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- PDB-3km9: Structure of complement C5 in complex with the C-terminal beta-gr... -

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Basic information

Entry
Database: PDB / ID: 3km9
TitleStructure of complement C5 in complex with the C-terminal beta-grasp domain of SSL7
Components
  • Complement C5
  • Staphylococcal enterotoxin-like toxin
KeywordsIMMUNE SYSTEM / OB-fold / beta-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 ...: / 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
Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / : / Complement component 5, CUB domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain ...Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / : / Complement component 5, CUB domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / 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 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Staphylococcal superantigen-like 7 / Staphylococcal superantigen-like 7 / Complement C5
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 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 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_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 / _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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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 2.2Oct 30, 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: Staphylococcal enterotoxin-like toxin
B: Complement C5
Y: Staphylococcal enterotoxin-like toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)402,44613
Polymers400,5934
Non-polymers1,8539
Water00
1
A: Complement C5
X: Staphylococcal enterotoxin-like toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,2797
Polymers200,2962
Non-polymers9835
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C5
Y: Staphylococcal enterotoxin-like toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,1676
Polymers200,2962
Non-polymers8704
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.790, 144.790, 245.280
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 Staphylococcal enterotoxin-like toxin / SSL7


Mass: 11770.348 Da / Num. of mol.: 2 / Fragment: C-terminal beta-grasp domain, residues 129-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Newman / Plasmid: pET-32a-3c / Production host: Escherichia coli (E. coli) / References: UniProt: A6QE84, UniProt: A0A0H3K6Z8*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.: 5 / 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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.2
Details: Reservoir contains 50mM MgAc2, 50mM MES pH 6.2. Mixed 1:1 with concentrated protein, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2009
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. all: 41983 / Num. obs: 41914 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 115.36 Å2 / Rsym value: 0.141 / Net I/σ(I): 14.4
Reflection shellResolution: 4.2→4.4 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CU7 with the C345C domain removed

3cu7


Resolution: 4.2→49.752 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.751 / SU ML: 0.6 / σ(F): 1.99 / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2971 2029 4.85 %random
Rwork0.2333 39763 --
obs0.2364 41792 99.6 %-
all-41960 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 150 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 536.65 Å2 / Biso mean: 205.604 Å2 / Biso min: 77.33 Å2
Baniso -1Baniso -2Baniso -3
1-36.235 Å2-0 Å2-0 Å2
2--36.235 Å2-0 Å2
3----45.221 Å2
Refinement stepCycle: LAST / Resolution: 4.2→49.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24720 0 89 0 24809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01125344
X-RAY DIFFRACTIONf_angle_d1.55134334
X-RAY DIFFRACTIONf_chiral_restr0.0973922
X-RAY DIFFRACTIONf_plane_restr0.0074356
X-RAY DIFFRACTIONf_dihedral_angle_d20.6219212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2004-4.30540.36081400.31482865X-RAY DIFFRACTION100
4.3054-4.42170.28111320.27292850X-RAY DIFFRACTION100
4.4217-4.55170.27061570.24272835X-RAY DIFFRACTION100
4.5517-4.69860.30921440.22582844X-RAY DIFFRACTION100
4.6986-4.86630.28271430.22042806X-RAY DIFFRACTION100
4.8663-5.0610.24671720.1912848X-RAY DIFFRACTION99
5.061-5.29110.21441260.18682854X-RAY DIFFRACTION100
5.2911-5.56970.2821520.18842875X-RAY DIFFRACTION100
5.5697-5.91810.31630.20642771X-RAY DIFFRACTION100
5.9181-6.37420.29991380.22152869X-RAY DIFFRACTION100
6.3742-7.01410.29651270.21432840X-RAY DIFFRACTION100
7.0141-8.02540.29581760.20532836X-RAY DIFFRACTION100
8.0254-10.09730.23611250.16192854X-RAY DIFFRACTION99
10.0973-49.75540.29261340.23082816X-RAY DIFFRACTION98

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