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- PDB-6qu8: Adenovirus Serotype 26 (Ad26) in complex with sialic acid, pH8.0 -

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Basic information

Entry
Database: PDB / ID: 6qu8
TitleAdenovirus Serotype 26 (Ad26) in complex with sialic acid, pH8.0
ComponentsFiber
KeywordsVIRAL PROTEIN / Adenovirus / Adenovirus 26 / Ad26 / HAdV-D26 / Ad26K / HAdV-D26K / human adenovirus / human adenovirus 26 / mastadenovirus / Sialic Acid / NANA / SIA / N-Acetylneuraminic acid / neuraminic acid / species D / adenovirus species D / AdD / HAdV-D / protein IV / pIV / fiber-knob / fiber / head domain / knob domain / fiber protein / fibre protein / fibre-knob / knob / head
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, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / 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 / N-acetyl-beta-neuraminic acid / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 26
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsBaker, A.T. / Rizkallah, P.J. / Parker, A.L. / Mundy, R.M.
Citation
Journal: Sci Adv / Year: 2019
Title: Human adenovirus type 26 uses sialic acid-bearing glycans as a primary cell entry receptor.
Authors: Baker, A.T. / Mundy, R.M. / Davies, J.A. / Rizkallah, P.J. / Parker, A.L.
#1: Journal: To Be Published
Title: Adenovirus serotype 26 fiber-knob in complex with sialic acid at pH8.0
Authors: Baker, A.T. / Rizkallah, P.J. / Mundy, R.M.
History
DepositionFeb 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 1, 2020Group: Data collection / Category: chem_comp / Item: _chem_comp.type
Revision 2.0Jul 8, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_validate_close_contact.label_alt_id_1
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8356
Polymers24,0301
Non-polymers8055
Water2,846158
1
A: Fiber
hetero molecules

A: Fiber
hetero molecules

A: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,50418
Polymers72,0903
Non-polymers2,41415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11630 Å2
ΔGint11 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.920, 85.920, 85.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

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Components

#1: Protein Fiber


Mass: 24029.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 26 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: A4ZKM1
#2: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
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
#3: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M MIB, 25 % w/v PEG 1500, pH8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.19→42.96 Å / Num. obs: 67799 / % possible obs: 100 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.088 / Net I/σ(I): 20.7
Reflection shellResolution: 1.19→1.22 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FJN

6fjn


Resolution: 1.19→42.96 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17201 3441 5.1 %RANDOM
Rwork0.14176 ---
obs0.14322 64286 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.632 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.19→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 54 158 1681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131735
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171544
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.6822384
X-RAY DIFFRACTIONr_angle_other_deg2.3391.5893631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0685221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46823.79779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.828156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021964
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02347
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_it33.5553.193837
X-RAY DIFFRACTIONr_mcbond_other33.582836
X-RAY DIFFRACTIONr_mcangle_it30.0794.7131072
X-RAY DIFFRACTIONr_mcangle_other30.0661073
X-RAY DIFFRACTIONr_scbond_it18.0063.131898
X-RAY DIFFRACTIONr_scbond_other17.9963.132899
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other21.0254.5871312
X-RAY DIFFRACTIONr_long_range_B_refined34.0991932
X-RAY DIFFRACTIONr_long_range_B_other34.4021895
X-RAY DIFFRACTIONr_rigid_bond_restr9.24431726
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.19→1.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 278 -
Rwork0.375 4645 -
obs--100 %

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