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- PDB-6qpm: Adenovirus serotype 10 Fiber-Knob -

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Basic information

Entry
Database: PDB / ID: 6qpm
TitleAdenovirus serotype 10 Fiber-Knob
ComponentsFiber protein
KeywordsVIRAL PROTEIN / Adenovirus / AdV / HAdV / HAdV-D10 / Ad10 / serotype 10 / Fiber / Fiber-knob / Fibre / knob domain / head / pIV / protein IV / Adenoviridae
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
Biological speciesHuman adenovirus D10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.39 Å
AuthorsBaker, A.T. / Rizkallah, P.J.
CitationJournal: Mol Ther Oncolytics / Year: 2022
Title: Development of a low-seroprevalence, alpha v beta 6 integrin-selective virotherapy based on human adenovirus type 10.
Authors: Bates, E.A. / Davies, J.A. / Vanova, J. / Nestic, D. / Meniel, V.S. / Koushyar, S. / Cunliffe, T.G. / Mundy, R.M. / Moses, E. / Uusi-Kerttula, H.K. / Baker, A.T. / Cole, D.K. / Majhen, D. / ...Authors: Bates, E.A. / Davies, J.A. / Vanova, J. / Nestic, D. / Meniel, V.S. / Koushyar, S. / Cunliffe, T.G. / Mundy, R.M. / Moses, E. / Uusi-Kerttula, H.K. / Baker, A.T. / Cole, D.K. / Majhen, D. / Rizkallah, P.J. / Phesse, T. / Chester, J.D. / Parker, A.L.
History
DepositionFeb 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fiber protein
B: Fiber protein
C: Fiber protein
D: Fiber protein
E: Fiber protein
F: Fiber protein


Theoretical massNumber of molelcules
Total (without water)138,6546
Polymers138,6546
Non-polymers00
Water00
1
A: Fiber protein
B: Fiber protein
C: Fiber protein


Theoretical massNumber of molelcules
Total (without water)69,3273
Polymers69,3273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-29 kcal/mol
Surface area20770 Å2
MethodPISA
2
D: Fiber protein
E: Fiber protein
F: Fiber protein


Theoretical massNumber of molelcules
Total (without water)69,3273
Polymers69,3273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-33 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.570, 183.570, 94.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 187 - 369 / Label seq-ID: 23 - 205

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Fiber protein


Mass: 23108.965 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D10 / Gene: L5 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: B5BQ05
Has protein modificationN

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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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium nitrate 0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 3.39→79.49 Å / Num. obs: 25265 / % possible obs: 99.6 % / Redundancy: 11.3 % / Biso Wilson estimate: 118.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.104 / Net I/σ(I): 15.5
Reflection shellResolution: 3.39→3.58 Å / Rmerge(I) obs: 2.455 / CC1/2: 0.426 / Rrim(I) all: 2.569

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UXE

1uxe


Resolution: 3.39→79.49 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 69.905 / SU ML: 0.451 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23242 1235 4.9 %RANDOM
Rwork0.19934 ---
obs0.20096 23861 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 170.188 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å2-0 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 3.39→79.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8631 0 0 0 8631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138833
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177975
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.65312006
X-RAY DIFFRACTIONr_angle_other_deg1.2371.57218631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.77651083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19824.612399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.121151489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9271518
X-RAY DIFFRACTIONr_chiral_restr0.0780.21221
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029773
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021781
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_it8.62112.3054347
X-RAY DIFFRACTIONr_mcbond_other8.61912.3044346
X-RAY DIFFRACTIONr_mcangle_it13.18418.4745423
X-RAY DIFFRACTIONr_mcangle_other13.18418.4755424
X-RAY DIFFRACTIONr_scbond_it8.81112.8864486
X-RAY DIFFRACTIONr_scbond_other8.80212.8854483
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.91319.0716582
X-RAY DIFFRACTIONr_long_range_B_refined21.61936418
X-RAY DIFFRACTIONr_long_range_B_other21.61936414
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A57430.11
12B57430.11
21A57930.1
22C57930.1
31A53900.11
32D53900.11
41A55730.14
42E55730.14
51A57540.11
52F57540.11
61B58420.11
62C58420.11
71B54500.1
72D54500.1
81B56250.13
82E56250.13
91B58110.11
92F58110.11
101C54570.1
102D54570.1
111C56330.13
112E56330.13
121C58540.09
122F58540.09
131D53900.11
132E53900.11
141D54590.11
142F54590.11
151E56560.13
152F56560.13
LS refinement shellResolution: 3.395→3.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 65 -
Rwork0.36 1529 -
obs--86.16 %
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)
15.0144-1.0947-0.29573.9133-0.74836.09450.09480.749-0.8557-0.4078-0.0344-0.40461.1833-0.1055-0.06040.3002-0.10950.02840.3654-0.1440.3565-49.150355.8369-9.4887
25.94310.85910.46798.05311.06573.63330.06440.36250.53140.09880.16280.2767-0.1727-0.5507-0.22730.0339-0.04270.02310.49910.10220.0798-68.377574.469-4.1043
36.8886-0.46881.63413.8574-1.02124.0030.18811.80960.6812-0.69550.0974-0.5463-0.2174-0.1599-0.28550.2882-0.05350.23770.99240.28060.3077-51.660777.8496-25.4315
46.4082-0.7850.68972.71720.1382.20140.0144-1.2496-1.0590.9103-0.1292-0.38050.95010.18670.11481.4582-0.0953-0.09240.87570.46360.6308-57.605221.604237.95
53.5661.2924-1.42043.5809-1.3325.98740.1803-1.42420.2141.1705-0.2442-0.3456-0.15530.28720.06390.747-0.1953-0.35020.90070.01870.3516-51.419748.016835.4123
65.3359-0.654-0.06936.20360.92054.1826-0.0967-0.5433-0.35570.2093-0.21550.2310.4242-0.52770.31220.4767-0.2579-0.0020.32580.0050.0537-70.457736.648119.4092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A187 - 369
2X-RAY DIFFRACTION2B187 - 369
3X-RAY DIFFRACTION3C187 - 369
4X-RAY DIFFRACTION4D187 - 369
5X-RAY DIFFRACTION5E187 - 369
6X-RAY DIFFRACTION6F187 - 369

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