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- PDB-1eaj: DIMERIC STRUCTURE OF THE COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR ... -

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Basic information

Entry
Database: PDB / ID: 1eaj
TitleDIMERIC STRUCTURE OF THE COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR D1 DOMAIN AT 1.35 ANGSTROM RESOLUTION
ComponentsCOXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
KeywordsVIRUS/VIRAL PROTEIN RECEPTOR / IMMUNOGLOBULIN V DOMAIN FOLD / SYMMETRIC DIMER / VIRUS-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 / transepithelial transport ...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 / transepithelial transport / cell-cell junction organization / connexin binding / cardiac muscle cell development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / intercalated disc / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / PDZ domain binding / Cell surface interactions at the vascular wall / filopodium / adherens junction / mitochondrion organization / neuromuscular junction / beta-catenin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell junction / cell-cell junction / heart development / virus receptor activity / cell body / actin cytoskeleton organization / growth cone / basolateral plasma membrane / defense response to virus / neuron projection / membrane raft / signaling receptor binding / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / 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 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
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
Authorsvan Raaij, M.J. / Cusack, S.
CitationJournal: Structure / Year: 2000
Title: Dimeric structure of the coxsackievirus and adenovirus receptor D1 domain at 1.7 A resolution.
Authors: van Raaij, M.J. / Chouin, E. / van der Zandt, H. / Bergelson, J.M. / Cusack, S.
History
DepositionJul 12, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation.title / _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
B: COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2904
Polymers28,0982
Non-polymers1922
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.538, 68.538, 146.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.70567, -0.70834, 0.01682), (-0.70846, -0.70575, 0.00179), (0.01061, -0.01318, -0.99986)
Vector: 23.60664, 58.16456, 102.27028)
DetailsANALYTICAL ULTRACENTIFUGATION EXPERIMENTS PROVETHE EXISTENCE OF A DIMER ALSO IN SOLUTION, WITH ADISSOCIATION CONSTANT IN THE MICROMOLAR RANGE.SEE JRNL REFERENCE

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Components

#1: Protein COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR / COXSACKIEVIRUS B-ADENOVIRUS RECEPTOR / HCAR / CVB3 BINDING PROTEIN


Mass: 14048.972 Da / Num. of mol.: 2 / Fragment: D1 DOMAIN RESIDUES 15-140
Source method: isolated from a genetically manipulated source
Details: DISULFIDE BOND BETWEEN A41 AND A120 AND BETWEEN B41 AND B120
Source: (gene. exp.) HOMO SAPIENS (human) / Description: HELA CELL CDNA LIBRARY / Plasmid: PAB3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1BLUE / References: UniProt: P78310
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRECEPTOR FOR GROUP B COXSACKIEVIRUSES AND SUBGROUP C OF ADENOVIRUSES (AD2 AND AD5).
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: 3.1 Å3/Da / Density % sol: 59.5 %
Crystal growpH: 5.6
Details: AMMONIUM SULPHATE, SODIUM CITRATE, GLYCEROL, pH 5.60
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC 2X2 / Detector: CCD / Date: Jun 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.35→20 Å / Num. obs: 73582 / % possible obs: 95.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 5.9
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.1 / % possible all: 68.7

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KAC, CHAIN B

1kac


Resolution: 1.35→19 Å / SU B: 1.73 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R Free: 0.036
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REFLECTIONS FOR RFREE WERE SELECTED IN THIN SHELLS OF RESOLUTIO, INDEPENDENTLY FROM REFLECTIONS SELECTED FOR RFREE USED IN THE 1.7 ANGSTROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REFLECTIONS FOR RFREE WERE SELECTED IN THIN SHELLS OF RESOLUTIO, INDEPENDENTLY FROM REFLECTIONS SELECTED FOR RFREE USED IN THE 1.7 ANGSTROM STRUCTURE. TO ELIMINATE POSSIBLE BIAS FROM THE 1.7 ANGSTROM STRUCTURE, STRUCTURE SOLUTION WAS COMPLETELY REDONE, PLACING TWO COPIES OF CHAIN B FROM PDB-ENTRY 1KAC WITH THE PROGRAM AMORE
RfactorNum. reflection% reflectionSelection details
Rfree0.14828 2047 2.8 %THIN SHELLS OF RESOLUTION
Rwork0.13674 ---
obs0.13708 71453 100 %-
Refinement stepCycle: LAST / Resolution: 1.35→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 10 332 2249

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