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- PDB-3g6j: C3b in complex with a C3b specific Fab -

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Basic information

Entry
Database: PDB / ID: 3g6j
TitleC3b in complex with a C3b specific Fab
Components
  • Complement C3 alpha chain
  • Complement C3 beta chain
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / Complement / C3b / Fab / Antibody:Antigen / Age-related macular degeneration / Cleavage on pair of basic residues / Complement alternate pathway / Complement pathway / Disease mutation / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Phosphoprotein / Secreted / Thioester bond
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 lipid storage / positive regulation of G protein-coupled receptor signaling pathway ...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 lipid storage / positive regulation of G protein-coupled receptor signaling pathway / 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 / complement activation, classical pathway / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / 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 angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / blood microparticle / secretory granule lumen / immune response / inflammatory response / positive regulation of protein phosphorylation / 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 2 / Complement component 3, CUB domain 1 / 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/fibulin / Anaphylatoxin, complement system / 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 / Netrin domain / NTR domain profile. / 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 / 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: 3.1 Å
AuthorsWiesmann, C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and Functional Analysis of a C3b-specific Antibody That Selectively Inhibits the Alternative Pathway of Complement
Authors: Katschke, K.J. / Stawicki, S. / Yin, J. / Steffek, M. / Xi, H. / Sturgeon, L. / Hass, P.E. / Loyet, K.M. / Deforge, L. / Wu, Y. / van Lookeren Campagne, M. / Wiesmann, C.
History
DepositionFeb 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 C3 alpha chain
C: Complement C3 beta chain
D: Complement C3 alpha chain
E: Fab light chain
F: Fab heavy chain
G: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,15010
Polymers445,0708
Non-polymers802
Water0
1
A: Complement C3 beta chain
B: Complement C3 alpha chain
E: Fab light chain
F: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,5755
Polymers222,5354
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Complement C3 beta chain
D: Complement C3 alpha chain
G: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,5755
Polymers222,5354
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Fab light chain
F: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,1392
Polymers47,1392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-29 kcal/mol
Surface area19700 Å2
MethodPISA
4
G: Fab light chain
H: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,1392
Polymers47,1392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-30 kcal/mol
Surface area19460 Å2
MethodPISA
5
A: Complement C3 beta chain
B: Complement C3 alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,4353
Polymers175,3952
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-69 kcal/mol
Surface area69970 Å2
MethodPISA
6
C: Complement C3 beta chain
D: Complement C3 alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,4353
Polymers175,3952
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-70 kcal/mol
Surface area70000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.436, 180.417, 154.584
Angle α, β, γ (deg.)90.00, 115.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 71322.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#2: Protein Complement C3 alpha chain / Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1


Mass: 104073.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#3: Antibody Fab light chain / Fragment antigen-binding


Mass: 23345.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 23793.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: Crystals of the C3b:S77 complex were obtained within a week at 19\xB0 C from 4 ml hanging drops, consisting of a 1:1 ratio of protein solution (10 mg/ml protein in 50 mM NaCl, 25 mM TRIS pH ...Details: Crystals of the C3b:S77 complex were obtained within a week at 19\xB0 C from 4 ml hanging drops, consisting of a 1:1 ratio of protein solution (10 mg/ml protein in 50 mM NaCl, 25 mM TRIS pH 7.8) to mother liquor (10% PEG 4000, 0.2 M MgCl2, 100 mM Na-HEPES, pH 7.0), suspended over mother liquor, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2007 / Details: mirrors
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 101495 / Num. obs: 101590 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.0135
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 10108 / Rsym value: 0.667 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ICF

2icf


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.829 / SU B: 49.527 / SU ML: 0.401 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 4825 5 %RANDOM
Rwork0.21437 ---
all0.2178 96423 --
obs0.2178 96819 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.199 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20.23 Å2
2---1.05 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31006 0 2 0 31008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02231675
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221426
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.96443000
X-RAY DIFFRACTIONr_angle_other_deg0.7923.00252458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37153946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47724.8351390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.418155500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.62715154
X-RAY DIFFRACTIONr_chiral_restr0.0610.24872
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0235014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026078
X-RAY DIFFRACTIONr_nbd_refined0.1850.26407
X-RAY DIFFRACTIONr_nbd_other0.180.221828
X-RAY DIFFRACTIONr_nbtor_refined0.1740.215071
X-RAY DIFFRACTIONr_nbtor_other0.080.217890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2509
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2340.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1550.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9132.520473
X-RAY DIFFRACTIONr_mcbond_other0.1982.57972
X-RAY DIFFRACTIONr_mcangle_it3.208532052
X-RAY DIFFRACTIONr_scbond_it1.362.512994
X-RAY DIFFRACTIONr_scangle_it2.177510948
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.162 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.381 270 -
Rwork0.298 5332 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -47.5365 Å / Origin y: 19.9956 Å / Origin z: -34.7955 Å
111213212223313233
T-0.002 Å20.0254 Å20.0075 Å2--0.0026 Å2-0.0038 Å2---0.0009 Å2
L0.1188 °2-0.0117 °20.0034 °2-0.1187 °20.0568 °2--0.0719 °2
S0.0081 Å °-0.1141 Å °-0.0532 Å °0.01 Å °0.039 Å °-0.0805 Å °0.0068 Å °0.0028 Å °-0.0471 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION1A104 - 207
3X-RAY DIFFRACTION1A208 - 329
4X-RAY DIFFRACTION1A330 - 424
5X-RAY DIFFRACTION1A425 - 535
6X-RAY DIFFRACTION1A536 - 642
7X-RAY DIFFRACTION1B730 - 805
8X-RAY DIFFRACTION1B806 - 912
9X-RAY DIFFRACTION1B913 - 963
10X-RAY DIFFRACTION1B964 - 1266
11X-RAY DIFFRACTION1B1267 - 1334
12X-RAY DIFFRACTION1B1335 - 1480
13X-RAY DIFFRACTION1B1481 - 1497
14X-RAY DIFFRACTION1B1498 - 1630
15X-RAY DIFFRACTION1C1 - 103
16X-RAY DIFFRACTION1C104 - 207
17X-RAY DIFFRACTION1C208 - 329
18X-RAY DIFFRACTION1C330 - 424
19X-RAY DIFFRACTION1C425 - 535
20X-RAY DIFFRACTION1C536 - 642
21X-RAY DIFFRACTION1D730 - 805
22X-RAY DIFFRACTION1D806 - 912
23X-RAY DIFFRACTION1D913 - 963
24X-RAY DIFFRACTION1D964 - 1266
25X-RAY DIFFRACTION1D1267 - 1334
26X-RAY DIFFRACTION1D1335 - 1480
27X-RAY DIFFRACTION1D1481 - 1497
28X-RAY DIFFRACTION1D1498 - 1630
29X-RAY DIFFRACTION1E1 - 109
30X-RAY DIFFRACTION1E110 - 214
31X-RAY DIFFRACTION1F1 - 110
32X-RAY DIFFRACTION1F121 - 216
33X-RAY DIFFRACTION1G1 - 109
34X-RAY DIFFRACTION1G110 - 214
35X-RAY DIFFRACTION1H1 - 110
36X-RAY DIFFRACTION1H121 - 216

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