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- PDB-7joo: Crystal structure of ICOS in complex with antibody STIM003 and an... -

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Basic information

Entry
Database: PDB / ID: 7joo
TitleCrystal structure of ICOS in complex with antibody STIM003 and anti-kappa VHH domain
Components
  • Inducible T-cell costimulator
  • STIM003 Fab Heavy chain
  • STIM003 Fab Light chain
  • anti-kappa VHH
KeywordsIMMUNE SYSTEM / Immune checkpoint / glycoprotein / receptor / T-cell / antibody
Function / homology
Function and homology information


T cell tolerance induction / T follicular helper cell differentiation / Co-stimulation by ICOS / Nuclear events stimulated by ALK signaling in cancer / T cell costimulation / cell-cell adhesion / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / signaling receptor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling ...T cell tolerance induction / T follicular helper cell differentiation / Co-stimulation by ICOS / Nuclear events stimulated by ALK signaling in cancer / T cell costimulation / cell-cell adhesion / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / signaling receptor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / immune response / extracellular region / plasma membrane
Similarity search - Function
Inducible T-cell costimulator / ICOS V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Inducible T-cell costimulator
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRujas, E. / Sicard, T. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-1488 Canada
CitationJournal: Nat Commun / Year: 2020
Title: Structural characterization of the ICOS/ICOS-L immune complex reveals high molecular mimicry by therapeutic antibodies.
Authors: Rujas, E. / Cui, H. / Sicard, T. / Semesi, A. / Julien, J.P.
History
DepositionAug 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Dec 21, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_validate_torsion / struct_conf / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_validate_torsion.auth_comp_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_label_comp_id / _struct_conf.end_auth_comp_id / _struct_conf.end_label_comp_id / _struct_ref_seq_dif.details / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_label_comp_id
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: anti-kappa VHH
H: STIM003 Fab Heavy chain
L: STIM003 Fab Light chain
C: Inducible T-cell costimulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8546
Polymers73,5414
Non-polymers3132
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.855, 49.031, 91.817
Angle α, β, γ (deg.)90.000, 101.901, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Antibody , 3 types, 3 molecules KHL

#1: Antibody anti-kappa VHH


Mass: 11326.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#2: Antibody STIM003 Fab Heavy chain


Mass: 24164.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody STIM003 Fab Light chain


Mass: 23619.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules C

#4: Protein Inducible T-cell costimulator / Activation-inducible lymphocyte immunomediatory molecule


Mass: 14430.349 Da / Num. of mol.: 1 / Mutation: N23Q, C136A, C137A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICOS, AILIM / Production host: Homo sapiens (human) / References: UniProt: Q9Y6W8
#6: 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.: 1
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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Non-polymers , 2 types, 167 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-sodium hydrogen phosphate and 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979341 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979341 Å / Relative weight: 1
ReflectionResolution: 2.38→40 Å / Num. obs: 30150 / % possible obs: 99.2 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.045 / Net I/σ(I): 13.3
Reflection shellResolution: 2.38→2.48 Å / Redundancy: 6 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3223 / CC1/2: 0.732 / Rpim(I) all: 0.258 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I8L, internal database

1i8l


Resolution: 2.4→28.48 Å / SU ML: 0.4469 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.9037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2966 1485 5 %
Rwork0.2413 28203 -
obs0.244 29688 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4855 0 20 166 5041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224982
X-RAY DIFFRACTIONf_angle_d0.60826779
X-RAY DIFFRACTIONf_chiral_restr0.0442765
X-RAY DIFFRACTIONf_plane_restr0.0043877
X-RAY DIFFRACTIONf_dihedral_angle_d20.02281713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.41281340.32082549X-RAY DIFFRACTION99.93
2.48-2.570.35921330.31452523X-RAY DIFFRACTION100
2.57-2.670.36981340.31012543X-RAY DIFFRACTION99.96
2.67-2.790.46021330.32382542X-RAY DIFFRACTION99.96
2.79-2.940.35951340.2982528X-RAY DIFFRACTION99.92
2.94-3.120.33391350.26552557X-RAY DIFFRACTION99.93
3.12-3.360.30151330.25212555X-RAY DIFFRACTION99.89
3.36-3.70.27421360.22442568X-RAY DIFFRACTION99.93
3.7-4.230.25881350.2182567X-RAY DIFFRACTION99.96
4.23-5.330.24171370.19522599X-RAY DIFFRACTION100
5.33-28.480.26981410.22192672X-RAY DIFFRACTION99.89

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