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- PDB-2j12: Ad37 fibre head in complex with CAR D1 -

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Basic information

Entry
Database: PDB / ID: 2j12
TitleAd37 fibre head in complex with CAR D1
Components
  • COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
  • FIBER PROTEIN
KeywordsVIRAL PROTEIN/RECEPTOR / VIRAL PROTEIN-RECEPTOR COMPLEX / CAR / AD37 / HAD37 / COMPLEX / MEMBRANE / RECEPTOR / COXSACKIEVIRUS / PHOSPHORYLATION / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / CELL ADHESION / TRANSMEMBRANE / TIGHT JUNCTION / PALMITATE / ADENOVIRUS / LIPOPROTEIN / GLYCOPROTEIN
Function / homology
Function and homology information


AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / connexin binding ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / connexin binding / transepithelial transport / cell-cell junction organization / adhesion receptor-mediated virion attachment to host cell / cardiac muscle cell development / heterophilic cell-cell adhesion / intercalated disc / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / Cell surface interactions at the vascular wall / mitochondrion organization / filopodium / adherens junction / PDZ domain binding / neuromuscular junction / beta-catenin binding / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / cell junction / viral capsid / heart development / cell body / growth cone / virus receptor activity / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / cell adhesion / neuron projection / membrane raft / signaling receptor binding / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / protein-containing complex / extracellular space / extracellular region / nucleoplasm / metal ion binding / identical protein binding / plasma membrane / cytoplasm
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 ...: / 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 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coxsackievirus and adenovirus receptor / Fiber / Fiber protein
Similarity search - Component
Biological speciesHuman adenovirus D37
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeiradake, E. / Lortat-Jacob, H. / Billet, O. / Kremer, E.J. / Cusack, S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and Mutational Analysis of Human Ad37 and Canine Adenovirus 2 Fiber Heads in Complex with the D1 Domain of Coxsackie and Adenovirus Receptor.
Authors: Seiradake, E. / Lortat-Jacob, H. / Billet, O. / Kremer, E.J. / Cusack, S.
History
DepositionAug 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 11, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / entity_src_gen / pdbx_database_related / reflns_shell
Item: _atom_site.occupancy / _audit_author.name ..._atom_site.occupancy / _audit_author.name / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_database_related.details / _reflns_shell.percent_possible_all
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBER PROTEIN
B: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0083
Polymers35,9682
Non-polymers401
Water5,170287
1
A: FIBER PROTEIN
B: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
hetero molecules

A: FIBER PROTEIN
B: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
hetero molecules

A: FIBER PROTEIN
B: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0249
Polymers107,9036
Non-polymers1203
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
MethodPQS
Unit cell
Length a, b, c (Å)131.780, 131.780, 131.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-2082-

HOH

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Components

#1: Protein FIBER PROTEIN / ADENOVIRUS 37 FIBRE HEAD


Mass: 21716.535 Da / Num. of mol.: 1 / Fragment: FIBRE HEAD, RESIDUES 177-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D37 / Strain: TYPE 37 / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q64823, UniProt: Q80S15*PLUS
#2: Protein COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR / COXSACKIEVIRUS B-ADENOVIRUS RECEPTOR / HCAR / CVB3-BINDING PROTEIN / HCVADR / COXSACKIEVIRUS AND ...COXSACKIEVIRUS B-ADENOVIRUS RECEPTOR / HCAR / CVB3-BINDING PROTEIN / HCVADR / COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR DOMAIN D1


Mass: 14251.245 Da / Num. of mol.: 1 / Fragment: DOMAIN D1, RESIDUES 15-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PAB3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: P78310
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 53 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 59884 / % possible obs: 99 % / Redundancy: 7 % / Rmerge(I) obs: 0.07
Reflection shellRmerge(I) obs: 0.4 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1UXA, 1KAC

1uxa

1kac


Resolution: 1.5→93.25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.737 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.169 3029 5.1 %RANDOM
Rwork0.148 ---
obs0.149 56854 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→93.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 1 287 2663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222543
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9643483
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01125.943106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04315464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.988154
X-RAY DIFFRACTIONr_chiral_restr0.0890.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021898
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3270.21131
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21771
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9931.51623
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.522580
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.38131068
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3774.5883
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.212 198
Rwork0.162 3675

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