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- PDB-4xl8: Crystal Structure of Human Adenovirus 52 Short Fiber Knob in Comp... -

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Basic information

Entry
Database: PDB / ID: 4xl8
TitleCrystal Structure of Human Adenovirus 52 Short Fiber Knob in Complex with 2-O-Methyl-5-N-Acetylneuraminic Acid
ComponentsFiber-1
KeywordsVIRAL PROTEIN / sialic acid / viral attachment / fiber knob / protein carbohydrate interaction
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
ALANINE / GLUTAMIC ACID / 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid / Fiber-1
Similarity search - Component
Biological speciesHuman adenovirus 52
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsStehle, T. / Liaci, A.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 685 Germany
CitationJournal: Plos Pathog. / Year: 2015
Title: Human Adenovirus 52 Uses Sialic Acid-containing Glycoproteins and the Coxsackie and Adenovirus Receptor for Binding to Target Cells.
Authors: Lenman, A. / Liaci, A.M. / Liu, Y. / Ardahl, C. / Rajan, A. / Nilsson, E. / Bradford, W. / Kaeshammer, L. / Jones, M.S. / Frangsmyr, L. / Feizi, T. / Stehle, T. / Arnberg, N.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Other
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Jul 22, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_audit_support / pdbx_validate_close_contact / pdbx_validate_symm_contact / 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.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 2.2Jul 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.3Jan 10, 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-1
B: Fiber-1
C: Fiber-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,63711
Polymers67,2633
Non-polymers1,3748
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-58 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.770, 81.610, 92.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 5 molecules ABC

#1: Protein Fiber-1 / Adenovirus 52 short fiber knob


Mass: 22420.875 Da / Num. of mol.: 3 / Fragment: UNP Residues 183-363
Source method: isolated from a genetically manipulated source
Details: His-tagged knob domain of short fiber (fiber-1) / Source: (gene. exp.) Human adenovirus 52 / Plasmid: pQE-30Xa / Production host: Escherichia Coli BL21(DE3) (bacteria) / References: UniProt: A0MK70
#2: Sugar ChemComp-MNA / 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid / 2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID


Type: D-saccharide / Mass: 323.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21NO9
IdentifierTypeProgram
2-O-methyl-5-N-acetyl-a-D-neuraminic acidIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 7 types, 357 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#6: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% (w/V) PEG1000, 12.5% (w/V) PEG3350, 12.5% (w/V) MPD, 0.02 mM of each Na L glutamate, DL alanine, glycine, DL lysine HCl, and DL serine, 0.1 M Tris/Bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 27, 2013
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 58970 / % possible obs: 99.7 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rsym value: 0.109 / Net I/σ(I): 25.4
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 2 / CC1/2: 0.683 / Rsym value: 1.303 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nob

1nob


Resolution: 1.65→37.48 Å / FOM work R set: 0.9067 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1737 2946 5 %
Rwork0.151 56017 -
obs0.1522 58963 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.43 Å2 / Biso mean: 18.95 Å2 / Biso min: 5.42 Å2
Refinement stepCycle: final / Resolution: 1.65→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 93 351 4230
Biso mean--25.47 30.91 -
Num. residues----499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114177
X-RAY DIFFRACTIONf_angle_d1.395769
X-RAY DIFFRACTIONf_chiral_restr0.101687
X-RAY DIFFRACTIONf_plane_restr0.007741
X-RAY DIFFRACTIONf_dihedral_angle_d12.7441569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6474-1.67450.26011320.2682508X-RAY DIFFRACTION94
1.6745-1.70330.24891370.22992610X-RAY DIFFRACTION100
1.7033-1.73430.24731410.21922662X-RAY DIFFRACTION100
1.7343-1.76770.23061370.20382605X-RAY DIFFRACTION100
1.7677-1.80370.23331390.1942646X-RAY DIFFRACTION100
1.8037-1.8430.22011390.1862652X-RAY DIFFRACTION100
1.843-1.88580.2211400.17132654X-RAY DIFFRACTION100
1.8858-1.9330.16941400.16472653X-RAY DIFFRACTION100
1.933-1.98530.1781380.15382645X-RAY DIFFRACTION100
1.9853-2.04370.15941410.1432679X-RAY DIFFRACTION100
2.0437-2.10960.17681390.14172632X-RAY DIFFRACTION100
2.1096-2.1850.18391380.13982639X-RAY DIFFRACTION100
2.185-2.27250.16491410.14212670X-RAY DIFFRACTION100
2.2725-2.37590.18751410.14042675X-RAY DIFFRACTION100
2.3759-2.50110.16441410.13862684X-RAY DIFFRACTION100
2.5011-2.65780.15671410.14692682X-RAY DIFFRACTION100
2.6578-2.86290.15311410.14362668X-RAY DIFFRACTION100
2.8629-3.15090.18491430.1462722X-RAY DIFFRACTION100
3.1509-3.60650.15291420.13232705X-RAY DIFFRACTION100
3.6065-4.54260.14881450.12292749X-RAY DIFFRACTION100
4.5426-37.48920.15761500.15692877X-RAY DIFFRACTION100

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