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- PDB-4f9p: Crystal Structure of the Human BTN3A1 Ectodomain in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 4f9p
TitleCrystal Structure of the Human BTN3A1 Ectodomain in Complex with the 103.2 Single Chain Antibody
Components
  • 103.2 anti-BTN3A1 antibody fragment
  • Butyrophilin 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 / signaling receptor binding / external side of plasma membrane / plasma membrane
Similarity search - Function
Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain ...Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.519 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 19, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Butyrophilin subfamily 3 member A1
B: Butyrophilin subfamily 3 member A1
D: 103.2 anti-BTN3A1 antibody fragment
C: 103.2 anti-BTN3A1 antibody fragment


Theoretical massNumber of molelcules
Total (without water)100,6144
Polymers100,6144
Non-polymers00
Water00
1
A: Butyrophilin subfamily 3 member A1
B: Butyrophilin subfamily 3 member A1


Theoretical massNumber of molelcules
Total (without water)47,2812
Polymers47,2812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 103.2 anti-BTN3A1 antibody fragment


Theoretical massNumber of molelcules
Total (without water)26,6661
Polymers26,6661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 103.2 anti-BTN3A1 antibody fragment


Theoretical massNumber of molelcules
Total (without water)26,6661
Polymers26,6661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: 103.2 anti-BTN3A1 antibody fragment


Theoretical massNumber of molelcules
Total (without water)26,6661
Polymers26,6661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.360, 117.680, 121.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'D' and (resseq 1:113 or resseq 137:141 or resseq 143:244 )D1 - 113
121chain 'D' and (resseq 1:113 or resseq 137:141 or resseq 143:244 )D137 - 141
131chain 'D' and (resseq 1:113 or resseq 137:141 or resseq 143:244 )D143 - 244
211chain 'C' and (resseq 1:113 or resseq 137:141 or resseq 143:244 )C1 - 113
221chain 'C' and (resseq 1:113 or resseq 137:141 or resseq 143:244 )C137 - 141
231chain 'C' and (resseq 1:113 or resseq 137:141 or resseq 143:244 )C143 - 244
112chain 'A' and (resseq 1:181 or resseq 188:198 or resseq 200:213 )A1 - 181
122chain 'A' and (resseq 1:181 or resseq 188:198 or resseq 200:213 )A188 - 198
132chain 'A' and (resseq 1:181 or resseq 188:198 or resseq 200:213 )A200 - 213
212chain 'B' and (resseq 1:181 or resseq 188:198 or resseq 200:213 )B1 - 181
222chain 'B' and (resseq 1:181 or resseq 188:198 or resseq 200:213 )B188 - 198
232chain 'B' and (resseq 1:181 or resseq 188:198 or resseq 200:213 )B200 - 213

NCS ensembles :
ID
1
2

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Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 23640.660 Da / Num. of mol.: 2 / 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: Antibody 103.2 anti-BTN3A1 antibody fragment


Mass: 26666.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IgG / Plasmid: pAK300 / Production host: Escherichia coli (E. coli) / Strain (production host): 33D3
Has protein modificationY

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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: 60.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH7.5, 1M Sodium Chloride, 15% PEG 8000, 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 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. all: 16002 / Num. obs: 16002 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 113.52 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.45-3.51199.6
3.51-3.57199.6
3.57-3.641100
3.64-3.721100
3.72-3.8199.5
3.8-3.89199.1
3.89-3.98199.6
3.98-4.09199.4
4.09-4.21196.8
4.21-4.35196.8
4.35-4.5198
4.5-4.68199.9
4.68-4.891100
4.89-5.15199.9
5.15-5.471100
5.47-5.9199.9
5.9-6.491100
6.49-7.43199.9
7.43-9.35199.9
9.35-50196.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 48F0, 3DIF, 1XGP

48f0

3dif

1xgp


Resolution: 3.519→41.54 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5927 / SU ML: 1.43 / σ(F): 1.33 / Phase error: 44.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4076 668 4.91 %
Rwork0.3731 --
obs0.3748 13608 83.32 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 130.54 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 500 Å2 / Biso mean: 126.4291 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--6.9566 Å2-0 Å20 Å2
2---0.066 Å2-0 Å2
3---2.1287 Å2
Refinement stepCycle: LAST / Resolution: 3.519→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 0 0 5552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085645
X-RAY DIFFRACTIONf_angle_d1.3777783
X-RAY DIFFRACTIONf_chiral_restr0.09913
X-RAY DIFFRACTIONf_plane_restr0.0061043
X-RAY DIFFRACTIONf_dihedral_angle_d15.3031599
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D1437X-RAY DIFFRACTIONPOSITIONAL0.05
12C1437X-RAY DIFFRACTIONPOSITIONAL0.05
21A1134X-RAY DIFFRACTIONPOSITIONAL0.054
22B1134X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.519-3.79060.4479440.43851199124339
3.7906-4.17170.42471310.42812423255480
4.1717-4.77460.39121700.3662977314798
4.7746-6.01260.40931630.381531113274100
6.0126-41.54260.40811600.34993230339099

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