SASDG44: Adenovirus Ad3 fibre knob in complex with the EC2-EC3 fragment of...

Basic information

• Entry: Database: SASBDB / ID: SASDG44

Sample

Adenovirus Ad3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2

• Human adenovirus serotype 3 fibre knob (protein), HAd3K, Human adenovirus serotype 3
• Human desmoglein 2 extracellular domain 2 and 3 (protein), EC2-EC3, Homo sapiens

Function / homology

Function:

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 / RAC2 GTPase cycle / RAC3 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

Domain/homology:

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

Component:

Fiber protein / Desmoglein-2

• Biological species: Human adenovirus serotype 3; Homo sapiens (human)

Contact author

• Wim Burmeister (IBS, Institut de Biologie Structurale, Grenoble, France)

Models

• Model #3651: ; Type: atomic / Symmetry: 3-fold; Comment: 3:1 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.; Chi-square value: 0.795; Search similar-shape structures of this assembly by Omokage search (details)
• Model #3652: ; Type: atomic / Symmetry: 3-fold; Comment: 3:2 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.; Chi-square value: 0.514; Search similar-shape structures of this assembly by Omokage search (details)
• Model #3653: ; Type: atomic / Symmetry: 3-fold; Comment: 3:1 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.; Chi-square value: 0.40 / P-value: 0.000001; Search similar-shape structures of this assembly by Omokage search (details)
• Model #3654: ; Type: atomic / Symmetry: 3-fold; Comment: 3:1 complex built from asymmetric unit structure. HAd3K has 3-fold symmetry, EC2-EC3 has not.; Chi-square value: 0.40 / P-value: 0.000001; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Adenovirus Ad3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2; Specimen concentration: 2.4 mg/ml / Entity id: 1854 / 1855
• Buffer: Name: 20 mM Tris-HCl, 150 mM NaCl, 3 mM CaCl2 / pH: 8

Entity #1854

Name: HAd3K / Type: protein / Description: Human adenovirus serotype 3 fibre knob / Formula weight: 23.072 / Num. of mol.: 3 / Source: Human adenovirus serotype 3 / References: UniProt: P04501
Sequence:

HHHHHHSQDP ANSIALKNNT LWTGPKPEAN CIIEYGKQNP DSKLTLILVK NGGIVNGYVT LMGASDYVNT LFKNKNVSIN VELYFDATGH ILPDSSSLKT DLELKYKQTA DFSARGFMPS TTAYPFVLPN AGTHNENYIF GQCYYKASDG ALFPLEVTVM LNKRLPDSRT SYVMTFLWSL NAGLAPETTQ ATLITSPFTF SYIREDD

Entity #1855

Name: EC2-EC3 / Type: protein
Description: Human desmoglein 2 extracellular domain 2 and 3
Formula weight: 27.339 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q14126
Sequence:

QGAMEVLDIN DNEPVFTQDV FVGSVEELSA AHTLVMKINA TDADEPNTLN SKISYRIVSL EPAYPPVFYL NKDTGEIYTT SVTLDREEHS SYTLTVEARD GNGEVTDKPV KQAQVQIRIL DVNDNIPVVE NKVLEGMVEE NQVNVEVTRI KVFDADEIGS DNWLANFTFA SGNEGGYFHI ETDAQTNEGI VTLIKEVDYE EMKNLDFSVI VANKAAFHKS IRSKYKPTPI PIKVKVKNVK EGI

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.864 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Adenovirus Ad3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2
Measurement date: Jan 26, 2017 / Storage temperature: 293 °C / Cell temperature: 293 °C / Exposure time: 1 sec. / Number of frames: 2000 / Unit: 1/A /

	Min	Max
Q	0.0141	0.2005

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 321 /

	Min	Max
Q	0.0202871	0.200536
P(R) point	1	321
R	0	111.7

Result

Type of curve: sec
Comments: Three different stoichiometries are possible for the Had3K: human desmoglein 2 EC2-EC3 complex : 3:1, 3:2 and 3:3. The SAXS experiment is used in order to determine the possible stoichiometries in solution.

	Experimental	Porod
MW	119 kDa	114 kDa
Volume	-	188 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	258.3	255.03	0.61
Radius of gyration, Rg	3.5 nm	3.42 nm	0.1

	Min	Max
D	-	11.17
Guinier point	12	35