[English] 日本語
Yorodumi
- PDB-3km9: Structure of complement C5 in complex with the C-terminal beta-gr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3km9
TitleStructure of complement C5 in complex with the C-terminal beta-grasp domain of SSL7
Components
  • Complement C5Complement component 5
  • 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 / inflammatory response / G protein-coupled receptor signaling pathway / 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/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial ...Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / : / Complement component 5, CUB domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Superantigen toxin, C-terminal / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / 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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
Components

#1: Protein Complement C5 / Complement component 5 / 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 / N-Acetylglucosamine


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
Sequence details802TH IS ILE IN THIS ENTRY, WHICH IS A NATURAL VARIANT REFERRED IN P01031 IN UNIPROT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more