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- PDB-6x4g: Crystal structure of ICOS in complex with ICOS-L and an anti ICOS... -

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Basic information

Entry
Database: PDB / ID: 6x4g
TitleCrystal structure of ICOS in complex with ICOS-L and an anti ICOS-L VNAR domain
Components
  • ICOS ligand
  • Inducible T-cell costimulator
  • anti ICOS-L VHH domain VNAR
KeywordsIMMUNE SYSTEM / Immune checkpoint / receptors / glycoproteins / T-cell / B-cell
Function / homology
Function and homology information


T cell tolerance induction / hyperosmotic response / Costimulation by the CD28 family / positive regulation of activated T cell proliferation / B cell activation / Nuclear events stimulated by ALK signaling in cancer / T cell costimulation / regulation of cytokine production / T cell activation / defense response ...T cell tolerance induction / hyperosmotic response / Costimulation by the CD28 family / positive regulation of activated T cell proliferation / B cell activation / Nuclear events stimulated by ALK signaling in cancer / T cell costimulation / regulation of cytokine production / T cell activation / defense response / cell-cell adhesion / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / adaptive immune response / immune response / external side of plasma membrane / intracellular membrane-bounded organelle / signaling receptor binding / signal transduction / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Inducible T-cell costimulator / ICOS V-set domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...Inducible T-cell costimulator / ICOS V-set domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ICOS ligand / Inducible T-cell costimulator
Similarity search - Component
Biological speciesHomo sapiens (human)
Orectolobus maculatus (spotted wobbegong)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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
DepositionMay 22, 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 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 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
A: Inducible T-cell costimulator
C: ICOS ligand
N: anti ICOS-L VHH domain VNAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,41212
Polymers54,1713
Non-polymers3,2419
Water00
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)104.015, 104.015, 123.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 2 types, 2 molecules AC

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


Mass: 13412.229 Da / Num. of mol.: 1
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
#2: Protein ICOS ligand / B7 homolog 2 / B7-H2 / B7-like protein Gl50 / B7-related protein 1 / B7RP-1


Mass: 26771.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICOSLG, B7H2, B7RP1, ICOSL, KIAA0653 / Production host: Homo sapiens (human) / References: UniProt: O75144

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Antibody / Non-polymers , 2 types, 2 molecules N

#3: Antibody anti ICOS-L VHH domain VNAR


Mass: 13987.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orectolobus maculatus (spotted wobbegong)
Production host: Homo sapiens (human)
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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Sugars , 2 types, 8 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 6
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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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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.0, and 30% (v/v) Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 10227 / % possible obs: 95.7 % / Redundancy: 11.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.079 / Net I/σ(I): 10
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 406 / CC1/2: 0.63 / Rpim(I) all: 0.23 / % possible all: 97.9

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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, 4I0K, 1T6V

1i8l

4i0k

1t6v


Resolution: 3.5→39.73 Å / SU ML: 0.5761 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2665 434 5 %
Rwork0.2241 8242 -
obs0.2262 8676 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.77 Å2
Refinement stepCycle: LAST / Resolution: 3.5→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 212 0 3513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01043575
X-RAY DIFFRACTIONf_angle_d1.13084848
X-RAY DIFFRACTIONf_chiral_restr0.0845602
X-RAY DIFFRACTIONf_plane_restr0.0094600
X-RAY DIFFRACTIONf_dihedral_angle_d26.0043582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-4.010.37091300.27522485X-RAY DIFFRACTION89.89
4.01-5.050.26451480.2052810X-RAY DIFFRACTION100
5.05-39.730.22921560.21832947X-RAY DIFFRACTION99.87

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