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- PDB-4v1p: BTN3 Structure -

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Basic information

Entry
Database: PDB / ID: 4v1p
TitleBTN3 Structure
ComponentsBUTYROPHILIN SUBFAMILY 3 MEMBER A1
KeywordsIMMUNE SYSTEM / IMMUNE SIGNALLING
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / activated T cell proliferation / regulation of cytokine production / positive regulation of cytokine production / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / signaling receptor binding / plasma membrane
Similarity search - Function
Butyrophilin subfamily 3, PRY/SPRY domain / : / SPRY domain / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain ...Butyrophilin subfamily 3, PRY/SPRY domain / : / SPRY domain / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.04 Å
AuthorsJames, L.C.
CitationJournal: J.Immunol. / Year: 2015
Title: Activation of Human Gammadelta T Cells by Cytosolic Interactions of Btn3A1 with Soluble Phosphoantigens and the Cytoskeletal Adaptor Periplakin.
Authors: Rhodes, D.A. / Chen, H. / Price, A.J. / Keeble, A.H. / Davey, M.S. / James, L.C. / Eberl, M. / Trowsdale, J.
History
DepositionSep 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BUTYROPHILIN SUBFAMILY 3 MEMBER A1


Theoretical massNumber of molelcules
Total (without water)21,7001
Polymers21,7001
Non-polymers00
Water2,144119
1
A: BUTYROPHILIN SUBFAMILY 3 MEMBER A1

A: BUTYROPHILIN SUBFAMILY 3 MEMBER A1


Theoretical massNumber of molelcules
Total (without water)43,3992
Polymers43,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1280 Å2
ΔGint-11.2 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.620, 124.664, 38.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BUTYROPHILIN SUBFAMILY 3 MEMBER A1 / BUTYROPHILIN


Mass: 21699.689 Da / Num. of mol.: 1 / Fragment: RESIDUES 325-512 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: O00481
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.56 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→31 Å / Num. obs: 14316 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.08

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.04→31.19 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.77 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22205 702 5 %RANDOM
Rwork0.16507 ---
obs0.1678 13333 97.92 %-
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 mean: 31.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--1.1 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.04→31.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 0 119 1650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191578
X-RAY DIFFRACTIONr_bond_other_d0.0010.021472
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9472146
X-RAY DIFFRACTIONr_angle_other_deg0.87333401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5815187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17423.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7815262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.191510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
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_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0663.686751
X-RAY DIFFRACTIONr_mcbond_other5.0653.685750
X-RAY DIFFRACTIONr_mcangle_it5.5096.182937
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.9544.323827
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.045→2.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 64 -
Rwork0.186 872 -
obs--92.22 %

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