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- PDB-3n0i: Crystal Structure of Ad37 fiber knob in complex with GD1a oligosa... -

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Basic information

Entry
Database: PDB / ID: 3n0i
TitleCrystal Structure of Ad37 fiber knob in complex with GD1a oligosaccharide
ComponentsFiber
KeywordsCELL ADHESION / adenovirus / fiber knob / ganglioside / GD1a / virus-receptor complex / oligosaccharide structure / protein carbohydrate interaction
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
Biological speciesHuman adenovirus 37
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNilsson, E.C. / Storm, R.J. / Bauer, J. / Johansson, S.M.C. / Lookene, A. / Angstroem, J. / Hedenstroem, M. / Fraengsmyr, L. / Rinaldi, S. / Willison, H. ...Nilsson, E.C. / Storm, R.J. / Bauer, J. / Johansson, S.M.C. / Lookene, A. / Angstroem, J. / Hedenstroem, M. / Fraengsmyr, L. / Rinaldi, S. / Willison, H. / Domelloef, F.P. / Stehle, T. / Arnberg, N.
CitationJournal: NAT.MED. (N.Y.) / Year: 2011
Title: The GD1a glycan is a cellular receptor for adenoviruses causing epidemic keratoconjunctivitis.
Authors: Nilsson, E.C. / Storm, R.J. / Bauer, J. / Johansson, S.M. / Lookene, A. / Angstrom, J. / Hedenstrom, M. / Eriksson, T.L. / Frangsmyr, L. / Rinaldi, S. / Willison, H.J. / Domellof, F.P. / Stehle, T. / Arnberg, N.
History
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6367
Polymers65,1503
Non-polymers1,4864
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-111 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.990, 69.770, 74.900
Angle α, β, γ (deg.)90.00, 94.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fiber / Fiber protein


Mass: 21716.535 Da / Num. of mol.: 3 / Fragment: UNP residues 177-365
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: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1290.140 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2-3/a4-b1_b3-c2_b4-d1_d3-e1_e3-f2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 26% PEG 8000, 0.05M zinc acetate, 0.1M HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2009 / Details: mirrors
RadiationMonochromator: DCM Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.65→32.9 Å / Num. all: 75294 / Num. obs: 74636 / % possible obs: 99.1 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2 / Redundancy: 4.1 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.2
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5420 / % possible all: 98.4

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1uxe

1uxe


Resolution: 1.65→32.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.871 / SU ML: 0.06 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2.2 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1494 2 %2.0% of reflections
Rwork0.16 ---
all0.16 74636 --
obs0.16 73139 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.587 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.8 Å2
2--0.27 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4335 0 91 527 4953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224577
X-RAY DIFFRACTIONr_bond_other_d0.0020.022996
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.976252
X-RAY DIFFRACTIONr_angle_other_deg1.09137390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81825.351185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67515751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.403157
X-RAY DIFFRACTIONr_chiral_restr0.0930.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214986
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02886
X-RAY DIFFRACTIONr_mcbond_it1.75162784
X-RAY DIFFRACTIONr_mcbond_other0.94761117
X-RAY DIFFRACTIONr_mcangle_it2.41354549
X-RAY DIFFRACTIONr_scbond_it2.60871793
X-RAY DIFFRACTIONr_scangle_it3.4261697
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 108 -
Rwork0.25 5297 -
obs-21215 98.5 %
Refinement TLS params.Method: refined / Origin x: -15.9383 Å / Origin y: 0.7706 Å / Origin z: -19.1258 Å
111213212223313233
T0.0576 Å20.0576 Å2-0.0014 Å2-0.0859 Å20.0367 Å2--0.0928 Å2
L0.9434 °20.5095 °2-0.4618 °2-1.3449 °2-0.6885 °2--1.3157 °2
S-0.0244 Å °-0.107 Å °-0.0795 Å °-0.0496 Å °-0.1394 Å °-0.2539 Å °0.1218 Å °0.2181 Å °0.1638 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A182 - 549
2X-RAY DIFFRACTION1B181 - 511
3X-RAY DIFFRACTION1C183 - 562

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