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- PDB-1qiu: A triple beta-spiral in the adenovirus fibre shaft reveals a new ... -

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Basic information

Entry
Database: PDB / ID: 1qiu
TitleA triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for biological fibres
ComponentsADENOVIRUS FIBRE
KeywordsFIBRE PROTEIN / TRIPLE BETA-SPIRAL / ADENOVIRUS
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
reovirus attachment protein sigma1; domain 1 / 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 ...reovirus attachment protein sigma1; domain 1 / 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 / Laminin / Ribbon / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHUMAN ADENOVIRUS 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Authorsvan Raaij, M.J. / Lavigne, G. / Mitraki, A. / Cusack, S.
CitationJournal: 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.
History
DepositionJun 16, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.title / _citation_author.name
Revision 1.4Dec 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
Revision 1.5Feb 7, 2024Group: Structure summary / Category: entity / Item: _entity.pdbx_fragment

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENOVIRUS FIBRE
B: ADENOVIRUS FIBRE
C: ADENOVIRUS FIBRE
D: ADENOVIRUS FIBRE
E: ADENOVIRUS FIBRE
F: ADENOVIRUS FIBRE


Theoretical massNumber of molelcules
Total (without water)171,5266
Polymers171,5266
Non-polymers00
Water10,431579
1
A: ADENOVIRUS FIBRE
B: ADENOVIRUS FIBRE
C: ADENOVIRUS FIBRE


Theoretical massNumber of molelcules
Total (without water)85,7633
Polymers85,7633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: ADENOVIRUS FIBRE
E: ADENOVIRUS FIBRE
F: ADENOVIRUS FIBRE


Theoretical massNumber of molelcules
Total (without water)85,7633
Polymers85,7633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)165.510, 95.870, 211.770
Angle α, β, γ (deg.)90.00, 106.83, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE MOLECULE CONSISTS IS A HOMO- TRIMER.CHAINS A, B AND C FORM ONE TRIMER CHAINS D, E AND F THE OTHER TRIMER

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Components

#1: Protein
ADENOVIRUS FIBRE


Mass: 28587.725 Da / Num. of mol.: 6
Fragment: FRAGMENT CONTAINING THE FOUR DISTAL SHAFT REPEATS PLUS THE HEAD DOMAIN.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN ADENOVIRUS 2 / Gene: LOCUS AD2H2 / Plasmid: PT7.7 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P03275
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 4.6 Å3/Da / Density % sol: 73 %
Crystal growpH: 4
Details: 0.8 M AMMONIUM SULPHATE, 100 MM SODIUM CITRATE, PH 4.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
20.8 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.948
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 103327 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.132 / Net I/σ(I): 4.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.287 / % possible all: 54.9
Reflection
*PLUS
Rmerge(I) obs: 0.132
Reflection shell
*PLUS
% possible obs: 59.9 % / Num. unique obs: 10696 / Rmerge(I) obs: 0.287

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Processing

Software
NameVersionClassification
CNS0.4refinement
MOSFLMdata reduction
SCALAdata scaling
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QHV

1qhv


Resolution: 2.4→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2480815.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1662 1.6 %SHELLS
Rwork0.232 ---
obs0.232 103325 84 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å25.19 Å2
2---3.52 Å20 Å2
3---5.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12042 0 0 579 12621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.53 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.365 208 2.2 %
Rwork0.312 9430 -
obs--54.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor obs: 0.312

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