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- PDB-6j0g: Crystal structure of intracellular B30.2 domain of BTN3A3 mutant ... -

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Basic information

Entry
Database: PDB / ID: 6j0g
TitleCrystal structure of intracellular B30.2 domain of BTN3A3 mutant in complex with HMBPP
ComponentsButyrophilin subfamily 3 member A3
KeywordsSIGNALING PROTEIN / Butyrophilin
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / T cell mediated immunity / regulation of cytokine production / T cell receptor signaling pathway / nuclear body / signaling receptor binding / external side of plasma membrane / intracellular membrane-bounded organelle / nucleoplasm / membrane ...Butyrophilin (BTN) family interactions / T cell mediated immunity / regulation of cytokine production / T cell receptor signaling pathway / nuclear body / signaling receptor binding / external side of plasma membrane / intracellular membrane-bounded organelle / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain ...Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-H6P / Butyrophilin subfamily 3 member A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYang, Y.Y. / Liu, W.D. / Cai, N.N. / Chen, C.C. / Guo, R.T. / Zhang, Y.H.
CitationJournal: Immunity / Year: 2019
Title: A Structural Change in Butyrophilin upon Phosphoantigen Binding Underlies Phosphoantigen-Mediated V gamma 9V delta 2 T Cell Activation.
Authors: Yang, Y. / Li, L. / Yuan, L. / Zhou, X. / Duan, J. / Xiao, H. / Cai, N. / Han, S. / Ma, X. / Liu, W. / Chen, C.C. / Wang, L. / Li, X. / Chen, J. / Kang, N. / Chen, J. / Shen, Z. / Malwal, S. ...Authors: Yang, Y. / Li, L. / Yuan, L. / Zhou, X. / Duan, J. / Xiao, H. / Cai, N. / Han, S. / Ma, X. / Liu, W. / Chen, C.C. / Wang, L. / Li, X. / Chen, J. / Kang, N. / Chen, J. / Shen, Z. / Malwal, S.R. / Liu, W. / Shi, Y. / Oldfield, E. / Guo, R.T. / Zhang, Y.
History
DepositionDec 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Butyrophilin subfamily 3 member A3
B: Butyrophilin subfamily 3 member A3
C: Butyrophilin subfamily 3 member A3
D: Butyrophilin subfamily 3 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1388
Polymers101,0904
Non-polymers1,0484
Water14,952830
1
A: Butyrophilin subfamily 3 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5352
Polymers25,2721
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Butyrophilin subfamily 3 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5352
Polymers25,2721
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Butyrophilin subfamily 3 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5352
Polymers25,2721
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Butyrophilin subfamily 3 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5352
Polymers25,2721
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.109, 67.108, 75.436
Angle α, β, γ (deg.)85.78, 86.88, 86.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Butyrophilin subfamily 3 member A3


Mass: 25272.418 Da / Num. of mol.: 4 / Fragment: UNP residues 328-515 / Mutation: R351H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A3, BTF3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00478
#2: Chemical
ChemComp-H6P / (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate


Mass: 262.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O8P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / 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: 1.95 Å3/Da / Density % sol: 36.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Sodium Acetate trihydrate , Tris Hydrochloride ,Polyethylene Glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 97578 / % possible obs: 96.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.11
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 9312 / CC1/2: 0.951

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7U

4n7u


Resolution: 1.6→24.685 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 37.74
RfactorNum. reflection% reflection
Rfree0.2893 4885 5.03 %
Rwork0.2424 --
obs0.2448 97186 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→24.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6170 0 60 830 7060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066463
X-RAY DIFFRACTIONf_angle_d0.9088824
X-RAY DIFFRACTIONf_dihedral_angle_d16.6233818
X-RAY DIFFRACTIONf_chiral_restr0.056911
X-RAY DIFFRACTIONf_plane_restr0.0061140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5934-1.61150.36921290.34592366X-RAY DIFFRACTION74
1.6115-1.63050.3591500.32233022X-RAY DIFFRACTION92
1.6305-1.65030.34721560.32172994X-RAY DIFFRACTION93
1.6503-1.67120.35871500.31223029X-RAY DIFFRACTION94
1.6712-1.69320.32391780.29343087X-RAY DIFFRACTION95
1.6932-1.71640.28991560.28393048X-RAY DIFFRACTION95
1.7164-1.74090.33541550.27383038X-RAY DIFFRACTION95
1.7409-1.76690.34981640.27423193X-RAY DIFFRACTION96
1.7669-1.79450.36171460.27053032X-RAY DIFFRACTION95
1.7945-1.82390.29661550.26443105X-RAY DIFFRACTION96
1.8239-1.85530.27391610.26663122X-RAY DIFFRACTION96
1.8553-1.88910.28511740.27253083X-RAY DIFFRACTION96
1.8891-1.92540.33281590.26293063X-RAY DIFFRACTION96
1.9254-1.96470.31491470.26643123X-RAY DIFFRACTION96
1.9647-2.00740.34621740.25233062X-RAY DIFFRACTION96
2.0074-2.05410.2991460.24553191X-RAY DIFFRACTION97
2.0541-2.10540.3491600.26643067X-RAY DIFFRACTION96
2.1054-2.16230.30421710.25763164X-RAY DIFFRACTION97
2.1623-2.22590.32181670.25043116X-RAY DIFFRACTION97
2.2259-2.29770.30771320.2493153X-RAY DIFFRACTION97
2.2977-2.37970.30251820.25133080X-RAY DIFFRACTION97
2.3797-2.47490.31391690.25463154X-RAY DIFFRACTION97
2.4749-2.58740.32692090.25683126X-RAY DIFFRACTION98
2.5874-2.72370.35521820.26793107X-RAY DIFFRACTION98
2.7237-2.89410.27341390.24273158X-RAY DIFFRACTION97
2.8941-3.11720.27271640.23623144X-RAY DIFFRACTION98
3.1172-3.43010.24371620.22513175X-RAY DIFFRACTION98
3.4301-3.92470.22861810.19523174X-RAY DIFFRACTION98
3.9247-4.93830.24241760.20473130X-RAY DIFFRACTION97
4.9383-24.68830.29721910.22432995X-RAY DIFFRACTION94

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