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- PDB-3mj7: Crystal structure of the complex of JAML and Coxsackie and Adenov... -

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Basic information

Entry
Database: PDB / ID: 3mj7
TitleCrystal structure of the complex of JAML and Coxsackie and Adenovirus receptor, CAR
Components
  • Coxsackievirus and adenovirus receptor homolog
  • Junctional adhesion molecule-like
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN TANDEM DOMAIN / IMMUNE RECEPTOR COMPLEX / CELL ADHESION / CELL JUNCTION / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / MEMBRANE / TRANSMEMBRANE / COSTIMULATION / PHOSPHOPROTEIN / RECEPTOR / SECRETED / TIGHT JUNCTION
Function / homology
Function and homology information


monocyte extravasation / 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 / Cell surface interactions at the vascular wall / epithelial structure maintenance / negative regulation of cardiac muscle cell proliferation / regulation of AV node cell action potential / positive regulation of epithelial cell proliferation involved in wound healing ...monocyte extravasation / 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 / Cell surface interactions at the vascular wall / epithelial structure maintenance / negative regulation of cardiac muscle cell proliferation / regulation of AV node cell action potential / positive regulation of epithelial cell proliferation involved in wound healing / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / connexin binding / cell-cell junction organization / cardiac muscle cell development / heterophilic cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / intercalated disc / regulation of synaptic vesicle endocytosis / bicellular tight junction / cardiac muscle cell proliferation / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / mitochondrion organization / filopodium / adherens junction / PDZ domain binding / cell-cell adhesion / beta-catenin binding / GABA-ergic synapse / cell-cell junction / heart development / presynaptic membrane / cell body / growth cone / actin cytoskeleton organization / basolateral plasma membrane / neuron projection / membrane raft / glutamatergic synapse / protein homodimerization activity / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / Myelin P0 protein-related / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...: / Myelin P0 protein-related / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coxsackievirus and adenovirus receptor homolog / Junctional adhesion molecule-like
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVerdino, P. / Wilson, I.A.
Citation
Journal: Science / Year: 2010
Title: The molecular interaction of CAR and JAML recruits the central cell signal transducer PI3K.
Authors: Verdino, P. / Witherden, D.A. / Havran, W.L. / Wilson, I.A.
#1: Journal: Science / Year: 2010
Title: The junctional adhesion molecule JAML is a costimulatory receptor for epithelial gammadelta T cell activation.
Authors: Witherden, D.A. / Verdino, P. / Rieder, S.E. / Garijo, O. / Mills, R.E. / Teyton, L. / Fischer, W.H. / Wilson, I.A. / Havran, W.L.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Junctional adhesion molecule-like
B: Coxsackievirus and adenovirus receptor homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2345
Polymers55,6942
Non-polymers1,5403
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint17 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.865, 89.865, 127.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein Junctional adhesion molecule-like / Dendritic cell-specific protein CREA7 / mCrea7


Mass: 30647.387 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (UNP RESIDUES 21-280) / Mutation: K124R, R211Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Amica1, Gm638, Jaml / Plasmid: PMT/BIP/V5-HIS A / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q80UL9
#2: Protein Coxsackievirus and adenovirus receptor homolog / CAR / mCAR


Mass: 25046.229 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (UNP RESIDUES 18-236)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Car, Cxadr / Plasmid: PBAC6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97792
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.25 M LI-SULFATE, 0.1 M MES, 24% PEG 3350, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2007
Details: SI(111) DOUBLE CRYSTAL MONOCHROMETER. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 14679 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 12.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.529 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.4.0069refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→38.92 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 40.735 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R: 2.932 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 729 5 %RANDOM
Rwork0.227 ---
obs0.229 13927 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.44 Å20 Å2
2--0.89 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 102 0 3440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223513
X-RAY DIFFRACTIONr_bond_other_d0.0020.022421
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9974758
X-RAY DIFFRACTIONr_angle_other_deg13.0035877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7124.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.20915626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9461522
X-RAY DIFFRACTIONr_chiral_restr0.060.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9832078
X-RAY DIFFRACTIONr_mcbond_other0.1493844
X-RAY DIFFRACTIONr_mcangle_it1.97653384
X-RAY DIFFRACTIONr_scbond_it3.47181435
X-RAY DIFFRACTIONr_scangle_it5.724111374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 54 -
Rwork0.339 1000 -
obs--99.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.45640.9923-2.29034.8715-0.65546.12210.0547-0.34240.2055-0.0650.17630.2132-0.3231-0.7405-0.231-0.3588-0.1023-0.056-0.14630.0585-0.337615.4786-23.3421-3.5617
26.67562.4503-2.6633.3248-1.27695.66040.4787-0.60630.45320.3139-0.3405-0.1205-1.04130.4492-0.13820.1437-0.2865-0.1061-0.2791-0.0062-0.248636.949-5.055-10.6205
34.27350.96091.38232.4418-0.5284.0191-0.0286-0.4694-0.0179-0.22130.36410.52130.2309-1.2365-0.3355-0.4082-0.2309-0.03510.53480.2841-0.0574-2.0593-37.80492.9744
47.95541.69624.89851.6137-1.912511.13190.0291-0.2623-0.0977-0.3065-0.79840.3141-0.4603-0.27480.76930.10380.1346-0.07750.2935-0.12520.4264-29.4149-52.2047-24.7645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 121
2X-RAY DIFFRACTION1A401 - 501
3X-RAY DIFFRACTION2A122 - 239
4X-RAY DIFFRACTION3B3 - 120
5X-RAY DIFFRACTION3B301 - 302
6X-RAY DIFFRACTION4B121 - 210

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