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- PDB-2y7l: Structure of N-terminal domain of Candida albicans Als9-2 in comp... -

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Basic information

Entry
Database: PDB / ID: 2y7l
TitleStructure of N-terminal domain of Candida albicans Als9-2 in complex with human fibrinogen gamma peptide
Components
  • AGGLUTININ-LIKE ALS9 PROTEIN
  • FIBRINOGEN GAMMA CHAIN, ISOFORM CRA_A
KeywordsCELL ADHESION / ADHESIN / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


cell adhesion involved in multi-species biofilm formation / platelet maturation / fungal-type cell wall / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cell adhesion involved in single-species biofilm formation / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) ...cell adhesion involved in multi-species biofilm formation / platelet maturation / fungal-type cell wall / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cell adhesion involved in single-species biofilm formation / 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 / side of membrane / 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 activation / platelet aggregation / cell-cell adhesion / 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 / Platelet degranulation / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / positive regulation of ERK1 and ERK2 cascade / blood microparticle / cell adhesion / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / structural molecule activity / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Fibrinogen gamma chain / : / Agglutinin-like protein, N-terminal domain, N2 subdomain / Agglutinin-like protein repeat / Agglutinin-like protein, N-terminal / Agglutinin-like protein / Agglutinin-like protein, N-terminal, N2 subdomain / Candida agglutinin-like (ALS) / Agglutinin-like protein, N-terminal domain / Cell-wall agglutinin N-terminal ligand-sugar binding ...Fibrinogen gamma chain / : / Agglutinin-like protein, N-terminal domain, N2 subdomain / Agglutinin-like protein repeat / Agglutinin-like protein, N-terminal / Agglutinin-like protein / Agglutinin-like protein, N-terminal, N2 subdomain / Candida agglutinin-like (ALS) / Agglutinin-like protein, N-terminal domain / Cell-wall agglutinin N-terminal ligand-sugar binding / Immunoglobulin-like - #1280 / Fibrogen-binding domain 1 / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / 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. / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Agglutinin-like protein 9 / Fibrinogen gamma chain, isoform CRA_a / Fibrinogen gamma chain / :
Similarity search - Component
Biological speciesCANDIDA ALBICANS (yeast)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsSalgado, P.S. / Cota, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural Basis for the Broad Specificity to Host- Cell Ligands by the Pathogenic Fungus Candida Albicans.
Authors: Salgado, P.S. / Yan, R. / Taylor, J.D. / Burchell, L. / Jones, R. / Hoyer, L.L. / Matthews, S.J. / Simpson, P.J. / Cota, E.
History
DepositionJan 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 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: AGGLUTININ-LIKE ALS9 PROTEIN
B: FIBRINOGEN GAMMA CHAIN, ISOFORM CRA_A


Theoretical massNumber of molelcules
Total (without water)35,2922
Polymers35,2922
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-4.4 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.581, 69.273, 122.223
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AGGLUTININ-LIKE ALS9 PROTEIN / NT_ALS9-2


Mass: 33599.988 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 18-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Plasmid: PET32 XA/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): ORIGAMI / References: UniProt: Q5A8T1, UniProt: A0A1D8PQ86*PLUS
#2: Protein/peptide FIBRINOGEN GAMMA CHAIN, ISOFORM CRA_A


Mass: 1691.780 Da / Num. of mol.: 1 / Fragment: RESIDUES 318-334 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: D3DP16, UniProt: P02679*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE EXCLUDES N-TERMINAL SIGNAL SEQUENCE (18 RESIDUES) FULL 17MER PEPTIDE SEQUENCE ...SEQUENCE EXCLUDES N-TERMINAL SIGNAL SEQUENCE (18 RESIDUES) FULL 17MER PEPTIDE SEQUENCE GEGQQHHLGGAKQAGDV ONLY LAST 6 RESIDUES PRESENT IN PDB

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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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 8 / Details: 0.2MM AMMONIUM FLUORIDE, 20% PEG3350, PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 50160 / % possible obs: 98 % / Observed criterion σ(I): 9.3 / Redundancy: 13.7 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 36.4
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 9.3 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y7M

2y7m


Resolution: 1.49→34.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.222 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22429 2540 5.1 %RANDOM
Rwork0.19633 ---
obs0.19771 47530 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.735 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.49→34.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 0 313 2725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222489
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.9353415
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88625.15299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69315367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.021155
X-RAY DIFFRACTIONr_chiral_restr0.140.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211886
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
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: 1.485→1.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 153 -
Rwork0.224 3014 -
obs--85.78 %

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