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- PDB-3kls: Structure of complement C5 in complex with SSL7 -

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Basic information

Entry
Database: PDB / ID: 3kls
TitleStructure of complement C5 in complex with SSL7
Components
  • Complement C5
  • Exotoxin 1
KeywordsIMMUNE SYSTEM / OB-fold / b-grasp domain / FN3 domain / Cleavage on pair of basic residues / Complement alternate pathway / Complement pathway / Cytolysis / Disulfide bond / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Membrane attack complex / Secreted
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Peptide ligand-binding receptors / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Pheromone ER-1 / Pheromone ER-1 - #10 / Jelly Rolls - #1540 / Anaphylotoxins (complement system) / Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Alpha-macroglobulin, receptor-binding domain / S-adenosyl-L-methionine-dependent methyltransferases ...Pheromone ER-1 / Pheromone ER-1 - #10 / Jelly Rolls - #1540 / Anaphylotoxins (complement system) / Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Alpha-macroglobulin, receptor-binding domain / S-adenosyl-L-methionine-dependent methyltransferases / Influenza Virus Matrix Protein; Chain A, domain 1 / Macroglobulin (MG2) domain / Immunoglobulin-like - #1940 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / : / Complement component 5, CUB domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / 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 / Enterotoxin / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Single Sheet / Helix non-globular / Special / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Jelly Rolls / Roll / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Exotoxin 1 / Complement C5 / Exotoxin 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsLaursen, N.S. / Gordon, N. / Hermans, S. / Lorenz, N. / Jackson, N. / Wines, B. / Spillner, E. / Christensen, J.B. / Jensen, M. / Fredslund, F. ...Laursen, N.S. / Gordon, N. / Hermans, S. / Lorenz, N. / Jackson, N. / Wines, B. / Spillner, E. / Christensen, J.B. / Jensen, M. / Fredslund, F. / Bjerre, M. / Sottrup-Jensen, L. / Fraser, J.D. / Andersen, G.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for inhibition of complement C5 by the SSL7 protein from Staphylococcus aureus
Authors: Laursen, N.S. / Gordon, N. / Hermans, S. / Lorenz, N. / Jackson, N. / Wines, B. / Spillner, E. / Christensen, J.B. / Jensen, M. / Fredslund, F. / Bjerre, M. / Sottrup-Jensen, L. / Fraser, J.D. / Andersen, G.R.
History
DepositionNov 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 30, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C5
X: Exotoxin 1
B: Complement C5
Y: Exotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,38417
Polymers429,0814
Non-polymers2,30313
Water00
1
A: Complement C5
X: Exotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,7489
Polymers214,5412
Non-polymers1,2087
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-27 kcal/mol
Surface area83390 Å2
MethodPISA
2
B: Complement C5
Y: Exotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,6368
Polymers214,5412
Non-polymers1,0956
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-24 kcal/mol
Surface area75780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.875, 143.875, 241.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Complement C5 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4 / Complement C5 beta chain / ...C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4 / Complement C5 beta chain / Complement C5 alpha chain / C5a anaphylatoxin / Complement C5 alpha' chain


Mass: 188526.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Outdated plasma pools / Source: (natural) Homo sapiens (human) / Tissue: Blood / References: UniProt: P01031
#2: Protein Exotoxin 1 / SSL7


Mass: 26014.383 Da / Num. of mol.: 2 / Mutation: E35G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MRSA252 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GJP2, UniProt: A0A7U7ETZ3*PLUS
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#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
Sequence details802TH IS ILE IN THIS ENTRY, WHICH IS A NATURAL VARIANT REFERRED IN P01031 IN UNIPROT.

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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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.2
Details: Reservoir contains 50mM MgAc2, 50 mM MES pH 6.2, mixed 1:1 with protein, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 18, 2008
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 3.6→29.047 Å / Num. all: 64230 / Num. obs: 64555 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 110.89 Å2 / Rsym value: 0.085 / Net I/σ(I): 11
Reflection shellResolution: 3.6→3.8 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CU7 chain A residues 20-1510

3cu7


Resolution: 3.6→29.047 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.803 / SU ML: 0.37 / σ(F): 1.99 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 3205 4.99 %random
Rwork0.1977 61025 --
obs0.2009 64230 99.49 %-
all-64555 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 120.556 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso max: 414.93 Å2 / Biso mean: 156.921 Å2 / Biso min: 43.25 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.6→29.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27590 0 93 0 27683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01228268
X-RAY DIFFRACTIONf_angle_d1.65838275
X-RAY DIFFRACTIONf_chiral_restr0.1054359
X-RAY DIFFRACTIONf_plane_restr0.0074875
X-RAY DIFFRACTIONf_dihedral_angle_d21.16310296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6002-3.65380.34751680.30422584X-RAY DIFFRACTION100
3.6538-3.71080.39971490.30012654X-RAY DIFFRACTION99
3.7108-3.77150.38231400.29212678X-RAY DIFFRACTION99
3.7715-3.83640.32031310.27172637X-RAY DIFFRACTION100
3.8364-3.9060.3511370.24432666X-RAY DIFFRACTION99
3.906-3.98090.2741290.23972648X-RAY DIFFRACTION100
3.9809-4.0620.27861430.21762636X-RAY DIFFRACTION99
4.062-4.15010.26271610.20792649X-RAY DIFFRACTION100
4.1501-4.24630.24821350.19832705X-RAY DIFFRACTION100
4.2463-4.35220.25241210.18972628X-RAY DIFFRACTION100
4.3522-4.46940.24341400.17312726X-RAY DIFFRACTION100
4.4694-4.60050.22951390.16142586X-RAY DIFFRACTION100
4.6005-4.74830.18331560.15422676X-RAY DIFFRACTION100
4.7483-4.91730.20841540.15542632X-RAY DIFFRACTION100
4.9173-5.11310.22181070.14372689X-RAY DIFFRACTION100
5.1131-5.34450.22261520.15312672X-RAY DIFFRACTION100
5.3445-5.62430.20231420.17242620X-RAY DIFFRACTION100
5.6243-5.97380.27941490.17482700X-RAY DIFFRACTION100
5.9738-6.43050.26491250.19412638X-RAY DIFFRACTION100
6.4305-7.06910.2891150.19082675X-RAY DIFFRACTION99
7.0691-8.07280.30851650.1922625X-RAY DIFFRACTION99
8.0728-10.09930.20061200.16112674X-RAY DIFFRACTION99
10.0993-29.04760.25561270.20582627X-RAY DIFFRACTION98

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