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- PDB-5hm7: The Intracellular domain of Butyrophilin 3A1 protein -

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Basic information

Entry
Database: PDB / ID: 5hm7
TitleThe Intracellular domain of Butyrophilin 3A1 protein
ComponentsButyrophilin subfamily 3 member A1
KeywordsIMMUNE SYSTEM / Immunological protein / intracellular domain
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: 1.93 Å
AuthorsAdams, E.J. / Gu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIHR01-AI115471 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on V gamma 9V delta 2 T cell activation.
Authors: Gu, S. / Sachleben, J.R. / Boughter, C.T. / Nawrocka, W.I. / Borowska, M.T. / Tarrasch, J.T. / Skiniotis, G. / Roux, B. / Adams, E.J.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification
Revision 1.2Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Butyrophilin subfamily 3 member A1
B: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,88911
Polymers57,2512
Non-polymers6379
Water2,522140
1
A: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8985
Polymers28,6261
Non-polymers2734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9906
Polymers28,6261
Non-polymers3655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.430, 145.840, 44.910
Angle α, β, γ (deg.)90.00, 105.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A55 - 243
2010B55 - 243
Detailsmonomer based on MALS

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Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 28625.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1, BTF5 / Production host: Escherichia coli (E. coli) / References: UniProt: O00481
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.06 Å3/Da / Density % sol: 40.36 % / Description: Rod-shaped crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 22% PEG 3350, 0.2M Magnesium chloride, 0.1M HEPES 7.0
PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.93→72.92 Å / Num. obs: 34081 / % possible obs: 98.7 % / Redundancy: 17.1 % / Net I/σ(I): 5.63
Reflection shellResolution: 1.93→2.02 Å / Mean I/σ(I) obs: 1.52 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data scaling
iMOSFLMdata reduction
PHASERphasing
ARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7I

4n7i


Resolution: 1.93→72.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.306 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1661 4.9 %RANDOM
Rwork0.197 ---
obs0.198 32419 98.6 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.28 Å2
2---0.49 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.93→72.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 36 140 3418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193394
X-RAY DIFFRACTIONr_bond_other_d0.0050.023186
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9564599
X-RAY DIFFRACTIONr_angle_other_deg1.0833.0017357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87223.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19815565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.121523
X-RAY DIFFRACTIONr_chiral_restr0.0910.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213753
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02786
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_it4.4362.0371598
X-RAY DIFFRACTIONr_mcbond_other4.432.0361597
X-RAY DIFFRACTIONr_mcangle_it5.5353.0361998
X-RAY DIFFRACTIONr_mcangle_other5.5363.0371999
X-RAY DIFFRACTIONr_scbond_it7.6842.7361796
X-RAY DIFFRACTIONr_scbond_other7.6722.7361796
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.7843.7792601
X-RAY DIFFRACTIONr_long_range_B_refined10.99417.2773692
X-RAY DIFFRACTIONr_long_range_B_other10.98717.2753692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23302 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.93→1.98 Å
RfactorNum. reflection% reflection
Rfree0.356 124 -
Rwork0.319 2428 -
obs--99.96 %

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