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- PDB-6qpn: Adenovirus species D serotype 49 Fiber-Knob -

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Basic information

Entry
Database: PDB / ID: 6qpn
TitleAdenovirus species D serotype 49 Fiber-Knob
ComponentsFiber
KeywordsVIRAL PROTEIN / Adenovirus / Fiber-knob / Fiber / Knob / Head / Adenoviridae / Protein IV / wild type / wildtype / pIV / HAdV-D49 / species D / serotype 49 / Ad49
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell
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 49
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsBaker, A.T. / Rizkallah, P.J.
CitationJournal: Journal of Virology / Year: 2021
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. / Rizkallah, P.J.
History
DepositionFeb 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 2.0Aug 25, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / database_2 / entity / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_ncs_dom_lim / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_FOM_work_R_set / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.overall_SU_R_Cruickshank_DPI / _refine.overall_SU_R_free / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr_ncs.pdbx_number / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_all / _reflns.B_iso_Wilson_estimate / _reflns.number_all / _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_number_measured_all / _software.version / _struct_conn.pdbx_dist_value / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_sheet.number_strands
Description: Atomic clashes / Details: New refinement for better geometry / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 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

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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)150,7099
Polymers150,4206
Non-polymers2883
Water1629
1
A: Fiber
B: Fiber
C: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4025
Polymers75,2103
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-73 kcal/mol
Surface area23520 Å2
MethodPISA
2
D: Fiber
E: Fiber
F: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3064
Polymers75,2103
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-31 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.830, 56.280, 115.700
Angle α, β, γ (deg.)90.000, 112.950, 90.000
Int Tables number3
Space group name H-MP121
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: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALAAA395 - 59323 - 221
21GLUGLUALAALABB395 - 59323 - 221
12GLUGLUALAALAAA395 - 59323 - 221
22GLUGLUALAALACC395 - 59323 - 221
13ASNASNALAALAAA396 - 59324 - 221
23ASNASNALAALADD396 - 59324 - 221
14GLUGLUASPASPAA395 - 59223 - 220
24GLUGLUASPASPEE395 - 59223 - 220
15GLUGLUALAALAAA395 - 59323 - 221
25GLUGLUALAALAFF395 - 59323 - 221
16GLUGLUALAALABB395 - 59323 - 221
26GLUGLUALAALACC395 - 59323 - 221
17ASNASNALAALABB396 - 59324 - 221
27ASNASNALAALADD396 - 59324 - 221
18GLUGLUALAALABB395 - 59323 - 221
28GLUGLUALAALAEE395 - 59323 - 221
19GLUGLUALAALABB395 - 59323 - 221
29GLUGLUALAALAFF395 - 59323 - 221
110ASNASNGLUGLUCC396 - 59424 - 222
210ASNASNGLUGLUDD396 - 59424 - 222
111GLUGLUGLUGLUCC395 - 59423 - 222
211GLUGLUGLUGLUEE395 - 59423 - 222
112GLUGLUALAALACC395 - 59323 - 221
212GLUGLUALAALAFF395 - 59323 - 221
113ASNASNGLUGLUDD396 - 59424 - 222
213ASNASNGLUGLUEE396 - 59424 - 222
114ASNASNASPASPDD396 - 59224 - 220
214ASNASNASPASPFF396 - 59224 - 220
115GLUGLUALAALAEE395 - 59323 - 221
215GLUGLUALAALAFF395 - 59323 - 221

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 /


Mass: 25070.061 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 49 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q09TX9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PACT Premier condition D5 (0.1M MMT [Malic acid, MES, Tris], pH8.0, 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: 0.97628 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.74→106.54 Å / Num. obs: 33350 / % possible obs: 99.1 % / Redundancy: 3.7 % / CC1/2: 0.988 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.09 / Rrim(I) all: 0.176 / Net I/σ(I): 6.8 / Num. measured all: 122219
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
2.74-2.813.71.633917924610.40.9791.91198.9
12.25-106.543.20.08212994090.9810.0510.09718.196.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNB

1knb


Resolution: 2.74→106.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2528 / WRfactor Rwork: 0.2003 / FOM work R set: 0.7079 / SU B: 54.108 / SU ML: 0.429 / SU R Cruickshank DPI: 0.3695 / SU Rfree: 0.3873 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 1609 4.8 %RANDOM
Rwork0.2114 ---
obs0.2136 31740 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 233.49 Å2 / Biso mean: 94.271 Å2 / Biso min: 42.83 Å2
Baniso -1Baniso -2Baniso -3
1-3.35 Å20 Å22.92 Å2
2---1.2 Å2-0 Å2
3----3.4 Å2
Refinement stepCycle: final / Resolution: 2.74→106.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9059 0 15 9 9083
Biso mean--148.58 58.22 -
Num. residues----1165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139275
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178704
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.65112593
X-RAY DIFFRACTIONr_angle_other_deg1.211.58920205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.77451154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19125.573393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.157151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3931512
X-RAY DIFFRACTIONr_chiral_restr0.0760.21258
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210410
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021990
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A55180.1
12B55180.1
21A58290.11
22C58290.11
31A58650.08
32D58650.08
41A59810.09
42E59810.09
51A59050.08
52F59050.08
61B54920.1
62C54920.1
71B55440.09
72D55440.09
81B55080.09
82E55080.09
91B55170.1
92F55170.1
101C58160.09
102D58160.09
111C58420.1
112E58420.1
121C58030.1
122F58030.1
131D58820.08
132E58820.08
141D58560.08
142F58560.08
151E58260.1
152F58260.1
LS refinement shellResolution: 2.74→2.811 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 141 -
Rwork0.379 2318 -
all-2459 -
obs--98.48 %
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)
16.7351-1.3051-2.14992.20550.39655.63130.119-0.2089-0.10360.02730.10380.2254-0.0266-0.3272-0.22270.163-0.00310.03210.05310.0250.04341.217611.785819.9031
25.0695-0.2081-1.11876.35142.68393.88250.5677-0.76831.1494-0.46660.2026-0.4294-0.79850.5348-0.77020.2987-0.13880.27840.273-0.22790.361325.490718.892412.2977
37.3978-1.8199-0.69133.33970.30724.82540.128-1.67680.61780.41090.283-0.3772-0.30061.0527-0.41090.3465-0.10010.0481.2069-0.5010.248918.988519.432738.6046
47.00531.1208-1.65642.60030.30423.5744-0.04940.1572-0.16420.1968-0.05860.2891-0.1141-0.44610.1080.16720.04430.05540.15390.04980.08760.647649.031915.9504
54.8434-0.11150.70752.83951.01525.7655-0.3063-0.492-0.87280.16340.0672-0.07380.87730.69410.23910.5610.21560.28150.30410.29670.379475.326529.401325.8471
64.4880.3706-1.01876.62750.19283.7465-0.3367-0.792-0.33170.49190.11250.27640.10030.14720.22420.43210.0760.19140.51140.20190.149559.587344.081642.3973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A395 - 593
2X-RAY DIFFRACTION2B395 - 593
3X-RAY DIFFRACTION3C395 - 593
4X-RAY DIFFRACTION4D396 - 594
5X-RAY DIFFRACTION5E395 - 594
6X-RAY DIFFRACTION6F395 - 593

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