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- PDB-2wbw: Ad37 fibre head in complex with CAR D1 and sialic acid -

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Basic information

Entry
Database: PDB / ID: 2wbw
TitleAd37 fibre head in complex with CAR D1 and sialic acid
Components
  • COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
  • FIBER PROTEINScleroprotein
KeywordsSTRUCTURAL PROTEIN / ALTERNATIVE SPLICING / IMMUNOGLOBULIN DOMAIN / TRANSMEMBRANE / PHOSPHOPROTEIN / DISULFIDE BOND / PHOSPHORYLATION / HEMAGGLUTINATION / RECEPTOR / PALMITATE / ADENOVIRUS / ERYTHROCYTE / LIPOPROTEIN / SIALIC ACID / POLYMORPHISM / GLYCOPROTEIN / CELL JUNCTION / CELL MEMBRANE / CELL ADHESION / CAR / AD37 / HAD37 / COMPLEX / MEMBRANE / SECRETED / TIGHT JUNCTION / RED BLOOD CELL / COXSACKIEVIRUS / HOST-VIRUS INTERACTION / VIRAL PROTEIN-RECEPTOR COMPLEX
Function / homology
Function and homology information


cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell-bundle of His cell adhesion involved in cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport ...cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell-bundle of His cell adhesion involved in cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport / cardiac muscle fiber development / negative regulation of cardiac muscle cell proliferation / cell-cell junction organization / connexin binding / adhesion receptor-mediated virion attachment to host cell / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / intercalated disc / bicellular tight junction / actin cytoskeleton reorganization / acrosomal vesicle / mitochondrion organization / filopodium / cell adhesion molecule binding / PDZ domain binding / neutrophil chemotaxis / adherens junction / neuromuscular junction / beta-catenin binding / virus receptor activity / viral capsid / cell body / cell junction / cell-cell junction / growth cone / integrin binding / defense response to virus / regulation of immune response / heart development / leukocyte migration / basolateral plasma membrane / viral entry into host cell / cell adhesion / virion attachment to host cell / neuron projection / membrane raft / host cell nucleus / signaling receptor binding / integral component of plasma membrane / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / metal ion binding / cytoplasm
Adenoviral fibre protein, repeat/shaft region / Immunoglobulin V-set domain / Adenovirus pIV-like, attachment domain / Adenovirus fibre protein / Immunoglobulin subtype / Attachment protein shaft domain superfamily / Immunoglobulin / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Adenoviral fibre protein (knob domain) ...Adenoviral fibre protein, repeat/shaft region / Immunoglobulin V-set domain / Adenovirus pIV-like, attachment domain / Adenovirus fibre protein / Immunoglobulin subtype / Attachment protein shaft domain superfamily / Immunoglobulin / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Adenoviral fibre protein (knob domain) / Immunoglobulin V-set domain / Immunoglobulin subtype 2 / Adenoviral fibre protein, knob / Immunoglobulin-like domain / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Fiber / Fiber protein / Coxsackievirus and adenovirus receptor
Biological speciesHUMAN ADENOVIRUS 37
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSeiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. ...Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / Finberg, R.W. / Cusack, S. / Kremer, E.J.
CitationJournal: Plos Pathog. / Year: 2009
Title: The Cell Adhesion Molecule "Car" and Sialic Acid on Human Erythrocytes Influence Adenovirus in Vivo Biodistribution.
Authors: Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / ...Authors: Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / Finberg, R.W. / Cusack, S. / Kremer, E.J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBER PROTEIN
B: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2754
Polymers35,9262
Non-polymers3492
Water7,206400
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-4.3 kcal/mol
Surface area17770 Å2
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)132.010, 132.010, 132.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-2094-

HOH

21B-2123-

HOH

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Components

#1: Protein FIBER PROTEIN / Scleroprotein / HUMAN ADENOVIRUS TYPE 37 FIBRE HEAD


Mass: 21716.535 Da / Num. of mol.: 1 / Fragment: FIBRE HEAD, RESIDUES 22-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN ADENOVIRUS 37 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR / References: UniProt: Q80S15, UniProt: Q64823*PLUS
#2: Protein COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR / COXSACKIEVIRUS B-ADENOVIRUS RECEPTOR / HCVADR / CVB3-BINDING PROTEIN / HCAR


Mass: 14209.165 Da / Num. of mol.: 1 / Fragment: D1, RESIDUES 15-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: P78310
#3: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CA / CALCIUM ION / Calcium


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 17% POLYETHYLENE GLYCOL 6000, 0.5 M LICL, 0.1 M TRIS, PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 1.55→93 Å / Num. obs: 55340 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 11 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J12
Resolution: 1.55→93.25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.885 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2807 5.1 %RANDOM
Rwork0.171 ---
Obs0.171 52533 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.63 Å2
Refinement stepCycle: LAST / Resolution: 1.55→93.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 22 400 2797
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 196 -
Rwork0.218 3893 -
Obs--99.98 %

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