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- PDB-2xnx: BC1 fragment of streptococcal M1 protein in complex with human fi... -

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Basic information

Entry
Database: PDB / ID: 2xnx
TitleBC1 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


platelet maturation / 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 / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) ...platelet maturation / 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 / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein secretion / protein polymerization / cellular response to interleukin-1 / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / cell adhesion molecule binding / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Platelet degranulation / cell cortex / ER-Phagosome pathway / protein-folding chaperone binding / protein-containing complex assembly / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / blood microparticle / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Helix Hairpins - #780 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 ...Helix Hairpins - #780 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
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: 3.3 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

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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
G: FIBRINOGEN ALPHA CHAIN
H: FIBRINOGEN BETA CHAIN
I: FIBRINOGEN GAMMA CHAIN
J: FIBRINOGEN ALPHA CHAIN
K: FIBRINOGEN BETA CHAIN
L: FIBRINOGEN GAMMA CHAIN
M: M PROTEIN
N: M PROTEIN


Theoretical massNumber of molelcules
Total (without water)371,16114
Polymers371,16114
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55430 Å2
ΔGint-331.9 kcal/mol
Surface area164660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.723, 216.866, 140.807
Angle α, β, γ (deg.)90.00, 102.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41J
12B
22E
32H
42K
13C
23F
33I
43L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A141 - 190
2115D141 - 190
3115G141 - 190
4115J141 - 190
1125B150 - 197
2125E150 - 197
3125H150 - 197
4125K150 - 197
1225B201 - 278
2225E201 - 278
3225H201 - 278
4225K201 - 278
1325B283 - 334
2325E283 - 334
3325H283 - 334
4325K283 - 334
1425B388 - 423
2425E388 - 423
3425H388 - 423
4425K388 - 423
1525B445 - 458
2525E445 - 458
3525H445 - 458
4525K445 - 458
1135C105 - 141
2135F105 - 141
3135I105 - 141
4135L105 - 141
1235C164 - 279
2235F164 - 279
3235I164 - 279
4235L164 - 279
1335C340 - 392
2335F340 - 392
3335I340 - 392
4335L340 - 392

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
FIBRINOGEN ALPHA CHAIN / HUMAN FIBRINOGEN


Mass: 10244.963 Da / Num. of mol.: 4 / 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


Mass: 37691.992 Da / Num. of mol.: 4 / 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.: 4 / 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 / M1-BC1


Mass: 17260.252 Da / Num. of mol.: 2 / Fragment: BC1 FRAGMENT OF M1, RESIDUES 128-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: 5448 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q48WD8

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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: 4.89 Å3/Da / Density % sol: 74.67 % / Description: NONE
Crystal growDetails: 16% PEG 3350, 0.2 M SODIUM TARTRATE WITH SEEDS GROWN IN 0.6 M K2/NA2 PO4, 0.12 M (NH4)2SO4, 0.1 M HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Apr 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.3→116.25 Å / Num. obs: 90704 / % possible obs: 96.7 % / Observed criterion σ(I): 1.4 / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.8
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E1I

3e1i


Resolution: 3.3→116.25 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.808 / SU B: 29.604 / SU ML: 0.477 / Cross valid method: THROUGHOUT / ESU R: 1.052 / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.325 4832 5.1 %RANDOM
Rwork0.277 ---
obs0.279 90704 96.5 %-
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: 77.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å2-0.16 Å2
2---0.3 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 3.3→116.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23867 0 0 0 23867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02224424
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.93432956
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29552945
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57224.8651262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.86154370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.25715138
X-RAY DIFFRACTIONr_chiral_restr0.0830.23363
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218790
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.211547
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.216106
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2875
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.24
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A200medium positional0.330.5
12D200medium positional0.350.5
13G200medium positional0.410.5
14J200medium positional0.410.5
21B908medium positional0.430.5
22E908medium positional0.320.5
23H908medium positional0.380.5
24K908medium positional0.430.5
31C824medium positional0.390.5
32F824medium positional0.310.5
33I824medium positional0.360.5
34L824medium positional0.430.5
11A205loose positional0.735
12D205loose positional0.745
13G205loose positional0.875
14J205loose positional0.795
21B926loose positional0.825
22E926loose positional0.625
23H926loose positional0.785
24K926loose positional0.885
31C850loose positional0.615
32F850loose positional0.535
33I850loose positional0.65
34L850loose positional0.645
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 293 -
Rwork0.333 6318 -
obs--90.76 %

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