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- PDB-2xny: A fragment of streptococcal M1 protein in complex with human fibr... -

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Basic information

Entry
Database: PDB / ID: 2xny
TitleA fragment of streptococcal M1 protein in complex with human fibrinogen
Components
  • FIBRINOGEN ALPHA CHAIN
  • FIBRINOGEN BETA CHAIN
  • FIBRINOGEN GAMMA CHAIN
  • M PROTEIN
KeywordsCELL ADHESION / VIRULENCE FACTOR / STREPTOCOCCAL TOXIC SHOCK SYNDROME
Function / homology
Function and homology information


blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of vasoconstriction / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein secretion / positive regulation of exocytosis / protein polymerization / cellular response to interleukin-1 / Integrin cell surface interactions / Common Pathway of Fibrin Clot Formation / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / cell adhesion molecule binding / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / platelet alpha granule lumen / cell-matrix adhesion / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to calcium ion / platelet aggregation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / Platelet degranulation / extracellular vesicle / protein-folding chaperone binding / : / ER-Phagosome pathway / protein-containing complex assembly / cell cortex / protein-macromolecule adaptor activity / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / innate immune response / external side of plasma membrane / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain ...Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
Fibrinogen alpha chain / Fibrinogen beta chain / Fibrinogen gamma chain / :
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.5 Å
AuthorsMacheboeuf, P. / Y Fu, C. / Zinkernagel, A.S. / Johnson, J.E. / Nizet, V. / Ghosh, P.
CitationJournal: Nature / Year: 2011
Title: Streptococcal M1 Protein Constructs a Pathological Host Fibrinogen Network
Authors: Macheboeuf, P. / Buffalo, C. / Fu, C.Y. / Zinkernagel, A.S. / Cole, J.N. / Johnson, J.E. / Nizet, V. / Nizet, V. / Ghosh, P.
History
DepositionAug 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBRINOGEN ALPHA CHAIN
B: FIBRINOGEN BETA CHAIN
C: FIBRINOGEN GAMMA CHAIN
D: FIBRINOGEN ALPHA CHAIN
E: FIBRINOGEN BETA CHAIN
F: FIBRINOGEN GAMMA CHAIN
M: M PROTEIN
N: M PROTEIN


Theoretical massNumber of molelcules
Total (without water)192,4538
Polymers192,4538
Non-polymers00
Water00
1
A: FIBRINOGEN ALPHA CHAIN
B: FIBRINOGEN BETA CHAIN
C: FIBRINOGEN GAMMA CHAIN


Theoretical massNumber of molelcules
Total (without water)84,1603
Polymers84,1603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-64.2 kcal/mol
Surface area33880 Å2
MethodPISA
2
D: FIBRINOGEN ALPHA CHAIN
E: FIBRINOGEN BETA CHAIN
F: FIBRINOGEN GAMMA CHAIN


Theoretical massNumber of molelcules
Total (without water)84,1603
Polymers84,1603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-64.3 kcal/mol
Surface area33920 Å2
MethodPISA
3
M: M PROTEIN
N: M PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,1332
Polymers24,1332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-11.6 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.687, 165.687, 289.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein FIBRINOGEN ALPHA CHAIN / FIBRINOPEPTIDE A / HUMAN FIBRINOGEN


Mass: 10244.963 Da / Num. of mol.: 2 / Fragment: FRAGMENT D, RESIDUES 130-216 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P02671
#2: Protein FIBRINOGEN BETA CHAIN / HUMAN FIBRINOGEN / FIBRINOPEPTIDE B


Mass: 37691.992 Da / Num. of mol.: 2 / Fragment: FRAGMENT D, RESIDUES 164-491 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P02675
#3: Protein FIBRINOGEN GAMMA CHAIN / HUMAN FIBRINOGEN


Mass: 36223.281 Da / Num. of mol.: 2 / Fragment: FRAGMENT D, RESIDUES 114-432 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P02679
#4: Protein M PROTEIN


Mass: 12066.417 Da / Num. of mol.: 2 / Fragment: N-TERMINAL FRAGMENT, RESIDUES 42-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: 5448 / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q48WD8
Has protein modificationY

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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: 5.86 Å3/Da / Density % sol: 79 % / Description: NONE
Crystal growDetails: 1.3 M AMMONIUM TARTRATE, 0.1 M MES, PH 6.25.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 6→142.8 Å / Num. obs: 5481 / % possible obs: 92.1 % / Observed criterion σ(I): 1.8 / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.7
Reflection shellResolution: 7.5→7.7 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.8 / % possible all: 56.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E1I

3e1i


Resolution: 7.5→142.86 Å / Cor.coef. Fo:Fc: 0.64 / Cor.coef. Fo:Fc free: 0.681 / Cross valid method: THROUGHOUT / ESU R Free: 4.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.408 286 5 %RANDOM
Rwork0.424 ---
obs0.423 5481 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.54 Å2
Baniso -1Baniso -2Baniso -3
1-11.56 Å25.78 Å20 Å2
2--11.56 Å20 Å2
3----17.34 Å2
Refinement stepCycle: LAST / Resolution: 7.5→142.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10956 0 0 0 10956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211220
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.92815139
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18451351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32124.674582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.536151970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.861566
X-RAY DIFFRACTIONr_chiral_restr0.0860.21520
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028668
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3330.25120
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.27480
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.290.2336
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.8030.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4660.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 7.5→7.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 6 -
Rwork0.463 248 -
obs--56.32 %

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