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- PDB-1v1i: Adenovirus fibre shaft sequence N-terminally fused to the bacteri... -

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Basic information

Entry
Database: PDB / ID: 1v1i
TitleAdenovirus fibre shaft sequence N-terminally fused to the bacteriophage T4 fibritin foldon trimerisation motif with a long linker
ComponentsFIBRITIN, FIBER PROTEIN
KeywordsADENOVIRUS / CHIMERA / FIBER PROTEIN
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / virion component / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #10 / reovirus attachment protein sigma1; domain 1 / 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 ...Wheat Germ Agglutinin (Isolectin 2); domain 1 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #10 / reovirus attachment protein sigma1; domain 1 / 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 / Fibritin C-terminal / Fibritin C-terminal region / Other non-globular / Laminin / Special / Ribbon / Mainly Beta
Similarity search - Domain/homology
Fiber protein / Fibritin
Similarity search - Component
Biological speciesHUMAN ADENOVIRUS C
ENTEROBACTERIA PHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPapanikolopoulou, K. / Teixeira, S. / Belrhali, H. / Forsyth, V.T. / Mitraki, A. / van Raaij, M.J.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Adenovirus Fibre Shaft Sequences Fold Into the Native Triple Beta-Spiral Fold When N-Terminally Fused to the Bacteriophage T4 Fibritin Foldon Trimerisation Motif
Authors: Papanikolopoulou, K. / Teixeira, S. / Belrhali, H. / Forsyth, V.T. / Mitraki, A. / van Raaij, M.J.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Formation of Highly Stable Chimeric Trimers by Fusion of an Adenovirus Fiber Shaft Fragment with the Foldon Domain of Bacteriophage T4 Fibritin
Authors: Papanikolopoulou, K. / Forge, V. / Goeltz, P. / Mitraki, A.
#2: Journal: Nature / Year: 1999
Title: A Triple Beta-Spiral in the Adenovirus Fibre Shaft Reveals a New Structural Motif for a Fibrous Protein
Authors: van Raaij, M.J. / Mitraki, A. / Lavigne, G. / Cusack, S.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of Bacteriophage T4 Fibritin M: A Troublesome Packing Arrangement
Authors: Strelkov, S. / Tao, Y. / Shneider, M.M. / Mesyanzhinov, V. / Rossmann, M.G.
History
DepositionApr 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2004Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Source and taxonomy
Revision 1.2Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBRITIN, FIBER PROTEIN
B: FIBRITIN, FIBER PROTEIN
C: FIBRITIN, FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,5293
Polymers34,5293
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.230, 43.270, 100.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.12087, -0.77467, 0.62071), (0.70931, -0.50485, -0.49195), (0.69446, 0.38082, 0.6105)-0.88325, 20.35965, 1.5734
2given(-0.11464, -0.78312, 0.61121), (0.72142, -0.48861, -0.49073), (0.68294, 0.38468, 0.62097)-0.51366, 19.9575, 1.17076
3given(-0.11908, -0.77334, 0.6227), (0.7158, -0.5015, -0.48594), (0.68808, 0.38786, 0.61327)-0.91706, 19.92031, 1.49919
4given(-0.46936, -0.70293, 0.5344), (0.86972, -0.26341, 0.41739), (-0.15263, 0.66069, 0.73498)-2.4625, 15.00239, -5.93603
5given(-0.50137, -0.67974, 0.53533), (0.85619, -0.30057, 0.42024), (-0.12475, 0.66904, 0.73268)-2.79445, 15.11898, -6.3232
6given(-0.43754, -0.72748, 0.52852), (0.88468, -0.24377, 0.39699), (-0.15996, 0.64136, 0.75038)-1.99557, 14.83177, -5.99442

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Components

#1: Protein FIBRITIN, FIBER PROTEIN / ARTIFICAL FUSION OF ADENOVIRUS FIBRE SHAFT WITH BACTERIOPHAGE T4 FIBRITIN FOLDON / WHISKER ANTIGEN ...ARTIFICAL FUSION OF ADENOVIRUS FIBRE SHAFT WITH BACTERIOPHAGE T4 FIBRITIN FOLDON / WHISKER ANTIGEN CONTROL PROTEIN / COLLAR PROTEIN


Mass: 11509.702 Da / Num. of mol.: 3
Fragment: SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
Source method: isolated from a genetically manipulated source
Details: ARTIFICIAL FUSION PROTEIN OF ADENOVIRUS TYPE 2 FIBRE SHAFT RESIDUES 319-398 - BACTERIOPHAGE T4 FIBRITIN FOLDON RESIDUES 457-483 WITH A GLY-SER LINKER IN BETWEEN
Source: (gene. exp.) HUMAN ADENOVIRUS C, (gene. exp.) ENTEROBACTERIA PHAGE T4 (virus)
Plasmid: PT7.7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P03275, UniProt: P10104
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Compound detailsADENOVIRUS FIBRE IS RESPONSIBLE FOR ADENOVIRUS RECEPTOR BINDING AND CONTAINS A VIRUS-BINDING N- ...ADENOVIRUS FIBRE IS RESPONSIBLE FOR ADENOVIRUS RECEPTOR BINDING AND CONTAINS A VIRUS-BINDING N-TERMINAL DOMAIN, A MIDDLE SHAFT DOMAIN AND A C-TERMINAL RECEPTOR-BINDING DOMAIN, BINDING TO THE HUMAN COXSACKIEVIRUS AND ADENOVIRUS PROTEIN. THE FIBRITIN CHAPERONE IS RESPONSIBLE FOR ATTACHMENT OF LONG TAIL FIBRES TO VIRUS PARTICLE. DURING PHAGE ASSEMBLY, 6 FIBRITIN MOLECULES ATTACH TO EACH VIRION NECK THROUGH THEIR N-TERMINAL DOMAINS, TO FORM A COLLAR WITH SIX FIBERS ('WHISKERS'). MOLECULES ATTACH TO EACH VIRION NECK THROUGH THEIR N-TERMINAL

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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: 44.8 %
Crystal growpH: 7
Details: 10 MM HEPES-NAOH PH 7.0 0.2 M MAGNESIUM ACETATE, 20 % (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9202
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 25299 / % possible obs: 99.9 % / Redundancy: 13.8 % / Biso Wilson estimate: 25.453 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.33 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
MOLREPphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QIU, PDB ENTRY 1AVY

1qiu

1avy


Resolution: 1.9→19.9 Å / SU B: 4.5422 / SU ML: 0.1332 / Cross valid method: THROUGHOUT / ESU R: 0.1933 / ESU R Free: 0.1788
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1522 6 %THIN SHELLS OF RESOLUTION
Rwork0.232 ---
obs-23720 99.9 %-
Displacement parametersBiso mean: 32.746 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.89 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 0 237 2471

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