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- PDB-4xqa: CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SI... -

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Basic information

Entry
Database: PDB / ID: 4xqa
TitleCRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SIALIC ACID INHIBITOR ME0462
ComponentsFiber
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-423 / ACETATE ION / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 37
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4072 Å
AuthorsStehle, T. / Liaci, A.M.
Funding support Germany, Sweden, 6items
OrganizationGrant numberCountry
German Research FoundationSFB 685 Germany
Swedish Research Council521-2010-3078 Sweden
Swedish Research Council621-2010-4746 Sweden
Knut and Alice Wallenberg Foundation2009.0009 Sweden
Stiftelsen foer Strategisk ForskningF06-0011 Sweden
Torsten Soederbergs StiftelseM4/11 Sweden
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
DepositionJan 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jul 6, 2016Group: Refinement description
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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.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_symmetry / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 2.2Jan 10, 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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)66,84811
Polymers65,1503
Non-polymers1,6998
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-92 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.230, 75.620, 131.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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
Details: FRAGMENT: FIBER KNOB / Source: (gene. exp.) Human adenovirus 37 / Gene: L5 / Plasmid: PPROEX HTB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q64823
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-423 / (1-{2-[bis(2-{4-[({(6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranonosyl}oxy)methyl]-1H-1,2,3-triazol-1-yl}ethyl)amino]ethyl}-1H-1,2,3-triazol-4-yl)methyl (6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranosidonic acid


Mass: 1266.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H75N13O27
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 26% PEG 8000, 0.1M HEPES, 0.05M zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2014
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: 1.4072→50 Å / Num. obs: 131319 / % possible obs: 99.6 % / Redundancy: 12.75 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.5
Reflection shellResolution: 1.4072→1.49 Å / Redundancy: 12.63 % / Rmerge(I) obs: 1.545 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.844 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.8.1069refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uxe

1uxe


Resolution: 1.4072→47.272 Å / FOM work R set: 0.8955 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1723 6567 5.26 %
Rwork0.1435 124753 -
obs0.1449 131319 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.43 Å2 / Biso mean: 33.16 Å2 / Biso min: 18.21 Å2
Refinement stepCycle: final / Resolution: 1.4072→47.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4329 0 107 540 4976
Biso mean--35.58 44.81 -
Num. residues----551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134578
X-RAY DIFFRACTIONf_angle_d1.4946246
X-RAY DIFFRACTIONf_chiral_restr0.109721
X-RAY DIFFRACTIONf_plane_restr0.008781
X-RAY DIFFRACTIONf_dihedral_angle_d12.0761675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4072-1.42310.32662030.2753865406893
1.4231-1.43990.27162150.22994084429999
1.4399-1.45750.2412190.195741544373100
1.4575-1.47590.24932140.188540804294100
1.4759-1.49530.25542170.177341314348100
1.4953-1.51580.22072170.159341274344100
1.5158-1.53750.182160.14754099431599
1.5375-1.56040.19532170.14241184335100
1.5604-1.58480.1952160.13794102431899
1.5848-1.61080.16852190.123341614380100
1.6108-1.63860.1422160.117240954311100
1.6386-1.66840.16562180.110441514369100
1.6684-1.70040.1662190.108341474366100
1.7004-1.73520.17262170.110441394356100
1.7352-1.77290.15722180.112741304348100
1.7729-1.81410.16532190.109441664385100
1.8141-1.85950.16912170.109841334350100
1.8595-1.90980.16132190.113641564375100
1.9098-1.9660.15682190.113341624381100
1.966-2.02940.16212200.117341674387100
2.0294-2.1020.16472200.116941854405100
2.102-2.18610.15562190.120141614380100
2.1861-2.28560.15582200.126141854405100
2.2856-2.40610.17152210.136441964417100
2.4061-2.55690.17132210.143542044425100
2.5569-2.75430.19422220.149942094431100
2.7543-3.03140.18562220.15242294451100
3.0314-3.46990.16222240.152442534477100
3.4699-4.37120.17162260.145442904516100
4.3712-47.29850.16812360.172544744710100

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