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- PDB-4f9l: Crystal Structure of the Human BTN3A1 Ectodomain in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 4f9l
TitleCrystal Structure of the Human BTN3A1 Ectodomain in Complex with the 20.1 Single Chain Antibody
Components
  • 20.1 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 / 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 / B30.2/SPRY domain superfamily ...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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1404 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 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
D: 20.1 anti-BTN3A1 antibody fragment
C: 20.1 anti-BTN3A1 antibody fragment
B: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3506
Polymers101,9074
Non-polymers4422
Water00
1
A: Butyrophilin subfamily 3 member A1
B: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7244
Polymers47,2812
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-6 kcal/mol
Surface area20810 Å2
MethodPISA
2
D: 20.1 anti-BTN3A1 antibody fragment


Theoretical massNumber of molelcules
Total (without water)27,3131
Polymers27,3131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 20.1 anti-BTN3A1 antibody fragment


Theoretical massNumber of molelcules
Total (without water)27,3131
Polymers27,3131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.136, 165.136, 53.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHEGLYGLYchain 'A' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )AA2 - 1275 - 130
121ILEILEGLYGLYchain 'A' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )AA133 - 183136 - 186
131GLUGLUSERSERchain 'A' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )AA187 - 195190 - 198
141GLYGLYILEILEchain 'A' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )AA199 - 208202 - 211
211PHEPHEGLYGLYchain 'B' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )BD2 - 1275 - 130
221ILEILEGLYGLYchain 'B' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )BD133 - 183136 - 186
231GLUGLUSERSERchain 'B' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )BD187 - 195190 - 198
241GLYGLYILEILEchain 'B' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )BD199 - 208202 - 211
112ASPASPASPASPchain 'D' and (resseq 1:105 )DB1 - 1051 - 105
212ASPASPASPASPchain 'C' and (resseq 1:105 )CC1 - 1051 - 105

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 20.1 anti-BTN3A1 antibody fragment


Mass: 27312.916 Da / Num. of mol.: 2
Fragment: domains of the heavy and light chains of the 20.1 antibody
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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.6 Å3/Da / Density % sol: 65.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.15M Potassium Fluoride, 14% PEG 3350, pH 7.2, VAPOR 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.14→50 Å / Num. all: 25881 / Num. obs: 25881 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 75.17 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.14-3.2199.1
3.2-3.26199.9
3.26-3.331100
3.33-3.391100
3.39-3.471100
3.47-3.551100
3.55-3.641100
3.64-3.731100
3.73-3.841100
3.84-3.971100
3.97-4.111100
4.11-4.271100
4.27-4.471100
4.47-4.71100
4.7-51100
5-5.381100
5.38-5.931100
5.93-6.781100
6.78-8.54199.9
8.54-50199.3

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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 4F80, 1IGT

4f80

1igt


Resolution: 3.1404→45.8 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7634 / SU ML: 0.74 / σ(F): 1.33 / Phase error: 30.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3026 1326 5.13 %
Rwork0.2538 --
obs0.2564 25831 99.72 %
all-25881 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.127 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 233.2 Å2 / Biso mean: 85.6031 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--4.7611 Å2-0 Å20 Å2
2---4.7611 Å2-0 Å2
3---9.5221 Å2
Refinement stepCycle: LAST / Resolution: 3.1404→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 28 0 6598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076811
X-RAY DIFFRACTIONf_angle_d1.2199269
X-RAY DIFFRACTIONf_chiral_restr0.0751049
X-RAY DIFFRACTIONf_plane_restr0.0051193
X-RAY DIFFRACTIONf_dihedral_angle_d19.7832367
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1424X-RAY DIFFRACTIONPOSITIONAL0.052
12B1424X-RAY DIFFRACTIONPOSITIONAL0.052
21D802X-RAY DIFFRACTIONPOSITIONAL0.081
22C802X-RAY DIFFRACTIONPOSITIONAL0.081
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1404-3.26610.38331370.3432672280999
3.2661-3.41470.37631330.314727112844100
3.4147-3.59470.31921410.289627222863100
3.5947-3.81980.34941370.270426752812100
3.8198-4.11460.30061550.265927252880100
4.1146-4.52830.27291410.223327152856100
4.5283-5.18280.25861520.212327162868100
5.1828-6.52670.29761610.253327382899100
6.5267-45.80530.29941690.24122831300099

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