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- PDB-4k6t: Crystal structure of Ad37 fiber knob in complex with trivalent si... -

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Basic information

Entry
Database: PDB / ID: 4k6t
TitleCrystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor ME0385
ComponentsFiber protein
KeywordsVIRAL PROTEIN / adenovirus / fiber knob / protein carbohydrate interaction / sialic acid / carbohydrate mimic / multivalent ligand
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 / metal ion binding
Similarity search - Function
Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-1P0 / ACETATE ION / N-acetyl-alpha-neuraminic acid / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 37
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStehle, T. / Bauer, J.
CitationJournal: Org.Biomol.Chem. / Year: 2015
Title: Triazole linker-based trivalent sialic acid inhibitors of adenovirus type 37 infection of human corneal epithelial cells.
Authors: Caraballo, R. / Saleeb, M. / Bauer, J. / Liaci, A.M. / Chandra, N. / Storm, R.J. / Frangsmyr, L. / Qian, W. / Stehle, T. / Arnberg, N. / Elofsson, M.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
E: Fiber protein
F: Fiber protein
G: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,29960
Polymers130,2996
Non-polymers5,00054
Water14,808822
1
A: Fiber protein
B: Fiber protein
C: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,64528
Polymers65,1503
Non-polymers2,49525
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Fiber protein
F: Fiber protein
G: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,65432
Polymers65,1503
Non-polymers2,50529
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.940, 67.180, 121.430
Angle α, β, γ (deg.)90.00, 96.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 12 molecules ABCEFG

#1: Protein
Fiber protein


Mass: 21716.535 Da / Num. of mol.: 6 / Fragment: fiber knob
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 37 / Gene: L5 / Plasmid: pPROEX Htb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q64823
#2: Sugar
ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 9 types, 870 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-1P0 / 2,2',2''-[nitrilotris(methanediyl-1H-1,2,3-triazole-4,1-diyl)]triethanol


Mass: 392.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N10O3
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 24% PEG 8000, 0.1M HEPES, 0.05M zinc acetate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2012
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 80721 / Num. obs: 80719 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5951 / % possible all: 99.1

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
REFMAC5.8.0025refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unliganded Ad37 trimer

Resolution: 2→37.26 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.618 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19957 1615 2 %RANDOM
Rwork0.15989 ---
obs0.1607 80719 99.34 %-
all-80719 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.745 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20.74 Å2
2---0.1 Å2-0 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 2→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8642 0 276 822 9740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.029235
X-RAY DIFFRACTIONr_bond_other_d0.0020.028524
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.96912593
X-RAY DIFFRACTIONr_angle_other_deg0.8443.00119701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7651166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48825.474369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.656151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1531512
X-RAY DIFFRACTIONr_chiral_restr0.0820.21467
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022073
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 119 -
Rwork0.252 5809 -
obs-5651 99.11 %
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)
11.9580.19280.31261.4776-0.40921.39-0.02250.06790.0961-0.07370.0001-0.179-0.06450.11850.02240.0104-0.00510.00620.0179-0.01330.058524.3603-10.58240.0493
21.1570.297-0.29231.921-0.05291.05660.0653-0.08720.19430.1547-0.03750.1213-0.0837-0.1259-0.02780.01970.00950.01010.0585-0.04540.06072.4862-10.912416.389
31.9428-0.7053-0.6451.58230.53771.8792-0.0552-0.3137-0.01090.32810.0593-0.26890.16070.2094-0.00410.09890.0125-0.07920.0670.00790.073524.1431-26.366222.3195
41.6337-0.4969-0.43672.21310.49741.50160.09880.10840.1726-0.1527-0.0539-0.171-0.08470.1485-0.04480.01470.00010.01460.05010.03080.038165.138819.495843.2351
52.16140.3276-0.84181.0623-0.26731.36880.01750.3314-0.1419-0.2395-0.00090.18720.0995-0.1822-0.01660.07730.0016-0.05650.0799-0.04750.07642.88894.642838.0334
61.98820.19860.55451.3390.33981.43760.0125-0.10310.09640.0652-0.02190.132-0.0688-0.13670.00950.00940.0060.01110.0148-0.00410.032643.502820.538859.8959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A180 - 365
2X-RAY DIFFRACTION2B180 - 365
3X-RAY DIFFRACTION3C184 - 365
4X-RAY DIFFRACTION4E181 - 365
5X-RAY DIFFRACTION5F180 - 365
6X-RAY DIFFRACTION6G181 - 365

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