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- PDB-2i07: Human Complement Component C3b -

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Basic information

Entry
Database: PDB / ID: 2i07
TitleHuman Complement Component C3b
Components(Complement C3b) x 2
KeywordsIMMUNE SYSTEM / C3b consists of 12 domains
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: 4 Å
AuthorsJanssen, B.J.C. / Christodoulidou, A. / McCarthy, A. / Lambris, J.D. / Gros, P.
CitationJournal: Nature / Year: 2006
Title: Structure of C3b reveals conformational changes that underlie complement activity.
Authors: Janssen, B.J. / Christodoulidou, A. / McCarthy, A. / Lambris, J.D. / Gros, P.
History
DepositionAug 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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 / _atom_site.label_entity_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: 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
Remark 999SEQUENCE RESIDUE 991 HAS BEEN CONVERTED FROM A GLN TO A GLU IN THE CONVERSION OF C3 TO C3B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3b
B: Complement C3b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,2914
Polymers175,4842
Non-polymers8082
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-47 kcal/mol
Surface area69150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.910, 128.537, 147.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThere is one biological unit in the asymmetric unit

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Components

#1: Protein Complement C3b


Mass: 71409.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Secretion: Serum / References: UniProt: P01024
#2: Protein Complement C3b


Mass: 104074.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Secretion: Serum / References: UniProt: P01024
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 1
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

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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: 3.33 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: PEG-MME 2000, sodium acetate, Bis-Tris propane, taurine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 4→45 Å / Num. all: 20515 / Num. obs: 20474 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 100 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 10.1
Reflection shellResolution: 4→4.22 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2 / Num. unique all: 2911 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DNAdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A73, 2A74, 1C3D

2a73

2a74

1c3d


Resolution: 4→45 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.842 / SU B: 153.838 / SU ML: 0.935 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 1.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32293 1045 5.1 %RANDOM
Rwork0.27259 ---
all0.275 20412 --
obs0.27524 20474 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 174.051 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2--14.01 Å20 Å2
3----15.31 Å2
Refinement stepCycle: LAST / Resolution: 4→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12104 0 53 0 12157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02212411
X-RAY DIFFRACTIONr_angle_refined_deg0.741.97216839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.37851525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.0624.91558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.389152201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0921565
X-RAY DIFFRACTIONr_chiral_restr0.0520.21923
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029255
X-RAY DIFFRACTIONr_nbd_refined0.2330.35466
X-RAY DIFFRACTIONr_nbtor_refined0.3280.58401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.5532
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.371
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.53
X-RAY DIFFRACTIONr_mcbond_it01.57635
X-RAY DIFFRACTIONr_mcangle_it0212420
X-RAY DIFFRACTIONr_scbond_it034776
X-RAY DIFFRACTIONr_scangle_it04.54419
LS refinement shellResolution: 4→4.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 76 -
Rwork0.334 1392 -
obs--99.93 %
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)
110.02962.52472.337214.49515.023214.7951-0.4928-0.32440.4810.07750.4057-1.06820.55552.83010.087-0.70480.6271-0.2013-0.61960.0796-0.526728.5596-19.4144-24.0512
27.82142.37495.623111.26027.74921.04350.1911-0.2655-1.04280.70340.43840.02681.9751.6657-0.6295-0.98830.22810.0466-0.822-0.0605-0.806922.9441-32.7926-58.7246
314.60822.0387-8.70191.0154-1.578317.0259-0.13030.4195-0.330.41760.03490.0657-0.1856-1.25240.0954-0.8844-0.0187-0.1012-0.496-0.2882-0.8022-10.629-27.6419-68.758
417.7914-0.585513.87521.68770.436631.1845-0.7266-0.3220.7730.34780.0770.4434-0.7189-2.27340.6496-0.72250.13690.2179-0.9311-0.1908-0.6087-9.4915-14.6489-36.4683
59.9873-0.4029-2.64837.08881.949822.2171-0.1761-0.71260.74270.37330.46650.6854-0.8127-1.1871-0.2904-1.00160.366-0.1019-1.0431-0.0487-0.710110.157-7.4673-25.8258
66.83440.96273.73675.01723.492717.1134-0.74050.46290.8922-0.33350.2626-0.0728-1.35380.7690.4779-0.8117-0.29090.0459-0.7220.1273-0.689419.8457-13.3218-68.5331
78.9144-5.963-0.0617.3612-0.6417.3499-0.2341.01390.0354-1.47240.3536-0.5028-0.3476-0.0696-0.1196-0.5913-0.26550.06970.303-0.2565-1.001210.6608-27.567-96.2175
815.0044-1.2639-3.83947.2053-0.946917.97490.02911.2691-0.4271-0.41860.1834-0.42510.5340.0698-0.2125-0.7769-0.3863-0.04240.1289-0.4384-0.6762-8.8463-37.8723-95.4345
97.0845-2.8766-6.65861.47664.728820.2564-0.11190.4596-1.19630.83740.34480.36863.0744-4.1328-0.233-0.3429-0.0691-0.0779-1.51030.0032-0.211412.6468-23.0398-30.9601
108.2897-1.81871.429.51131.701110.5972-0.2845-0.1556-0.6722-0.3702-0.0087-0.83071.52221.15710.29310.4930.69190.1956-0.16960.5274-0.413737.5579-53.6079-9.5397
1118.5444-1.2726-0.45089.3819-0.238512.6810.0756-0.20630.16510.0167-0.272-0.01690.16140.67240.19640.58440.36560.14660.3337-0.1113-0.31423.2411-53.4229-122.3984
1235.3734-12.279728.745122.8888-32.7255119.2556-0.39274.26842.2203-1.8213-1.7607-1.8543-0.16113.77142.1534-0.059-0.42340.31020.05280.0864-0.588117.9393-18.4906-100.9597
139.8005-0.46576.99695.1672-2.427817.27640.14190.6735-0.04971.0483-0.35670.4258-0.27212.09490.21480.95750.36020.11120.2558-0.43540.207830.0197-55.9808-63.0359
1463.5587-31.190830.572323.9731-13.602714.9318-2.0486-4.79460.6353-1.3752.3236-2.0082.7528-0.9026-0.2750.41390.2310.56781.5048-1.1785-0.263614.0855-48.3717-102.8476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1031 - 103
2X-RAY DIFFRACTION1AC646 - 648
3X-RAY DIFFRACTION2AA104 - 204104 - 204
4X-RAY DIFFRACTION3AA205 - 329205 - 329
5X-RAY DIFFRACTION4AA330 - 424330 - 424
6X-RAY DIFFRACTION5AA425 - 535425 - 535
7X-RAY DIFFRACTION6AA536 - 590536 - 590
8X-RAY DIFFRACTION6BB745 - 80419 - 78
9X-RAY DIFFRACTION7BB805 - 91279 - 186
10X-RAY DIFFRACTION8BB1335 - 1476609 - 750
11X-RAY DIFFRACTION9AA591 - 642591 - 642
12X-RAY DIFFRACTION10BB969 - 1266243 - 540
13X-RAY DIFFRACTION11BB1496 - 1641770 - 915
14X-RAY DIFFRACTION12BB730 - 7444 - 18
15X-RAY DIFFRACTION13BB913 - 968187 - 242
16X-RAY DIFFRACTION13BB1267 - 1334541 - 608
17X-RAY DIFFRACTION13BD1
18X-RAY DIFFRACTION14BB1477 - 1495751 - 769

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