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- PDB-2wbv: Canine adenovirus 2 fibre head in complex with sialic acid -

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Basic information

Entry
Database: PDB / ID: 2wbv
TitleCanine adenovirus 2 fibre head in complex with sialic acid
ComponentsFIBER PROTEIN
KeywordsSTRUCTURAL PROTEIN / KNOB / HEAD / FIBER / VIRUS / FIBRE / ADENOVIRUS / HEMAGGLUTINATION / RED BLOOD CELL / SIALYL-LACTOSE / CELL ATTACHMENT / ERYTHROCYTE / SIALIC ACID / FIBER PROTEIN
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Fiber protein
Similarity search - Component
Biological speciesCANINE ADENOVIRUS 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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.
History
DepositionMar 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBER PROTEIN
B: FIBER PROTEIN
C: FIBER PROTEIN
D: FIBER PROTEIN
E: FIBER PROTEIN
F: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,32918
Polymers123,7586
Non-polymers2,57012
Water20,7531152
1
A: FIBER PROTEIN
B: FIBER PROTEIN
D: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2459
Polymers61,8793
Non-polymers1,3666
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-30.1 kcal/mol
Surface area20270 Å2
MethodPISA
2
C: FIBER PROTEIN
E: FIBER PROTEIN
F: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0839
Polymers61,8793
Non-polymers1,2046
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-33.1 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.000, 61.250, 143.110
Angle α, β, γ (deg.)90.00, 131.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
FIBER PROTEIN / CANINE ADENOVIRUS 2 FIBRE HEAD / PIV


Mass: 20626.408 Da / Num. of mol.: 6 / Fragment: FIBRE HEAD, RESIDUES 358-542
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANINE ADENOVIRUS 2 / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR / References: UniProt: Q65914
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar
ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 5
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1152 / 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: 2.54 Å3/Da / Density % sol: 51.18 % / Description: NONE
Crystal growDetails: 5% PEG 4000, 5% ISOPROPANOL, 0.1 M HEPES PH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Sep 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.9→46.1 Å / Num. obs: 109731 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.22
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.06 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J2J

2j2j


Resolution: 1.9→46.13 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.481 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS 6-FOLD NCS WHICH CAN BE DETECTED USING REGULAR CRYSTALLOGRAPHIC SOFTWARE.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 5480 5 %RANDOM
Rwork0.157 ---
obs0.159 104251 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.07 Å2
2--0.19 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8493 0 173 1152 9818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228972
X-RAY DIFFRACTIONr_bond_other_d0.0010.026026
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.96612269
X-RAY DIFFRACTIONr_angle_other_deg0.847314712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78651124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77323.507365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.407151381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8291558
X-RAY DIFFRACTIONr_chiral_restr0.070.21416
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021828
X-RAY DIFFRACTIONr_nbd_refined0.1860.21422
X-RAY DIFFRACTIONr_nbd_other0.1960.26444
X-RAY DIFFRACTIONr_nbtor_refined0.1690.24484
X-RAY DIFFRACTIONr_nbtor_other0.0810.24714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2870
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6021.55653
X-RAY DIFFRACTIONr_mcbond_other0.1121.52237
X-RAY DIFFRACTIONr_mcangle_it0.96329068
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.37333745
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2534.53187
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 390 -
Rwork0.194 7531 -
obs--98.61 %

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