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- PDB-9tac: Crystal Structure of Human Adenovirus 52 Short Fiber Knob Mutant ... -

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Basic information

Entry
Database: PDB / ID: 9tac
TitleCrystal Structure of Human Adenovirus 52 Short Fiber Knob Mutant K349R in Complex with alpha-(2,8)-Pentasialic Acid (DP5)
ComponentsFiber-1
KeywordsVIRAL PROTEIN / human adenovirus fiber knob
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
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
Similarity search - Domain/homology
Biological specieshuman adenovirus 52
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVonmetz, K. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2953 Germany
CitationJournal: To Be Published
Title: Crystal Structures of Human Adenovirus 52 Short Fiber Knob Mutants in Complex with alpha-(2,8)-Pentasialic Acid (DP5)
Authors: Vonmetz, K. / Stehle, T.
History
DepositionNov 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)69,03916
Polymers67,3473
Non-polymers1,69313
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-35 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.501, 82.245, 93.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Fiber-1


Mass: 22448.889 Da / Num. of mol.: 3 / Mutation: K349R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human adenovirus 52 / Production host: Escherichia coli (E. coli) / References: UniProt: A0MK70
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid


Type: oligosaccharide / Mass: 891.780 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Aca2-8DNeup5Aca2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[Aad21122h-2a_2-6_5*NCC/3=O]/1-1-1/a8-b2_b8-c2WURCSPDB2Glycan 1.1.0
[][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.82 Å3/Da / Density % sol: 32.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12.5 % (v/v) MPD; 12.5 % (w/v) PEG3350; 25 % (w/v) PEG1000; 0.1 M Tris/Bicine pH 8.5; 1.6 mM of each Glycine, Na L-Glutamate, DL-Alanine, DL-Lysine, DL-Serine; Seed stock N243R 1:100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999997 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999997 Å / Relative weight: 1
ReflectionResolution: 2.1→46.73 Å / Num. obs: 29147 / % possible obs: 99.8 % / Redundancy: 5.16 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.985 / Rrim(I) all: 0.291 / Net I/σ(I): 5.98
Reflection shellResolution: 2.1→2.22 Å / Mean I/σ(I) obs: 1.35 / Num. unique obs: 4647 / CC1/2: 0.497 / Rrim(I) all: 1.337 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.73 Å / SU ML: 0.2193 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1817
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219 1458 5 %
Rwork0.1984 27687 -
obs0.1994 29145 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.79 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 113 224 4162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01384033
X-RAY DIFFRACTIONf_angle_d1.90185500
X-RAY DIFFRACTIONf_chiral_restr0.1426649
X-RAY DIFFRACTIONf_plane_restr0.0125696
X-RAY DIFFRACTIONf_dihedral_angle_d20.16031376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.27511440.25222723X-RAY DIFFRACTION99.86
2.18-2.260.30471440.2622737X-RAY DIFFRACTION100
2.26-2.370.29841430.25592719X-RAY DIFFRACTION99.97
2.37-2.490.28931440.23072746X-RAY DIFFRACTION99.93
2.49-2.650.27491440.23332737X-RAY DIFFRACTION99.9
2.65-2.850.24891450.21662747X-RAY DIFFRACTION99.86
2.85-3.140.20751450.2022758X-RAY DIFFRACTION99.73
3.14-3.590.20281470.17872783X-RAY DIFFRACTION99.97
3.59-4.530.16031470.15872808X-RAY DIFFRACTION99.36
4.53-46.730.1831550.17112929X-RAY DIFFRACTION99.81

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