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- PDB-6hcn: Adenovirus Type 5 Fiber Knob protein at 1.49A resolution -

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Basic information

Entry
Database: PDB / ID: 6hcn
TitleAdenovirus Type 5 Fiber Knob protein at 1.49A resolution
Components(Fiber protein) x 2
KeywordsVIRAL PROTEIN / Fiber / Fiber-knob / tropism determinant / high resolution / structure determination. adenovirus / Mastadenovirus
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
Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman adenovirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsRizkallah, P.J. / Parker, A.L. / Baker, A.T.
CitationJournal: Nat Commun / Year: 2019
Title: Diversity within the adenovirus fiber knob hypervariable loops influences primary receptor interactions.
Authors: Baker, A.T. / Greenshields-Watson, A. / Coughlan, L. / Davies, J.A. / Uusi-Kerttula, H. / Cole, D.K. / Rizkallah, P.J. / Parker, A.L.
History
DepositionAug 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4779
Polymers61,1423
Non-polymers3356
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-18 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.160, 102.440, 77.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA396 - 5801 - 185
21GLNGLNBB396 - 5803 - 187
12GLUGLUAA396 - 5811 - 186
22GLUGLUCC396 - 5811 - 186
13GLNGLNBB396 - 5803 - 187
23GLNGLNCC396 - 5801 - 185

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Fiber protein / SPIKE / Protein IV


Mass: 20299.631 Da / Num. of mol.: 2
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: Protein Fiber protein / SPIKE / Protein IV


Mass: 20542.916 Da / Num. of mol.: 1
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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 3.3 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: DL-Malic acid, MES monohydrate, Tris, pH 7.0 (condition D4 of PACT premier suite from Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 1.49→61.56 Å / Num. obs: 131951 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 18.3 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.159 / Net I/σ(I): 7.1
Reflection shellResolution: 1.49→1.53 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.838 / Num. unique obs: 9638 / CC1/2: 0.565 / Rrim(I) all: 2.183 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNB

1knb


Resolution: 1.49→61.56 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.205 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23305 6388 4.8 %RANDOM
Rwork0.21091 ---
obs0.21201 125479 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.628 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å2-0 Å2
2---1.47 Å20 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.49→61.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4310 0 21 409 4740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0144523
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173997
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.6576179
X-RAY DIFFRACTIONr_angle_other_deg0.9291.6469371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.515579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.53124.715193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88615719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.118159
X-RAY DIFFRACTIONr_chiral_restr0.080.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025093
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02851
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_it1.1811.0442292
X-RAY DIFFRACTIONr_mcbond_other1.1853.7222291
X-RAY DIFFRACTIONr_mcangle_it1.561.5762879
X-RAY DIFFRACTIONr_mcangle_other1.566.1552880
X-RAY DIFFRACTIONr_scbond_it1.4841.1932231
X-RAY DIFFRACTIONr_scbond_other1.4841.1932231
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6971.7223301
X-RAY DIFFRACTIONr_long_range_B_refined2.6914874
X-RAY DIFFRACTIONr_long_range_B_other2.2424781
X-RAY DIFFRACTIONr_rigid_bond_restr17.2934508
X-RAY DIFFRACTIONr_sphericity_free39.1657
X-RAY DIFFRACTIONr_sphericity_bonded14.29654395
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A57090.1
12B57090.1
21A58260.08
22C58260.08
31B56890.1
32C56890.1
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 450 -
Rwork0.39 9182 -
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)
11.6925-0.11650.50552.5368-0.17690.9579-0.05-0.0338-0.0515-0.02450.04040.1119-0.0044-0.09140.00960.0027-0.00690.01310.1132-0.0050.3788-6.354228.9398-9.5287
22.9982-0.02540.04151.7552-0.78871.3791-0.0686-0.32790.09970.19720.0494-0.0309-0.03750.04520.01930.03530.0157-0.02480.18140.0010.357315.199834.92925.942
31.10740.23040.15651.6299-0.11422.3862-0.05210.04680.1254-0.1173-0.0407-0.1381-0.19580.0260.09280.062-0.01340.00730.10510.02690.42079.170850.4614-15.6567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A396 - 581
2X-RAY DIFFRACTION2B394 - 581
3X-RAY DIFFRACTION3C396 - 581

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