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- PDB-6uz4: Solution structure of AGL55-Kringle 2 complex -

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Basic information

Entry
Database: PDB / ID: 6uz4
TitleSolution structure of AGL55-Kringle 2 complex
Components
  • M protein
  • PlasminogenPlasmin
KeywordsPROTEIN BINDING / Plasminogen binding peptide
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 / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / 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 / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / 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 / 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 / endopeptidase activity / blood microparticle / 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
Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / Peptidase S1A, plasmin / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site ...Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / Peptidase S1A, plasmin / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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
Similarity search - Domain/homology
M protein / Plasminogen
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pyogenes NS88.2 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsQiu, C. / Yuan, Y. / Castellino, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HL013423 United States
CitationJournal: To Be Published
Title: Structural evolution of the A-domain in plasminogen-binding Group A streptococcal M-protein reflects improved adaptability of the pathogen to the host
Authors: Qiu, C. / Yuan, Y. / Ploplis, V.A. / Castellino, F.J.
History
DepositionNov 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasminogen
B: M protein


Theoretical massNumber of molelcules
Total (without water)16,9092
Polymers16,9092
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1040 Å2
ΔGint6 kcal/mol
Surface area10220 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Plasminogen / Plasmin


Mass: 10166.340 Da / Num. of mol.: 1 / Mutation: C11G, E63D, L79Y
Source method: isolated from a genetically manipulated source
Details: The terminal residues, YVEFSEE and AA, are not derived from kringle 2 domain of human plasminogen.
Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Komagataella pastoris (fungus) / References: UniProt: P00747, plasmin
#2: Protein M protein / AGL55


Mass: 6742.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes NS88.2 (bacteria)
Strain: NS88.2 / Gene: emm / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: M4I022

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D TROSY-[1H-15N] HSQC
121isotropic13D TROSY-HNCO
131isotropic13D TROSY-HN(CA)CO
141isotropic13D TROSY-HN(CA)CB
151isotropic13D TROSY-C(CO)NH
161isotropic13D TROSY-HBHA(CBCA)NH
171isotropic13D TROSY-H(CCO)NH
181isotropic12D NOESY
191isotropic13D NOESY
1101anisotropic12D IPAP
1112isotropic12D 1H-15N HSQC
1122isotropic13D NOESY
1132anisotropic12D IPAP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-99% 13C; U-99% 15N] AGL55, 1.2 mM Kringle 2, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O13C, 15N_sample_195% H2O/5% D2O
solution21.0 mM [U-99% 13C; U-99% 15N] Kringle 2, 1.2 mM AGL55, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O13C, 15N_sample_295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMAGL55[U-99% 13C; U-99% 15N]1
1.2 mMKringle 2natural abundance1
20 mMBis-Tris-d19[U-2H]1
2 ug/mLDSSnatural abundance1
2 ug/mLsodium azidenatural abundance1
1.0 mMKringle 2[U-99% 13C; U-99% 15N]2
1.2 mMAGL55natural abundance2
20 mMBis-Tris-d19[U-2H]2
2 ug/mLDSSnatural abundance2
2 ug/mLsodium azidenatural abundance2
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
HADDOCKBonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 2000 / Conformers submitted total number: 20

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