
3.2632-3.35920.30021260.27322651X-RAY DIFFRACTION99
3.3592-3.46760.36161390.32212480X-RAY DIFFRACTION95
3.4676-3.59140.30161420.2792639X-RAY DIFFRACTION98
3.5914-3.7350.32661230.31432514X-RAY DIFFRACTION95
3.735-3.90490.33521480.2772556X-RAY DIFFRACTION96
3.9049-4.11050.25631410.23732559X-RAY DIFFRACTION96
4.1105-4.36760.23691290.19882585X-RAY DIFFRACTION97
4.3676-4.70420.21441290.17072567X-RAY DIFFRACTION96
4.7042-5.17650.21341420.15282518X-RAY DIFFRACTION95
5.1765-5.92280.22471400.18262497X-RAY DIFFRACTION93
5.9228-7.4520.23891370.20152364X-RAY DIFFRACTION88
7.452-36.81130.19071270.16182449X-RAY DIFFRACTION90
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)
11.5926-0.5280.06520.4780.17160.0889-0.2910.8190.4114-1.23890.3535-0.41190.0769-0.02380.13122.3996-0.1345-0.17351.15350.29430.779330.370125.758721.5907
21.26970.32110.5660.8634-0.77362.4926-0.26570.43450.4324-0.8166-0.02570.2889-0.38610.03270.1451.0266-0.0625-0.17480.48410.17320.669926.134432.471345.8195
31.21071.1598-0.20751.8204-0.55252.1565-0.04360.12440.0924-0.8481-0.0920.27040.4765-0.16770.22380.54710.0228-0.01920.4684-0.02510.552718.60288.98370.6445
41.86530.11020.45241.2070.1763.70010.01560.2376-0.2578-1.0814-0.06970.39871.1088-0.40590.1581.2804-0.1658-0.10040.3544-0.04310.766314.3787-1.393658.7703
51.2981-0.21450.01331.02950.64060.6609-0.00380.4856-0.4142-1.0824-0.0852-0.050.86420.2566-0.12452.2613-0.068-0.00711.0029-0.18250.665424.37571.039929.8612
61.22780.5450.02911.06070.52731.1731-0.42070.2571-0.0817-1.3918-0.00520.34990.15971.292-0.04621.10570.0990.08780.95370.0720.569335.377113.036147.5398
70.51780.1920.1374-0.01590.02680.2508-0.19690.25090.1685-1.2095-0.00960.61570.0078-0.61470.01821.7635-0.0691-0.31160.78640.0230.643520.281317.322332.9585
828.1494-9.076921.99992-4.19669.1477.87962.1808-2.3694-10.886-33.01567.05646.5842.1674-0.49790.04671.82850.66932.3746.52719.635841.7992
91.7905-0.36160.03641.24190.00683.3838-0.0919-0.12410.02140.0187-0.0346-0.1836-0.13780.58610.10150.1981-0.05970.05630.54910.0650.565435.962820.812387.3773
102.2458-1.0046-0.17671.3727-0.84051.3657-0.1507-0.5652-0.2338-0.27590.78440.6402-0.4461-0.9816-0.18640.6320.0725-0.09190.64350.00060.66318.530845.91478.8785
110.2878-0.05092.5661-1.11070.3613.9472-0.7293-0.41140.78290.2405-0.29890.1232-0.9647-0.24240.31721.7334-0.2053-0.53460.8352-0.11931.0151-0.106553.423619.385
121.68080.9050.46862.178-1.01980.8323-0.30540.0649-0.0279-0.36040.6749-0.2218-0.09420.7652-0.34490.90950.0568-0.04990.7632-0.15130.859.917752.225865.3616
132.59860.06081.20511.73550.63654.4464-0.4338-0.08380.5626-1.0531-0.30611.5907-0.7635-1.0079-1.021-0.1029-0.04150.27760.88450.34760.76984.432816.1105100.0901
141.3045-0.58780.07532.39141.45821.88020.0231-0.2824-0.68550.91740.532-0.22580.89890.1172-0.04750.3123-0.01480.12720.60590.2920.862114.30653.9585100.466
150.59880.76071.10551.65440.5872.861-0.2016-0.0976-0.00820.18630.0482-0.0679-0.57250.10560.1450.41460.0660.070.76070.02440.546120.653326.6286111.0303
162.25250.44931.14913.11090.96563.8452-0.7362-0.54690.67470.0761-0.45480.6016-1.2138-1.15330.75161.110.1394-0.23310.6313-0.14110.797921.374343.316128.4389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 39 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 40 THROUGH 188 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 189 THROUGH 255 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 256 THROUGH 390 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 391 THROUGH 485 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 486 THROUGH 590 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 591 THROUGH 642 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 643 THROUGH 643 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 752 THROUGH 921 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 922 THROUGH 976 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 977 THROUGH 1284 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 1285 THROUGH 1350 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 1351 THROUGH 1400 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 1401 THROUGH 1456 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 1457 THROUGH 1544 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 1545 THROUGH 1663 )

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