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- PDB-4n7i: Crystal Structure of Intracellular B30.2 Domain of BTN3A1 -

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Basic information

Entry
Database: PDB / ID: 4n7i
TitleCrystal Structure of Intracellular B30.2 Domain of BTN3A1
ComponentsButyrophilin subfamily 3 member A1
KeywordsSIGNALING PROTEIN / Butyrophilin / CD277 / B30.2 / PTY/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
BETA-MERCAPTOETHANOL / Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4015 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 15, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn_type.id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2357
Polymers21,8351
Non-polymers4006
Water3,657203
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)44,47014
Polymers43,6702
Non-polymers80012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area1100 Å2
ΔGint-11 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.032, 44.957, 124.813
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-737-

HOH

21A-754-

HOH

31A-769-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 209 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 50.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M MgCl2, 22%PEG3350, pH 7.2, vapour diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MAR scanner 225mm plate / Detector: CCD / Date: Aug 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.4→25 Å / Num. all: 42389 / Num. obs: 42349 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.74 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.4-1.42190.9
1.42-1.45191.6
1.45-1.48193.5
1.48-1.51193.6
1.51-1.54194.3
1.54-1.58195.6
1.58-1.62195.9
1.62-1.66196.5
1.66-1.71197.9
1.71-1.76197.8
1.76-1.83197.3
1.83-1.9198
1.9-1.99198.3
1.99-2.09198.4
2.09-2.22198.5
2.22-2.39198.1
2.39-2.63198.5
2.63-3.01197.8
3.01-3.8198.1
3.8-25193.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WL1

2wl1


Resolution: 1.4015→21.03 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.9149 / SU ML: 0.1 / σ(F): 1.34 / Phase error: 14.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1664 2107 4.98 %RANDOM
Rwork0.1351 ---
obs0.1367 42349 96.14 %-
all-42389 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.73 Å2 / Biso mean: 13.8232 Å2 / Biso min: 2.63 Å2
Refinement stepCycle: LAST / Resolution: 1.4015→21.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 22 203 1739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041642
X-RAY DIFFRACTIONf_angle_d0.9692246
X-RAY DIFFRACTIONf_chiral_restr0.067239
X-RAY DIFFRACTIONf_plane_restr0.004289
X-RAY DIFFRACTIONf_dihedral_angle_d13.363625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4015-1.43410.19931240.13172436256089
1.4341-1.46990.16511370.12352539267693
1.4699-1.50970.16791200.12722597271793
1.5097-1.55410.16031310.1152616274794
1.5541-1.60420.1631230.11272631275495
1.6042-1.66150.15231340.11262673280797
1.6615-1.7280.1531330.1182677281097
1.728-1.80660.17481410.12162724286598
1.8066-1.90180.15331610.11762687284898
1.9018-2.02090.15541530.11462732288598
2.0209-2.17680.15611370.12492755289298
2.1768-2.39560.18231540.13462743289798
2.3956-2.74160.18161560.14972781293798
2.7416-3.45160.18071550.14622808296398
3.4516-21.0320.15291480.1532843299195

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