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- PDB-28nu: Human Adenovirus type C5 knob protein with the KO1 mutation -

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Basic information

Entry
Database: PDB / ID: 28nu
TitleHuman Adenovirus type C5 knob protein with the KO1 mutation
ComponentsFiber protein
KeywordsVIRAL PROTEIN / Adenovirus / C5 / Fiber Knob protein / KO1 mutation
Function / homology
Function and homology information


viral capsid, fiber / adhesion receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Fiber protein
Similarity search - Component
Biological speciesHuman adenovirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRizkallah, P.J. / Swift, E.A. / Parker, A.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: To Be Published
Title: Human Adenovirus type C5 knob protein with the KO1 mutation
Authors: Rizkallah, P.J. / Swift, E.A. / Parker, A.L.
History
DepositionFeb 10, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,18619
Polymers121,9906
Non-polymers1,19613
Water7,008389
1
A: Fiber protein
B: Fiber protein
C: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5409
Polymers60,9953
Non-polymers5456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-30 kcal/mol
Surface area20680 Å2
2
D: Fiber protein
E: Fiber protein
F: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,64610
Polymers60,9953
Non-polymers6517
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-20 kcal/mol
Surface area20840 Å2
Unit cell
Length a, b, c (Å)139.976, 139.976, 139.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515

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 / SPIKE / Protein IV


Mass: 20331.627 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 5 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: P11818
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane, 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: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.6→57.2 Å / Num. obs: 82777 / % possible obs: 100 % / Redundancy: 14.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.389 / Rpim(I) all: 0.106 / Rrim(I) all: 0.403 / Χ2: 0.98 / Net I/σ(I): 6.1
Reflection shellResolution: 2.6→2.65 Å / % possible obs: 99.8 % / Redundancy: 13.4 % / Rmerge(I) obs: 2.66 / Num. measured all: 60674 / Num. unique obs: 4515 / CC1/2: 0.424 / Rpim(I) all: 0.752 / Rrim(I) all: 2.765 / Χ2: 1.01 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→57.2 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 18.842 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25718 4315 5.2 %RANDOM
Rwork0.21408 ---
obs0.2163 78394 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.834 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 2.6→57.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8598 0 75 389 9062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138948
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158196
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.64512219
X-RAY DIFFRACTIONr_angle_other_deg1.2171.57418945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.59851134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.71424.688384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.006151398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6181518
X-RAY DIFFRACTIONr_chiral_restr0.0660.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210230
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021977
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_it2.2783.2984518
X-RAY DIFFRACTIONr_mcbond_other2.2793.2984517
X-RAY DIFFRACTIONr_mcangle_it3.8834.9375658
X-RAY DIFFRACTIONr_mcangle_other3.8824.9375659
X-RAY DIFFRACTIONr_scbond_it2.3663.3994430
X-RAY DIFFRACTIONr_scbond_other2.3663.3994431
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5235.0176562
X-RAY DIFFRACTIONr_long_range_B_refined6.73737.4889669
X-RAY DIFFRACTIONr_long_range_B_other6.71837.379610
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)
11A59420.04
12B59420.04
21A59380.05
22C59380.05
31A59370.05
32D59370.05
41A59090.05
42E59090.05
51A59180.05
52F59180.05
61B59420.05
62C59420.05
71B59450.04
72D59450.04
81B59590.03
82E59590.03
91B59690.01
92F59690.01
101C59480.05
102D59480.05
111C59210.05
112E59210.05
121C59240.05
122F59240.05
131D59080.05
132E59080.05
141D59230.04
142F59230.04
151E59260.03
152F59260.03
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 287 -
Rwork0.328 5813 -
obs--99.93 %
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)
12.40941.32320.13743.41471.63781.736-0.0058-0.0905-0.1437-0.00610.0968-0.40120.07150.3272-0.0910.01020.0258-0.00540.08940.00410.1271128.10130.987178.0931
23.4183-1.3658-1.47611.64520.01112.60620.12410.41320.0453-0.2923-0.08570.07580.091-0.0951-0.03840.06760.0047-0.04640.0689-0.00340.0916106.02511.554566.5777
31.7017-0.07741.52852.1091-1.36273.51-0.0765-0.06480.28880.1260.00070.0686-0.4128-0.01990.07580.0669-0.00060.00220.0092-0.03870.1649116.581823.119988.6793
42.2968-0.23991.4561.5216-1.49883.336-0.00660.099-0.0575-0.0861-0.094-0.28320.04150.39310.10060.00930.00170.03770.06770.00780.159993.08946.598655.7549
51.7786-1.3909-0.05023.58951.36912.3865-0.0747-0.3147-0.04690.41090.113-0.04080.1204-0.1055-0.03820.06040.00170.00980.070.03350.077481.541836.033277.8499
63.42071.2087-1.54442.3863-0.18611.66470.1073-0.01280.382-0.1024-0.02820.1069-0.3057-0.0703-0.07910.08130.02540.0130.00990.00760.124671.039558.118966.2843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A390 - 590
2X-RAY DIFFRACTION2B390 - 590
3X-RAY DIFFRACTION3C390 - 590
4X-RAY DIFFRACTION4D390 - 590
5X-RAY DIFFRACTION5E390 - 590
6X-RAY DIFFRACTION6F390 - 590

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