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- PDB-3oxu: Complement components factor H CCP19-20 and C3d in complex -

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Basic information

Entry
Database: PDB / ID: 3oxu
TitleComplement components factor H CCP19-20 and C3d in complex
Components
  • Complement C3
  • HF protein
KeywordsIMMUNE SYSTEM / C3d-ALPHA-ALPHA BARREL / COMPLEMENT COMPONENT / FACTOR H
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 / complement component C3b binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance ...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 / complement component C3b binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / regulation of complement activation / 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 / complement receptor mediated signaling pathway / positive regulation of type IIa hypersensitivity / complement-dependent cytotoxicity / heparan sulfate proteoglycan binding / positive regulation of D-glucose transmembrane transport / 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 / fatty acid metabolic process / 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 / heparin binding / positive regulation of protein phosphorylation / G alpha (i) signalling events / secretory granule lumen / blood microparticle / immune response / G protein-coupled receptor signaling pathway / inflammatory response / receptor ligand activity / endoplasmic reticulum lumen / 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 / Complement Module, domain 1 / : / 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 / Complement Module; domain 1 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Glycosyltransferase - #20 / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / 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 / 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 / Glycosyltransferase / Alpha/alpha barrel / Ribbon / Immunoglobulin-like fold / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Complement C3 / Complement factor H / HF protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMorgan, H.P. / Schmidt, C.Q. / Guariento, M. / Gillespie, D. / Herbert, A.P. / Mertens, H. / Blaum, B.S. / Svergun, D. / Johansson, C.M. / Uhrin, D. ...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.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural basis for engagement by complement factor H of C3b on a self surface.
Authors: 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.
History
DepositionSep 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 C3
D: HF protein
E: HF protein
F: HF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,39114
Polymers150,6556
Non-polymers7378
Water17,078948
1
B: Complement C3
F: HF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4024
Polymers50,2182
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Complement C3
E: HF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4024
Polymers50,2182
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement C3
D: HF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5876
Polymers50,2182
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.675, 82.990, 85.605
Angle α, β, γ (deg.)112.75, 110.14, 99.96
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1 / Complement C3 beta chain / ...C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1 / Complement C3 beta chain / Complement C3 alpha chain / C3a anaphylatoxin / Complement C3b alpha' chain / Complement C3c alpha' chain fragment 1 / Complement C3dg fragment / Complement C3g fragment / Complement C3d fragment / Complement C3f fragment / Complement C3c alpha' chain fragment 2


Mass: 35444.438 Da / Num. of mol.: 3 / Fragment: UNP residues 996-1303 / Mutation: C1010A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, complement H factor, CPAMD1 / Production host: Pichia pastoris (fungus) / References: UniProt: P01024
#2: Protein HF protein


Mass: 14773.793 Da / Num. of mol.: 3 / Fragment: UNP residues 533-657
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: complement component C3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14006, UniProt: P08603*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 948 / Source method: isolated from a natural source / Formula: H2O
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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 4% w/v PEG 8000, 0.1 M Tris HCl, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→41.6 Å / Num. obs: 93199 / % possible obs: 96.4 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 4.6 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.063 / Net I/σ(I): 14.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 5.1 / Num. unique all: 13657 / Rsym value: 0.523 / % possible all: 96.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2G7I, 1C3D

2g7i

1c3d


Resolution: 2.1→40.482 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 4681 5.02 %RANDOM
Rwork0.1706 ---
obs0.1724 93157 95.86 %-
all-93199 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.065 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2635 Å2-0.0438 Å2-0.0175 Å2
2---0.8986 Å2-0.5499 Å2
3---1.1621 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9895 0 48 948 10891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710277
X-RAY DIFFRACTIONf_angle_d1.01813909
X-RAY DIFFRACTIONf_dihedral_angle_d14.9913835
X-RAY DIFFRACTIONf_chiral_restr0.0711515
X-RAY DIFFRACTIONf_plane_restr0.0041798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.23961560.20012967X-RAY DIFFRACTION95
2.1239-2.14890.22331460.1842939X-RAY DIFFRACTION96
2.1489-2.17510.241370.17872963X-RAY DIFFRACTION96
2.1751-2.20260.25481380.18463004X-RAY DIFFRACTION97
2.2026-2.23160.25611480.18942948X-RAY DIFFRACTION96
2.2316-2.26210.23911560.20582986X-RAY DIFFRACTION96
2.2621-2.29450.2521480.18522936X-RAY DIFFRACTION96
2.2945-2.32870.22341420.17662993X-RAY DIFFRACTION97
2.3287-2.36510.21751600.17412973X-RAY DIFFRACTION96
2.3651-2.40390.24251720.17512931X-RAY DIFFRACTION97
2.4039-2.44530.21891760.17392978X-RAY DIFFRACTION96
2.4453-2.48980.25561560.17552964X-RAY DIFFRACTION97
2.4898-2.53760.22991510.17432962X-RAY DIFFRACTION97
2.5376-2.58940.24331390.17993016X-RAY DIFFRACTION97
2.5894-2.64570.21791640.18362937X-RAY DIFFRACTION97
2.6457-2.70730.26491580.18482959X-RAY DIFFRACTION97
2.7073-2.77490.23791670.18752997X-RAY DIFFRACTION97
2.7749-2.850.22041360.17612971X-RAY DIFFRACTION97
2.85-2.93380.22331610.17552964X-RAY DIFFRACTION96
2.9338-3.02850.20411590.17472963X-RAY DIFFRACTION96
3.0285-3.13670.23331600.17872949X-RAY DIFFRACTION96
3.1367-3.26220.22261640.17922939X-RAY DIFFRACTION96
3.2622-3.41060.21511780.17712882X-RAY DIFFRACTION95
3.4106-3.59030.21891390.17792956X-RAY DIFFRACTION95
3.5903-3.81510.19961720.16932865X-RAY DIFFRACTION94
3.8151-4.10940.17461490.16032855X-RAY DIFFRACTION93
4.1094-4.52240.17081410.14192630X-RAY DIFFRACTION86
4.5224-5.17570.16981810.13643009X-RAY DIFFRACTION98
5.1757-6.51640.19791660.18183017X-RAY DIFFRACTION99
6.5164-40.48960.13851610.15343023X-RAY DIFFRACTION98

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