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- PDB-3l3o: Staphylococcal Complement Inhibitor (SCIN) in complex with Human ... -

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Basic information

Entry
Database: PDB / ID: 3l3o
TitleStaphylococcal Complement Inhibitor (SCIN) in complex with Human Complement Component C3c
Components
  • (Complement C3) x 3
  • Staphylococcal complement inhibitor
KeywordsIMMUNE SYSTEM / Complement alternate pathway / Complement pathway / Converstase / Immune response / Inflammatory response / Innate immunity / Secreted / Virulence / Immune evasion
Function / homology
Function and homology information


C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / 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 / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment ...C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / 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 / 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 / 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 / Post-translational protein phosphorylation / response to bacterium / 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 / 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 / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Alpha-macroglobulin, receptor-binding domain / S-adenosyl-L-methionine-dependent methyltransferases / Macroglobulin (MG2) domain / Immunoglobulin-like - #1940 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 ...Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Alpha-macroglobulin, receptor-binding domain / S-adenosyl-L-methionine-dependent methyltransferases / Macroglobulin (MG2) domain / Immunoglobulin-like - #1940 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / N-terminal domain of TfIIb / 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 / Other non-globular / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Single Sheet / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Complement C3 / Staphylococcal complement inhibitor
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.405 Å
AuthorsGeisbrecht, B.V. / Garcia, B.G.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Molecular Basis for Complement Recognition and Inhibition Determined by Crystallographic Studies of the Staphylococcal Complement Inhibitor (SCIN) Bound to C3c and C3b.
Authors: Garcia, B.L. / Ramyar, K.X. / Tzekou, A. / Ricklin, D. / McWhorter, W.J. / Lambris, J.D. / Geisbrecht, B.V.
History
DepositionDec 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 6, 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
Revision 1.6Nov 6, 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
M: Staphylococcal complement inhibitor
P: Staphylococcal complement inhibitor
F: Complement C3
D: Complement C3
C: Complement C3
E: Complement C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,67510
Polymers289,2338
Non-polymers4422
Water00
1
A: Complement C3
B: Complement C3
M: Staphylococcal complement inhibitor
C: Complement C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8385
Polymers144,6164
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: Staphylococcal complement inhibitor
F: Complement C3
D: Complement C3
E: Complement C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8385
Polymers144,6164
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.110, 217.028, 115.654
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Complement C3


Mass: 71393.320 Da / Num. of mol.: 2 / Fragment: residues 23-667 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#2: Protein Complement C3


Mass: 23621.244 Da / Num. of mol.: 2 / Fragment: residues 749-954 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#3: Protein Staphylococcal complement inhibitor / SCIN


Mass: 10064.370 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: SAV1942, scn / Plasmid: pt7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q931M7
#4: Protein Complement C3


Mass: 39537.418 Da / Num. of mol.: 2 / Fragment: residues 1321-1663 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#5: 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
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: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 5mg/ml, 0.1M HEPES, 10% PEG 6000, 5% 2-Methyl-2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2009 / Details: mirrors
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 6.5 / Number: 152670 / Rmerge(I) obs: 0.161 / Χ2: 1.11 / D res high: 3.4 Å / D res low: 50 Å / Num. obs: 45397 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.325098.810.0680.4073.5
5.817.3299.610.1181.2193.5
5.085.8199.310.1251.2923.5
4.615.0898.910.1251.3793.5
4.284.6197.810.1491.2453.4
4.034.2897.610.1991.1293.4
3.834.0397.810.2741.123.4
3.663.8396.610.3361.0913.3
3.523.6695.910.411.1443.2
3.43.5293.110.4971.0472.8
ReflectionResolution: 3.4→50 Å / Num. all: 48213 / Num. obs: 45397 / % possible obs: 97.5 % / Observed criterion σ(F): 2.38 / Observed criterion σ(I): 2.38 / Redundancy: 3.4 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 5
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.38 / % possible all: 93.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.99 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.4 Å49.97 Å
Translation3.4 Å49.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A74,2QFF

2a74

2qff


Resolution: 3.405→34.522 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.38 / σ(F): 0.21 / Phase error: 27.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 1857 4.39 %
Rwork0.223 --
obs0.2251 42338 91.04 %
all-42376 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.458 Å2 / ksol: 0.256 e/Å3
Displacement parametersBiso mean: 108.06 Å2
Baniso -1Baniso -2Baniso -3
1--12.254 Å2-0 Å2-1.004 Å2
2---45.076 Å20 Å2
3----39.562 Å2
Refinement stepCycle: LAST / Resolution: 3.405→34.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19062 0 28 0 19090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00919478
X-RAY DIFFRACTIONf_angle_d1.19526366
X-RAY DIFFRACTIONf_dihedral_angle_d19.5057252
X-RAY DIFFRACTIONf_chiral_restr0.0713008
X-RAY DIFFRACTIONf_plane_restr0.0073386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.405-3.49690.38781200.31532643X-RAY DIFFRACTION78
3.4969-3.59970.411360.2962877X-RAY DIFFRACTION84
3.5997-3.71570.28681340.27592856X-RAY DIFFRACTION85
3.7157-3.84840.28081380.2733057X-RAY DIFFRACTION88
3.8484-4.00220.2911450.24993013X-RAY DIFFRACTION90
4.0022-4.18410.29821410.2373102X-RAY DIFFRACTION91
4.1841-4.40430.27041400.20743208X-RAY DIFFRACTION93
4.4043-4.67960.23731460.18173212X-RAY DIFFRACTION95
4.6796-5.03990.1841560.16623263X-RAY DIFFRACTION95
5.0399-5.54520.2551500.16513297X-RAY DIFFRACTION96
5.5452-6.34330.2291500.19493273X-RAY DIFFRACTION95
6.3433-7.97560.25371510.18883322X-RAY DIFFRACTION97
7.9756-34.52410.23071500.19893358X-RAY DIFFRACTION96

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