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- PDB-6sit: Pseudo-atomic crystal structure of the desmoglein 2 - human adeno... -

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Basic information

Entry
Database: PDB / ID: 6sit
TitlePseudo-atomic crystal structure of the desmoglein 2 - human adenovirus serotype 3 fibre knob complex
Components
  • Desmoglein-2
  • Fiber proteinFibrous protein
KeywordsVIRAL PROTEIN / virus receptor / extracellular domain / cell surface glycoprotein / desmosome
Function / homology
Function and homology information


Purkinje myocyte development / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / desmosome / Formation of the cornified envelope / cornified envelope / regulation of ventricular cardiac muscle cell action potential / Apoptotic cleavage of cell adhesion proteins ...Purkinje myocyte development / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / desmosome / Formation of the cornified envelope / cornified envelope / regulation of ventricular cardiac muscle cell action potential / Apoptotic cleavage of cell adhesion proteins / adhesion receptor-mediated virion attachment to host cell / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of heart rate by cardiac conduction / RHOG GTPase cycle / intercalated disc / maternal process involved in female pregnancy / lateral plasma membrane / RAC3 GTPase cycle / RAC2 GTPase cycle / cell adhesion molecule binding / response to progesterone / cell-cell adhesion / viral capsid / cell-cell junction / cell junction / cell adhesion / symbiont entry into host cell / apical plasma membrane / intracellular membrane-bounded organelle / host cell nucleus / calcium ion binding / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
Desmosomal cadherin / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Catenin binding domain superfamily / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Cadherin conserved site ...Desmosomal cadherin / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Catenin binding domain superfamily / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
Fiber protein / Desmoglein-2
Similarity search - Component
Biological speciesHuman adenovirus B3
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsBurmeister, W.P. / Fender, P. / Vassal-Stermann, E.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INSB-05-02 France
French National Research AgencyANR-10-LABX-49-01 France
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Intermediate-resolution crystal structure of the human adenovirus B serotype 3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2.
Authors: Vassal-Stermann, E. / Hutin, S. / Fender, P. / Burmeister, W.P.
History
DepositionAug 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fiber protein
D: Desmoglein-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1208
Polymers47,8802
Non-polymers2406
Water0
1
A: Fiber protein
D: Desmoglein-2
hetero molecules

A: Fiber protein
D: Desmoglein-2
hetero molecules

A: Fiber protein
D: Desmoglein-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,36124
Polymers143,6396
Non-polymers72118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)146.530, 146.530, 146.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Fiber protein / Fibrous protein / SPIKE / Protein IV


Mass: 21270.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus B3 / Gene: L5 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: P04501
#2: Protein Desmoglein-2 / / Cadherin family member 5 / HDGC


Mass: 26609.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: extracellular domain EC2 and EC3 / Source: (gene. exp.) Homo sapiens (human) / Gene: DSG2, CDHF5 / Plasmid: pETM-40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q14126
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.07 % / Description: prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 7 mg/mL complex in 20 mM Tris-HCl, pH 8, 150 mM NaCl, 3 mM CaCl2 using a reservoir solution of 15 % PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Na-acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 12, 2018
Details: Vertically focused by CRLs and horizontally focussed by a mirror in half-Kirkpatrick-Baez (KB) geometry
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 4.49→46.51 Å / Num. obs: 3184 / % possible obs: 97.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 233 Å2 / CC1/2: 0.997 / R split: 0.093 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.053 / Rrim(I) all: 0.108 / Χ2: 0.77 / Net I/av σ(I): 4.9 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
4.49-4.652.41.2590.62730.2110.9441.5851.2590.587.4
17.38-46.343.60.03822.7590.9970.0230.0450.0380.990.7

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Processing

Software
NameVersionClassification
CNSrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1h7z

1h7z


Resolution: 4.5→46.5 Å / SU R Cruickshank DPI: 1.7 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.37 137 4.3 %random selection
Rwork0.3666 ---
obs-3129 97.1 %-
Solvent computationBsol: 252.167 Å2
Displacement parametersBiso max: 382.5 Å2 / Biso mean: 252 Å2 / Biso min: 256.54 Å2
Refinement stepCycle: final / Resolution: 4.5→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 6 0 3378
Biso mean--297.18 --
Num. residues----429
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_d2.388
LS refinement shellResolution: 4.5→4.7 Å
RfactorNum. reflection% reflection
Rfree0.426 12 3.65 %
Rwork0.444 317 -
obs--88 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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