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- PDB-3mj6: Crystal structure of the gammadelta T cell costimulatory receptor... -

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Basic information

Entry
Database: PDB / ID: 3mj6
TitleCrystal structure of the gammadelta T cell costimulatory receptor Junctional Adhesion Molecule-Like Protein, JAML
ComponentsJunctional adhesion molecule-like
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN TANDEM DOMAIN / CELL ADHESION / CELL JUNCTION / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / MEMBRANE / COSTIMULATION / TRANSMEMBRANE
Function / homology
Function and homology information


monocyte extravasation / Cell surface interactions at the vascular wall / positive regulation of epithelial cell proliferation involved in wound healing / gamma-delta T cell activation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / bicellular tight junction / protein homodimerization activity / plasma membrane
Similarity search - Function
Myelin P0 protein-related / 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 ...Myelin P0 protein-related / 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
FORMIC ACID / Junctional adhesion molecule-like
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.19 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 / chem_comp ...atom_site / 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 / pdbx_struct_conn_angle / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Junctional adhesion molecule-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,84813
Polymers30,6471
Non-polymers1,20112
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.946, 61.946, 82.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 1 molecules A

#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

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 2
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

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Non-polymers , 3 types, 138 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: 3.25 M NA-FORMATE, 0.1 M IMIDAZOLE, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.07812, 0.99984
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2005 / Details: KOHZU: DOUBLE CRYSTAL SI(111)
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.078121
20.999841
ReflectionResolution: 2.19→50 Å / Num. obs: 15924 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 11.1
Reflection shellResolution: 2.19→2.24 Å / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2 / Rsym value: 0.415 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SHELXmodel building
RESOLVEmodel building
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: OBTAINED BY MAD PHASING OF A TA6BR12 SOAKED JAML CRYSTAL AND SUBSEQUENT MR INTO THE NATIVE HIGH RESOLUTION DATA

Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.735 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS WAS ALSO USED FOR THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 799 5 %RANDOM
Rwork0.17 ---
obs0.172 15098 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 77 129 2034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211967
X-RAY DIFFRACTIONr_bond_other_d0.010.021357
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.9882655
X-RAY DIFFRACTIONr_angle_other_deg1.2963.0023279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0075236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5523.93694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65715353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5731517
X-RAY DIFFRACTIONr_chiral_restr0.1270.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02384
X-RAY DIFFRACTIONr_nbd_refined0.2010.2270
X-RAY DIFFRACTIONr_nbd_other0.210.21380
X-RAY DIFFRACTIONr_nbtor_refined0.170.2889
X-RAY DIFFRACTIONr_nbtor_other0.0960.21165
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0310.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8621.51164
X-RAY DIFFRACTIONr_mcbond_other0.1831.5475
X-RAY DIFFRACTIONr_mcangle_it1.64221879
X-RAY DIFFRACTIONr_scbond_it2.6253825
X-RAY DIFFRACTIONr_scangle_it4.4144.5773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 57 -
Rwork0.21 1032 -
obs--94.2 %
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)
13.1244-0.4362-2.40361.88080.54677.1322-0.0622-0.03570.0615-0.04760.0377-0.0866-0.0644-0.02480.0245-0.2362-0.01210.0001-0.1808-0.021-0.147730.102814.2243-0.2836
23.97540.9059-1.88261.6649-0.46674.63040.07770.1514-0.18870.11770.10570.05180.1115-0.3087-0.1835-0.17310.0249-0.0374-0.1837-0.0139-0.17635.304512.88513.4525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 122
2X-RAY DIFFRACTION2A123 - 236

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