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- PDB-5nc1: Structure of the distal domain of mouse adenovirus 2 fibre bound ... -

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Basic information

Entry
Database: PDB / ID: 5nc1
TitleStructure of the distal domain of mouse adenovirus 2 fibre bound to N-acetyl-glucosamine
ComponentsFiber
KeywordsVIRAL PROTEIN / Triple beta-spiral / 3-bladed propeller / ABCJ-GHID topology / N-acetyl-glucosamine binding
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / virion component / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily
Similarity search - Domain/homology
Biological speciesMurine adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSingh, A.K. / van Raaij, M.J.
CitationJournal: J. Gen. Virol. / Year: 2018
Title: Structure and N-acetylglucosamine binding of the distal domain of mouse adenovirus 2 fibre.
Authors: Singh, A.K. / Nguyen, T.H. / Vidovszky, M.Z. / Harrach, B. / Benko, M. / Kirwan, A. / Joshi, L. / Kilcoyne, M. / Berbis, M.A. / Canada, F.J. / Jimenez-Barbero, J. / Menendez, M. / Wilson, S. ...Authors: Singh, A.K. / Nguyen, T.H. / Vidovszky, M.Z. / Harrach, B. / Benko, M. / Kirwan, A. / Joshi, L. / Kilcoyne, M. / Berbis, M.A. / Canada, F.J. / Jimenez-Barbero, J. / Menendez, M. / Wilson, S.S. / Bromme, B.A. / Smith, J.G. / van Raaij, M.J.
History
DepositionMar 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_struct_special_symmetry
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _entity.formula_weight
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Jul 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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 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
B: Fiber
C: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,24518
Polymers77,4333
Non-polymers1,81215
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Protein is trimeric on SDS-PAGE when sample is not boiled prior to analysis.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14460 Å2
ΔGint-201 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.410, 163.410, 163.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11C-932-

HOH

21C-980-

HOH

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Components

#1: Protein Fiber


Mass: 25810.922 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEF is an expression and purification tag. GALTAQGAS residues are disordered.
Source: (gene. exp.) Murine adenovirus 2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E7CH51
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.125 M lithium sulphate, 0.075 M HEPES-NaOH, 25% (v/v) glycerol, 10 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2→28.9 Å / Num. obs: 48930 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3642 / CC1/2: 0.714 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NBH

5nbh


Resolution: 2→28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.794 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.137 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20513 2409 4.9 %RANDOM
Rwork0.16538 ---
obs0.16736 46439 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.478 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 106 350 4953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024794
X-RAY DIFFRACTIONr_bond_other_d0.0020.024223
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9776543
X-RAY DIFFRACTIONr_angle_other_deg0.85939842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30623.854205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14115759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5421524
X-RAY DIFFRACTIONr_chiral_restr0.0830.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021018
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_it1.7372.7562346
X-RAY DIFFRACTIONr_mcbond_other1.7372.7552345
X-RAY DIFFRACTIONr_mcangle_it2.8864.1212936
X-RAY DIFFRACTIONr_mcangle_other2.8864.1222937
X-RAY DIFFRACTIONr_scbond_it2.13.052448
X-RAY DIFFRACTIONr_scbond_other2.13.052448
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3754.4893594
X-RAY DIFFRACTIONr_long_range_B_refined5.79633.1585039
X-RAY DIFFRACTIONr_long_range_B_other5.66332.914976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 165 -
Rwork0.269 3444 -
obs--100 %

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