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- PDB-4zdg: Structure of the Adenovirus 14p1 knob domain -

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Basic information

Entry
Database: PDB / ID: 4zdg
TitleStructure of the Adenovirus 14p1 knob domain
ComponentsFiber protein
KeywordsVIRAL PROTEIN / adenovirus 14 / strain p1 / fibre knob / head domain
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
Biological speciesHuman adenovirus 14p1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFender, P. / Ducournau, C. / Zubieta, C.
CitationJournal: J.Virol. / Year: 2015
Title: Intracellular Signaling and Desmoglein 2 Shedding Triggered by Human Adenoviruses Ad3, Ad14, and Ad14P1.
Authors: Wang, H. / Ducournau, C. / Saydaminova, K. / Richter, M. / Yumul, R. / Ho, M. / Carter, D. / Zubieta, C. / Fender, P. / Lieber, A.
History
DepositionApr 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_data_processing_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fiber protein
B: Fiber protein
C: Fiber protein


Theoretical massNumber of molelcules
Total (without water)71,7323
Polymers71,7323
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-34 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.414, 112.414, 79.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Fiber protein


Mass: 23910.504 Da / Num. of mol.: 3 / Fragment: knob domain, UNP residues 121-323 / Mutation: deletion of K251 and E252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 14p1 / Production host: Escherichia coli (E. coli) / References: UniProt: D6BP13

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1.65 M MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.2→48.68 Å / Num. all: 9525 / Redundancy: 6.8 % / Biso Wilson estimate: 79.58 Å2 / Rmerge(I) obs: 0.179
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 6.75 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.6 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XSCALEdata scaling
PHASERphasing
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F0Y

4f0y


Resolution: 3.2→48.68 Å / Cor.coef. Fo:Fc: 0.9071 / Cor.coef. Fo:Fc free: 0.8548 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.531
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 458 4.81 %RANDOM
Rwork0.1997 ---
obs0.2017 9525 99.76 %-
Displacement parametersBiso mean: 82.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.2511 Å20 Å20 Å2
2--2.2511 Å20 Å2
3----4.5023 Å2
Refine analyzeLuzzati coordinate error obs: 0.532 Å
Refinement stepCycle: LAST / Resolution: 3.2→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4561 0 0 0 4561
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014669HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.146393HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1524SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes123HARMONIC2
X-RAY DIFFRACTIONt_gen_planes686HARMONIC5
X-RAY DIFFRACTIONt_it4669HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.95
X-RAY DIFFRACTIONt_other_torsion15.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion678SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5519SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.58 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2878 150 5.66 %
Rwork0.2071 2501 -
all0.2116 2651 -
obs--99.76 %

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