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- PDB-1f5w: DIMERIC STRUCTURE OF THE COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR ... -

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Basic information

Entry
Database: PDB / ID: 1f5w
TitleDIMERIC STRUCTURE OF THE COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR D1 DOMAIN
ComponentsCOXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
KeywordsViral protein receptor / immunoglobulin V domain fold / symmetric dimer
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 / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / gamma-delta T cell activation / regulation of AV node cell action potential / germ cell migration / apicolateral plasma membrane / cell-cell junction organization ...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 / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / gamma-delta T cell activation / regulation of AV node cell action potential / germ cell migration / apicolateral plasma membrane / cell-cell junction organization / transepithelial transport / connexin binding / cardiac muscle cell development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / bicellular tight junction / intercalated disc / cell adhesion molecule binding / mitochondrion organization / neutrophil chemotaxis / acrosomal vesicle / filopodium / PDZ domain binding / Cell surface interactions at the vascular wall / adherens junction / neuromuscular junction / beta-catenin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / integrin binding / virus receptor activity / cell junction / cell body / heart development / growth cone / actin cytoskeleton organization / 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-like 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 / Immunoglobulins / Immunoglobulin-like fold / 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: 1.7 Å
Authorsvan Raaij, M.J. / Chouin, E. / van der Zandt, H. / Bergelson, J.M. / Cusack, S.
CitationJournal: Structure Fold.Des. / 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
DepositionJun 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)28,3865
Polymers28,0982
Non-polymers2883
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-35 kcal/mol
Surface area11940 Å2
MethodPISA
2
B: COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
hetero molecules

A: COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3865
Polymers28,0982
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y+1/2,-z+3/41
Buried area1370 Å2
ΔGint-39 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.337, 68.337, 146.356
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is the dimer formed by chains A and B

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Components

#1: Protein COXSACKIE VIRUS AND ADENOVIRUS RECEPTOR


Mass: 14048.972 Da / Num. of mol.: 2 / Fragment: D1 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HELA CELL CDNA LIBRARY / Plasmid: PAB3 / Production host: Escherichia coli (E. coli) / References: UniProt: P78310
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.04 Å3/Da / Density % sol: 59.3 %
Description: THE SIGMA(I) IN SCALA APPEARS TO BE OVERESTIMATED FOR OUR DATASET, GIVING LOW I/SIGMA(I) VALUES. THE Mn(I)/sd OVERALL AND FOR THE HIGH RESOLUTION SHELL ARE 10.8 AND 3.2, RESPECTIVELY TWO ...Description: THE SIGMA(I) IN SCALA APPEARS TO BE OVERESTIMATED FOR OUR DATASET, GIVING LOW I/SIGMA(I) VALUES. THE Mn(I)/sd OVERALL AND FOR THE HIGH RESOLUTION SHELL ARE 10.8 AND 3.2, RESPECTIVELY TWO MOLECULES COULD BE PLACED IN ASYMMETRIC UNIT BY MOLECULAR REPLACEMENT
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: ammonium sulphate, sodium citrate, glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium acetate1reservoir
225 %(v/v)glycerol1reservoir
345-60 %(v/v)satammonium sulfate1reservoir
412 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC / Detector: CCD / Date: Feb 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 36389 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.079 / Net I/σ(I): 2.4
Reflection shellResolution: 1.7→1.84 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 0.4 / Rsym value: 0.375 / % possible all: 70.2
Reflection
*PLUS
Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 70.2 % / Num. unique obs: 3806 / Rmerge(I) obs: 0.302

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kac, chain B

1kac


Resolution: 1.7→20 Å / SU B: 1.45946 / SU ML: 0.04749 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.10264 / ESU R Free: 0.08305 / Stereochemistry target values: Engh & Huber
Details: PEPTIDE PLANAR RMS 0.0243 ANGSTROM; AROMATIC PLANAR RMS 0.0134 ANGSTROM
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1564 4.3 %Thin shells of resolution
Rwork0.158 ---
all0.16 ---
obs0.16 34825 90.1 %-
Displacement parametersBiso mean: 22.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 15 232 2168
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.025
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_multtor_nbd0.2380.3
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_planar_d0.0340.06
X-RAY DIFFRACTIONp_mcbond_it3.2254
X-RAY DIFFRACTIONp_mcangle_it3.9625
X-RAY DIFFRACTIONp_scbond_it5.4736
X-RAY DIFFRACTIONp_scangle_it7.0868
X-RAY DIFFRACTIONp_chiral_restr0.1250.15
X-RAY DIFFRACTIONp_transverse_tor15.520
X-RAY DIFFRACTIONp_planar_tor4.45
X-RAY DIFFRACTIONp_staggered_tor13.215
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / σ(F): 0 / % reflection Rfree: 4.3 % / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_mcbond_it4
X-RAY DIFFRACTIONp_scbond_it6
X-RAY DIFFRACTIONp_mcangle_it5
X-RAY DIFFRACTIONp_scangle_it8
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.84 Å / Rfactor Rfree: 0.23 / Num. reflection Rfree: 222 / Num. reflection obs: 5948 / Rfactor obs: 0.15

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