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- PDB-6stu: Adenovirus 30 Fiber Knob protein -

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Basic information

Entry
Database: PDB / ID: 6stu
TitleAdenovirus 30 Fiber Knob protein
ComponentsFiber
KeywordsVIRAL PROTEIN / Adenovirus / Type 29 / Sialic Acid / 3D Structure / 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, 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
Similarity search - Domain/homology
GLUTAMIC ACID / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 30
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 Å
AuthorsBaker, A.T. / Mundy, R.M. / Rizkallah, P.J. / Parker, A.L.
Citation
Journal: npj Viruses / Year: 2023
Title: Broad sialic acid usage amongst species D human adenovirus
Authors: Mundy, R.M. / Baker, A.T. / Bates, E.A. / Cunliffe, T.G. / Teijeira-Crespo, A. / Moses, E. / Rizkallah, P.J. / Parker, A.L.
#1: Journal: Biorxiv / Year: 2020
Title: The fiber knob protein of human adenovirus type 49 mediates highly efficient and promiscuous infection of cancer cell lines using a novel cell entry mechanism
Authors: Baker, A.T. / Marlow, G. / Davies, J.A. / Moses, E. / Mundy, R.M. / Cole, D.K. / Rizkallah, P.J. / Parker, A.L.
History
DepositionSep 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.title

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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
D: Fiber
E: Fiber
F: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,0989
Polymers136,8266
Non-polymers2713
Water3,477193
1
A: Fiber
B: Fiber
C: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6225
Polymers68,4133
Non-polymers2092
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-23 kcal/mol
Surface area25470 Å2
MethodPISA
2
D: Fiber
E: Fiber
F: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4754
Polymers68,4133
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-27 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.350, 87.360, 217.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fiber


Mass: 22804.398 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 30 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: M0QTV3
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M SPG, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 X 500K / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.39→54.76 Å / Num. obs: 48896 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.049 / Rrim(I) all: 0.134 / Net I/σ(I): 11.2 / Num. measured all: 365841 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.39-2.457.81.4842811035890.6230.5611.5881.4100
10.69-54.766.30.03340646420.9970.0140.03639.799.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→54.76 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 27.729 / SU ML: 0.293 / SU R Cruickshank DPI: 0.5812 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.581 / ESU R Free: 0.297
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 2348 4.8 %RANDOM
Rwork0.217 ---
obs0.2194 46478 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 199.63 Å2 / Biso mean: 58.703 Å2 / Biso min: 27.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å20 Å2
2---5.34 Å2-0 Å2
3---5.48 Å2
Refinement stepCycle: final / Resolution: 2.39→54.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9426 0 18 193 9637
Biso mean--106.01 47.75 -
Num. residues----1220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139647
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178701
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.64913108
X-RAY DIFFRACTIONr_angle_other_deg1.2261.58320457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.68951214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.93826.897406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.363151640
X-RAY DIFFRACTIONr_chiral_restr0.0780.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021742
LS refinement shellResolution: 2.39→2.452 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 162 -
Rwork0.36 3416 -
all-3578 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.30720.0048-0.2342.1860.55851.89960.0822-0.2214-0.2661-0.0184-0.09950.26090.1375-0.14820.01730.0218-0.0396-0.00580.1064-0.01550.056221.6575-13.474938.417
23.0388-0.76920.59354.1562-1.01332.53840.01930.09180.3257-0.0904-0.0835-0.0186-0.21390.09940.06420.0543-0.06290.01670.127-0.02750.047237.69178.122437.0188
33.86630.69651.32522.48330.78993.60740.0298-0.36320.45040.0446-0.23070.6076-0.0602-0.32260.20090.02230.01730.02760.2047-0.14910.238212.314910.955644.8473
43.21970.2978-0.5034.2298-0.87585.02380.0805-0.4066-0.33110.7177-0.3122-0.96160.14460.30610.23170.2123-0.0134-0.17720.18660.12750.251527.1786-3.698595.7519
52.6789-0.0886-0.6566.14540.16731.37310.1131-0.2935-0.17120.8391-0.00630.6392-0.0581-0.1901-0.10680.2629-0.04440.12580.26180.08660.12230.8624-8.898498.1589
63.18340.8938-0.19944.6846-0.96491.5235-0.0006-0.03580.12820.08880.08930.3933-0.0847-0.1385-0.08870.04680.03290.01460.1190.01680.03559.274711.650383.194
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A394 - 601
2X-RAY DIFFRACTION2B396 - 598
3X-RAY DIFFRACTION3C391 - 596
4X-RAY DIFFRACTION4D396 - 596
5X-RAY DIFFRACTION5E396 - 596
6X-RAY DIFFRACTION6F394 - 601

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