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- PDB-4f80: Crystal Structure of the human BTN3A1 ectodomain -

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Basic information

Entry
Database: PDB / ID: 4f80
TitleCrystal Structure of the human BTN3A1 ectodomain
ComponentsButyrophilin subfamily 3 member A1
KeywordsIMMUNE SYSTEM / B7 superfamily / Butyrophilin / CD277
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-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-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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 Å
AuthorsPalakodeti, A. / Sandstrom, A. / Sundaresan, L. / Harly, C. / Nedellec, S. / Olive, D. / Scotet, E. / Bonneville, M. / Adams, E.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The molecular basis for modulation of human V(gamma)9V(delta)2 T cell responses by CD277/Butyrophilin-3 (BTN3A)-specific antibodies
Authors: Palakodeti, A. / Sandstrom, A. / Sundaresan, L. / Harly, C. / Nedellec, S. / Olive, D. / Scotet, E. / Bonneville, M. / Adams, E.J.
History
DepositionMay 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)24,4701
Polymers24,4701
Non-polymers00
Water93752
1
A: Butyrophilin subfamily 3 member A1

A: Butyrophilin subfamily 3 member A1


Theoretical massNumber of molelcules
Total (without water)48,9392
Polymers48,9392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1520 Å2
ΔGint-8 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.055, 77.988, 98.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 24469.541 Da / Num. of mol.: 1 / Fragment: Ectodomain (UNP Residues 30-246)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTF5, BTN3A1 / Plasmid: pAcGP67A / Production host: Trichoplusia Ni (cabbage looper) / References: UniProt: O00481
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M Citric acid pH4.0, 1.6M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 23011 / Num. obs: 23011 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.74 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.93-1.96189.9
1.96-2194.2
2-2.04198.1
2.04-2.08198.6
2.08-2.12196.4
2.12-2.17198.7
2.17-2.23195.9
2.23-2.29198.8
2.29-2.36195.8
2.36-2.43198.1
2.43-2.52195.4
2.26-2.52197.6
2.62-2.74195.5
2.74-2.88194.9
2.88-3.06195.4
3.06-3.3195
3.3-3.63193.4
3.36-4.16193.8
4.16-5.24191.5
5.24-50187.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BIK, 1TLK

3bik

1tlk


Resolution: 1.944→19.945 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8443 / SU ML: 0.26 / σ(F): 0 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1112 5.1 %RANDOM
Rwork0.2247 ---
obs0.2257 21794 92.88 %-
all-21794 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.647 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 213.25 Å2 / Biso mean: 30.8593 Å2 / Biso min: 11.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.4457 Å2-0 Å20 Å2
2---2.7021 Å2-0 Å2
3---3.1478 Å2
Refinement stepCycle: LAST / Resolution: 1.944→19.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1582 0 0 52 1634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111616
X-RAY DIFFRACTIONf_angle_d1.2312189
X-RAY DIFFRACTIONf_chiral_restr0.076246
X-RAY DIFFRACTIONf_plane_restr0.009283
X-RAY DIFFRACTIONf_dihedral_angle_d11.179583
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.944-2.03240.28781290.23622356248586
2.0324-2.13940.22551420.2162549269193
2.1394-2.27330.26571350.22072584271995
2.2733-2.44850.28061440.23452614275895
2.4485-2.69440.25831760.23722574275094
2.6944-3.0830.25011420.25122650279295
3.083-3.87960.23191200.21622671279195
3.8796-19.94640.22231240.21272684280890
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0649-0.17530.17382.0505-0.69240.61410.0641-0.1833-0.11330.1192-0.2075-0.61560.08720.24430.14180.1816-0.0081-0.02280.19320.05370.241521.6656-16.6995-19.2406
21.2581-0.05290.1720.4487-0.12770.3180.08440.23180.2508-0.1276-0.07760.12950.01970.00370.02920.10310.0024-0.01470.13720.00160.127714.4265-12.785-26.9809
30.0297-0.1265-0.07931.3169-0.31060.8356-0.06180.14520.2-0.1782-0.02480.4771-0.0947-0.5988-0.06510.14440.0202-0.04110.18520.05240.24384.2457-16.7702-25.4182
40.7049-0.17230.21040.2621-0.06230.33110.0522-0.06670.0271-0.0204-0.06090.04890.0230.0377-0.00040.139-0.00170.00360.13080.01340.141814.7853-15.1436-21.6707
5-0.0293-0.2712-0.18040.14460.06570.2564-0.12740.0150.0356-0.1488-0.0065-0.11640.24140.0281-0.01870.25670.03120.0520.19640.04020.190720.0589-43.2073-14.1235
60.2135-0.18290.3140.3589-0.12910.5074-0.0290.18430.02920.02910.0256-0.08670.01180.42530.03960.19880.07840.06440.29130.04470.191326.2656-47.1078-10.2384
70.32350.1144-0.13380.9207-0.07130.6847-0.17830.0083-0.2224-0.06440.10740.35920.1399-0.03-0.02150.14720.04740.00990.15490.00680.151920.4165-50.2265-15.0115
80.6718-0.22510.35560.5875-0.20890.5384-0.04730.06850.10030.1829-0.2754-0.17570.15950.35320.03690.27530.05090.05720.18460.05290.17326.24-51.6485-3.8613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:26)A1 - 26
2X-RAY DIFFRACTION2chain 'A' and (resseq 27:50)A27 - 50
3X-RAY DIFFRACTION3chain 'A' and (resseq 51:67)A51 - 67
4X-RAY DIFFRACTION4chain 'A' and (resseq 68:103)A68 - 103
5X-RAY DIFFRACTION5chain 'A' and (resseq 104:139)A104 - 139
6X-RAY DIFFRACTION6chain 'A' and (resseq 140:156)A140 - 156
7X-RAY DIFFRACTION7chain 'A' and (resseq 157:181)A157 - 181
8X-RAY DIFFRACTION8chain 'A' and (resseq 182:213)A182 - 213

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