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- PDB-6og4: plasminogen binding group A streptococcal M protein -

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Basic information

Entry
Database: PDB / ID: 6og4
Titleplasminogen binding group A streptococcal M protein
Components
  • Plasminogen-binding group A streptococcal M-like protein PAM
  • PlasminogenPlasmin
KeywordsHYDROLASE/PROTEIN BINDING / PAM / plasminogen / invasion / fibrinolysis / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / plasminogen activation / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / Schaffer collateral - CA1 synapse / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / blood microparticle / endopeptidase activity / protease binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Streptococcal M proteins C repeat profile. / Streptococcal M proteins D repeats region profile. / Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain ...Streptococcal M proteins C repeat profile. / Streptococcal M proteins D repeats region profile. / Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / YSIRK Gram-positive signal peptide / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Plasminogen / Plasminogen-binding group A streptococcal M-like protein PAM
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLaw, R.H.P. / Quek, A.J. / Whisstock, J.C. / Caradoc-Davies, T.T.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1127593 Australia
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Structure and Function Characterization of the a1a2 Motifs of Streptococcus pyogenes M Protein in Human Plasminogen Binding.
Authors: Quek, A.J.H. / Mazzitelli, B.A. / Wu, G. / Leung, E.W.W. / Caradoc-Davies, T.T. / Lloyd, G.J. / Jeevarajah, D. / Conroy, P.J. / Sanderson-Smith, M. / Yuan, Y. / Ayinuola, Y.A. / Castellino, ...Authors: Quek, A.J.H. / Mazzitelli, B.A. / Wu, G. / Leung, E.W.W. / Caradoc-Davies, T.T. / Lloyd, G.J. / Jeevarajah, D. / Conroy, P.J. / Sanderson-Smith, M. / Yuan, Y. / Ayinuola, Y.A. / Castellino, F.J. / Whisstock, J.C. / Law, R.H.P.
History
DepositionApr 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasminogen
B: Plasminogen
C: Plasminogen-binding group A streptococcal M-like protein PAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2665
Polymers29,0733
Non-polymers1922
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Shift in elution volumes relative to individual plasminogen KR2 and PAM VEK75, light scattering, Increase in molecular weight indicating that 2 plasminogen KR2 are bound to one PAM VEK75
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-42 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.599, 52.599, 198.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUHISHIS(chain 'A' and (resid 164 through 169 or resid 171...AA164 - 1686 - 10
12GLYGLYCYSCYS(chain 'A' and (resid 164 through 169 or resid 171...AA171 - 24313 - 85
23GLUGLUHISHIS(chain 'B' and (resid 164 through 169 or resid 171 through 243))BB164 - 1686 - 10
24GLYGLYCYSCYS(chain 'B' and (resid 164 through 169 or resid 171 through 243))BB171 - 24313 - 85

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Components

#1: Protein Plasminogen / Plasmin


Mass: 10017.235 Da / Num. of mol.: 2 / Fragment: Kringle 2 domain (UNP residues 183-264) / Mutation: C169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Plasmid: pSecTag2 A / Cell (production host): epithelial / Cell line (production host): HEK293 / Organ (production host): embryonic kidney / Production host: Homo sapiens (human) / References: UniProt: P00747, plasmin
#2: Protein Plasminogen-binding group A streptococcal M-like protein PAM / Plasminogen-binding Group A Streptococcal M protein VEK75


Mass: 9038.926 Da / Num. of mol.: 1 / Fragment: UNP residues 76-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: pam, emm / Production host: Escherichia coli (E. coli) / References: UniProt: P49054
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.84 % / Description: cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, pH 7.0, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.699→46.46 Å / Num. obs: 31726 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 26.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.0365 / Net I/σ(I): 15
Reflection shellResolution: 1.699→1.76 Å / Rmerge(I) obs: 0.236 / Num. unique obs: 3048 / CC1/2: 0.853 / Rrim(I) all: 0.334

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DUR

4dur


Resolution: 1.7→46.46 Å / SU ML: 0.1721 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.351
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1617 5.1 %Random
Rwork0.2029 ---
obs0.2038 31725 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.39 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 10 128 1733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591659
X-RAY DIFFRACTIONf_angle_d0.8592244
X-RAY DIFFRACTIONf_chiral_restr0.0522216
X-RAY DIFFRACTIONf_plane_restr0.0061297
X-RAY DIFFRACTIONf_dihedral_angle_d12.86131031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.28871230.23642397X-RAY DIFFRACTION98.09
1.75-1.810.28261170.21572473X-RAY DIFFRACTION100
1.81-1.870.24941310.21312471X-RAY DIFFRACTION100
1.87-1.940.23061240.20562466X-RAY DIFFRACTION100
1.94-2.030.21161280.19672487X-RAY DIFFRACTION99.96
2.03-2.140.22271280.19242479X-RAY DIFFRACTION100
2.14-2.270.20881500.19332469X-RAY DIFFRACTION99.66
2.27-2.450.21511370.2062499X-RAY DIFFRACTION99.89
2.45-2.70.24271480.21242494X-RAY DIFFRACTION99.81
2.7-3.090.22131350.2182560X-RAY DIFFRACTION99.81
3.09-3.890.2161320.19682575X-RAY DIFFRACTION99.78
3.89-46.480.20871640.19692738X-RAY DIFFRACTION99.35
Refinement TLS params.Method: refined / Origin x: -3.34118483407 Å / Origin y: 11.8579077148 Å / Origin z: 99.4405517233 Å
111213212223313233
T0.167159916915 Å20.0205128933025 Å2-0.0322519779658 Å2-0.162333747211 Å2-0.0070139384231 Å2--0.224808251646 Å2
L1.37047836494 °20.581675419995 °2-1.49315734165 °2-1.02820542971 °2-0.639758381913 °2--2.59797625889 °2
S0.0310213572373 Å °0.0536563858023 Å °0.150865545403 Å °-0.16254924304 Å °0.0616111414596 Å °0.161133509668 Å °-0.0318921096334 Å °-0.229807318236 Å °-0.0938601411852 Å °
Refinement TLS groupSelection details: all

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