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- PDB-3jz7: Crystal structure of the extracellular domains of coxsackie & ade... -

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Basic information

Entry
Database: PDB / ID: 3jz7
TitleCrystal structure of the extracellular domains of coxsackie & adenovirus receptor from mouse (mCAR)
ComponentsCoxsackievirus and adenovirus receptor homolog
KeywordsCELL ADHESION / cell adhesion molecule / immunoglobuline superfamily / adenovirus / coxsackievirus / Alternative splicing / Cell junction / Cell membrane / Disulfide bond / Glycoprotein / Immunoglobulin domain / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Receptor / Secreted / Tight junction / Transmembrane
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 / Cell surface interactions at the vascular wall / negative regulation of cardiac muscle cell proliferation / gamma-delta T cell activation / regulation of AV node cell action potential / positive regulation of epithelial cell proliferation involved in wound healing ...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 / Cell surface interactions at the vascular wall / negative regulation of cardiac muscle cell proliferation / gamma-delta T cell activation / regulation of AV node cell action potential / positive regulation of epithelial cell proliferation involved in wound healing / germ cell migration / apicolateral plasma membrane / cell-cell junction organization / transepithelial transport / connexin binding / cardiac muscle cell development / cardiac muscle cell proliferation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / bicellular tight junction / intercalated disc / cell adhesion molecule binding / mitochondrion organization / neutrophil chemotaxis / acrosomal vesicle / filopodium / PDZ domain binding / adherens junction / neuromuscular junction / cell-cell adhesion / beta-catenin binding / cell-cell junction / integrin binding / 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 / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin 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 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
ISOPROPYL ALCOHOL / Coxsackievirus and adenovirus receptor homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å
AuthorsMax, K.E.A. / Heinemann, U.
CitationJournal: J.Neurosci. / Year: 2010
Title: The coxsackievirus-adenovirus receptor reveals complex homophilic and heterophilic interactions on neural cells.
Authors: Patzke, C. / Max, K.E. / Behlke, J. / Schreiber, J. / Schmidt, H. / Dorner, A.A. / Kroger, S. / Henning, M. / Otto, A. / Heinemann, U. / Rathjen, F.G.
History
DepositionSep 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Sep 6, 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: Coxsackievirus and adenovirus receptor homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8513
Polymers23,7311
Non-polymers1202
Water2,288127
1
A: Coxsackievirus and adenovirus receptor homolog
hetero molecules

A: Coxsackievirus and adenovirus receptor homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7026
Polymers47,4622
Non-polymers2404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)53.369, 61.468, 86.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Coxsackievirus and adenovirus receptor homolog / mCAR / CAR


Mass: 23730.842 Da / Num. of mol.: 1 / Fragment: D1 & D2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Car, Cxadr / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P97792
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein buffer: 20mM TRIS 50mM NaCl protein concentration: 8mg / ml; crystallization buffer 0.1M HEPES pH 7.5 21% PEG 4000 15% isopropanol; crystalliztion setup: mixture 400nl protein sample ...Details: protein buffer: 20mM TRIS 50mM NaCl protein concentration: 8mg / ml; crystallization buffer 0.1M HEPES pH 7.5 21% PEG 4000 15% isopropanol; crystalliztion setup: mixture 400nl protein sample : 400nl crystallization buffer reservoir filled with 80 ul crystallization buffer; cryo solution: 25% PEG 4000 20% isopropanol 10% glycerol 0.1M HEPES pH 7.5 freezing of crystals: crystallization setup was overlayed with cryosolution, floating crystals were removed with a cryoloop and flash-frozen in liquid nitrogen., VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 16, 2008
Details: Mirror 1: Silicon, active surface 50nm Rh-coated. Double crystal monochromator: Si-111 crystal. Mirror 2: Glas, active surface 50nm Rh-coated
RadiationMonochromator: Mirrors & silicon-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 15245 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 47.774 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.003 / Net I/σ(I): 13.63
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.37 / Num. unique all: 1481 / Χ2: 0.999 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_FTF
Highest resolutionLowest resolution
Translation2.5 Å9.98 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EAJ (complete) for domain D1 2V5R (residues 5-40, 44-62, 68-76, 81-90) for domain D2

1eaj

2v5r


Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.783 / SU B: 6.441 / SU ML: 0.163 / SU R Cruickshank DPI: 0.231 / SU Rfree: 0.208 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 754 5 %RANDOM
Rwork0.209 ---
obs0.212 15150 98.482 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 81.05 Å2 / Biso mean: 38.075 Å2 / Biso min: 30.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2--1.14 Å20 Å2
3----0.68 Å2
Refine analyzeLuzzati coordinate error obs: 0.144 Å
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 8 127 1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221694
X-RAY DIFFRACTIONr_bond_other_d0.0030.021162
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.982304
X-RAY DIFFRACTIONr_angle_other_deg0.8713.0042862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9095214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73426.16473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33515298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.723155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021865
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02297
X-RAY DIFFRACTIONr_nbd_refined0.2080.2301
X-RAY DIFFRACTIONr_nbd_other0.2010.21195
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2783
X-RAY DIFFRACTIONr_nbtor_other0.0920.2952
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.212
X-RAY DIFFRACTIONr_mcbond_it1.65921362
X-RAY DIFFRACTIONr_mcbond_other0.2632422
X-RAY DIFFRACTIONr_mcangle_it2.09831729
X-RAY DIFFRACTIONr_scbond_it3.5324.5744
X-RAY DIFFRACTIONr_scangle_it4.8016573
LS refinement shellResolution: 2.188→2.245 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 41 -
Rwork0.266 1047 -
all-1088 -
obs-1481 98.19 %

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