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- PDB-4r0l: Anti-canine CD28 antibody, 1C6, bound canine CD28 -

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Basic information

Entry
Database: PDB / ID: 4r0l
TitleAnti-canine CD28 antibody, 1C6, bound canine CD28
Components
  • (Antibody 1C6 ...) x 2
  • T-cell costimulatory molecule CD28
KeywordsIMMUNE SYSTEM / Immunoglobulin / T-cell activation / CD28 / 1C6
Function / homology
Function and homology information


positive regulation of T cell proliferation / positive regulation of interleukin-2 production / positive regulation of mitotic nuclear division / immune response / membrane
Similarity search - Function
T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell-specific surface glycoprotein CD28
Similarity search - Component
Biological speciesMus musculus (house mouse)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGewe, M.M. / Strong, R.K.
CitationJournal: Transplant Direct / Year: 2015
Title: Anti-CD28 Antibody-Initiated Cytokine Storm in Canines.
Authors: Rosinski, S.L. / Storb, R. / Strong, R.K. / Sale, G.E. / Stone, D.M. / Gewe, M.M. / Friend, D.J. / Abrams, V.K. / Randolph-Habecker, J. / Graves, S.S.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody 1C6 Heavy chain
C: T-cell costimulatory molecule CD28
D: T-cell costimulatory molecule CD28
H: Antibody 1C6 Heavy chain
L: Antibody 1C6 Light chain
B: Antibody 1C6 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,64314
Polymers82,9726
Non-polymers2,6728
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.783, 86.783, 205.804
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
12B
22L
13C
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 110
2010H1 - 110
1020B1 - 112
2020L1 - 112
1030C2 - 117
2030D2 - 117

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 2 types, 4 molecules AHLB

#1: Antibody Antibody 1C6 Heavy chain


Mass: 13651.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein expressed as thrombin cleavable single chain Fv.
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22(b)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Antibody Antibody 1C6 Light chain


Mass: 12979.702 Da / Num. of mol.: 2 / Fragment: UNP residues 20-137
Source method: isolated from a genetically manipulated source
Details: Protein expressed as thrombin cleavable single chain Fv.
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22(b)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Protein / Non-polymers , 2 types, 4 molecules CD

#2: Protein T-cell costimulatory molecule CD28


Mass: 14854.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed as C-terminus TEV cleavable human siderocalin fusion polypeptide
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: CD28 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q9N0N8
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 8 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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: 5.4 Å3/Da / Density % sol: 77.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.9M AmSO4, 0.1M Cesium sulfate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.27 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2014
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 26171 / Num. obs: 25360 / % possible obs: 96.9 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.065 / Rsym value: 0.078 / Net I/σ(I): 15.1
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→42.46 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.872 / SU B: 54.67 / SU ML: 0.424 / Cross valid method: THROUGHOUT / ESU R: 0.909 / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29283 1292 5.1 %RANDOM
Rwork0.25609 ---
obs0.25792 24012 96.72 %-
all-25306 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0.6 Å20 Å2
2---1.2 Å20 Å2
3---3.89 Å2
Refinement stepCycle: LAST / Resolution: 3.3→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4711 0 174 2 4887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025034
X-RAY DIFFRACTIONr_bond_other_d0.0010.023977
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9686935
X-RAY DIFFRACTIONr_angle_other_deg0.72139042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4955680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71523.976166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04915475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.122154
X-RAY DIFFRACTIONr_chiral_restr0.0660.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215957
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021181
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_it7.6018.1812738
X-RAY DIFFRACTIONr_mcbond_other7.6018.1812737
X-RAY DIFFRACTIONr_mcangle_it11.28313.8183412
X-RAY DIFFRACTIONr_mcangle_other11.93417.8743403
X-RAY DIFFRACTIONr_scbond_it10.5048.7712296
X-RAY DIFFRACTIONr_scbond_other10.53511.592590
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.86119.4053939
X-RAY DIFFRACTIONr_long_range_B_refined19.98650.1965918
X-RAY DIFFRACTIONr_long_range_B_other19.98450.1995919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A4840.12
12H4840.12
21B5450.11
22L5450.11
31C5270.13
32D5270.13
LS refinement shellResolution: 3.298→3.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 98 -
Rwork0.382 1793 -
obs--96.04 %
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)
16.2575-0.23871.68533.6997-0.00496.0950.11431.0707-0.2833-0.5061-0.0652-0.16010.62640.3623-0.04910.19260.05530.01240.62330.01430.0321128.87833.3208-12.3112
26.366-2.69484.85613.6076-0.95646.2431-0.25730.10230.31270.1473-0.25710.0732-0.2497-0.34180.51440.0409-0.0753-0.01240.42690.05810.1433115.688317.7911-2.4588
34.221-1.4911.75094.3752-4.51425.2358-0.39640.19230.4285-0.01080.1559-0.50520.09190.0620.24040.0844-0.0152-0.08080.4825-0.04740.2253139.00287.716914.1493
44.6705-0.86424.38333.11860.21386.39940.10810.20660.54640.3625-0.1801-0.0006-0.0166-0.05660.0720.35880.13010.00930.11620.03510.2061153.7918-1.267439.6128
53.3829-0.92522.20593.0546-2.7196.4272-0.2836-0.9458-0.07480.52910.27820.23510.0672-0.75750.00540.42650.20220.03050.3895-0.06310.131155.4292-12.151366.5047
67.7094-2.38432.93662.1146-2.93655.8058-0.31970.24850.1205-0.0978-0.2013-0.26820.24380.5020.5210.41380.1278-0.05270.0957-0.01440.1385174.1984-16.068956.312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 109
2X-RAY DIFFRACTION2B1 - 110
3X-RAY DIFFRACTION3C2 - 118
4X-RAY DIFFRACTION4D2 - 119
5X-RAY DIFFRACTION5H1 - 108
6X-RAY DIFFRACTION6L1 - 109

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