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- PDB-4n7u: Crystal Structure of Intracellular B30.2 Domain of BTN3A1 in Comp... -

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Basic information

Entry
Database: PDB / ID: 4n7u
TitleCrystal Structure of Intracellular B30.2 Domain of BTN3A1 in Complex with CHDMAPP
ComponentsButyrophilin subfamily 3 member A1
KeywordsSIGNALING PROTEIN / Butyrophilin / CD277 / Phosphoantigen / B30.2 / PRY/SPRY
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 / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain ...Butyrophilin subfamily 3, PRY/SPRY domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin subtype / Immunoglobulin / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-2JA / Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4598 Å
AuthorsSandstrom, A. / Adams, E.J.
CitationJournal: Immunity / Year: 2014
Title: The Intracellular B30.2 Domain of Butyrophilin 3A1 Binds Phosphoantigens to Mediate Activation of Human V gamma 9V delta 2 T Cells.
Authors: Sandstrom, A. / Peigne, C.M. / Leger, A. / Crooks, J.E. / Konczak, F. / Gesnel, M.C. / Breathnach, R. / Bonneville, M. / Scotet, E. / Adams, E.J.
History
DepositionOct 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1873
Polymers21,8351
Non-polymers3522
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Butyrophilin subfamily 3 member A1
hetero molecules

A: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3746
Polymers43,6702
Non-polymers7044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_567x,-y+1,-z+21
Buried area1110 Å2
ΔGint-12 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.980, 44.952, 125.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-720-

HOH

21A-748-

HOH

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Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 21834.861 Da / Num. of mol.: 1 / Fragment: UNP Residues 328-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTF5, BTN3A1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O00481
#2: Chemical ChemComp-2JA / [(E)-4-methyl-5-oxidanyl-pent-3-enyl]-phosphonooxy-phosphinic acid


Mass: 260.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O7P2 / Details: Innate Pharma
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M MgCl2, 22%PEG3350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.4598→42.31 Å / Num. all: 37813 / Num. obs: 37549 / % possible obs: 96.3 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.4598-1.54188.7
4.62-42.31182.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N7I

4n7i


Resolution: 1.4598→37.22 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8823 / SU ML: 0.13 / σ(F): 1.34 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 1847 4.92 %R-free Flags imported from PDB ENTRY 4N7I
Rwork0.1533 ---
obs0.1552 37505 95.75 %-
all-37813 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.84 Å2 / Biso mean: 20.1575 Å2 / Biso min: 6.68 Å2
Refinement stepCycle: LAST / Resolution: 1.4598→37.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 0 21 211 1741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041588
X-RAY DIFFRACTIONf_angle_d0.9382161
X-RAY DIFFRACTIONf_chiral_restr0.062228
X-RAY DIFFRACTIONf_plane_restr0.004276
X-RAY DIFFRACTIONf_dihedral_angle_d13.276590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4598-1.49930.28541110.23762338244982
1.4993-1.54340.2541350.21612649278495
1.5434-1.59320.23891160.16792758287498
1.5932-1.65020.21351400.15642776291698
1.6502-1.71620.20691390.15162764290398
1.7162-1.79430.20631430.1492777292098
1.7943-1.88890.18931560.13672745290198
1.8889-2.00730.16641550.12672799295498
2.0073-2.16220.15661490.12752820296998
2.1622-2.37980.18841540.14372839299399
2.3798-2.72410.19751590.15692826298599
2.7241-3.43170.17871530.15332836298997
3.4317-37.23160.18631370.16392731286888

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