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- PDB-1p6a: STRUCTURAL BASIS FOR VARIATION IN ADENOVIRUS AFFINITY FOR THE CEL... -

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Basic information

Entry
Database: PDB / ID: 1p6a
TitleSTRUCTURAL BASIS FOR VARIATION IN ADENOVIRUS AFFINITY FOR THE CELLULAR RECEPTOR CAR (S489Y MUTANT)
Components
  • Coxsackievirus and adenovirus receptor
  • Fiber protein
KeywordsViral protein/receptor / VIRUS / VIRAL PROTEIN / Viral protein-receptor COMPLEX
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 / adherens junction / PDZ domain binding / filopodium / 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 / virus receptor activity / growth cone / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / cell adhesion / neuron projection / membrane raft / signaling receptor binding / symbiont entry into host cell / host cell nucleus / protein-containing complex / extracellular space / extracellular region / nucleoplasm / 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
Fiber protein / Coxsackievirus and adenovirus receptor
Similarity search - Component
Biological speciesHuman adenovirus A serotype 12
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsHowitt, J. / Bewley, M.C. / Graziano, V. / Flanagan, J.M. / Freimuth, P.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structural basis for variation in adenovirus affinity for the cellular coxsackievirus and adenovirus receptor.
Authors: Howitt, J. / Bewley, M.C. / Graziano, V. / Flanagan, J.M. / Freimuth, P.
#1: Journal: Science / Year: 1999
Title: Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR
Authors: Bewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M.
#2: Journal: J.Virol. / Year: 1999
Title: Coxsackievirus and adenovirus receptor amino-terminal immunoglobulin V-related domain binds adenovirus type 2 and fiber knob from adenovirus type 12
Authors: Freimuth, P. / Springer, K. / Berard, C. / Hainfeld, J. / Bewley, M.C. / Flanagan, J.M.
History
DepositionApr 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Aug 22, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _entity.src_method ..._entity.pdbx_fragment / _entity.src_method / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.5Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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 protein
B: Coxsackievirus and adenovirus receptor


Theoretical massNumber of molelcules
Total (without water)33,6612
Polymers33,6612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.926, 168.926, 168.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Fiber protein / SPIKE / Protein IV


Mass: 20020.572 Da / Num. of mol.: 1 / Fragment: knob domain (UNP residues 403-587) / Mutation: Y489S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus A serotype 12 / Genus: Mastadenovirus / Species: Human adenovirus A / Gene: L5 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36711
#2: Protein Coxsackievirus and adenovirus receptor / hCAR / CVB3-binding protein / Coxsackievirus B-adenovirus receptor / HCVADR


Mass: 13640.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXADR, CAR / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78310
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.97 Å3/Da / Density % sol: 79.39 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber /
RfactorSelection details
Rfree0.252 RANDOM
Rwork0.218 -
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 0 0 2366

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