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- PDB-6x4t: Crystal structure of ICOS-L in complex with Prezalumab and VNAR domain -

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Basic information

Entry
Database: PDB / ID: 6x4t
TitleCrystal structure of ICOS-L in complex with Prezalumab and VNAR domain
Components
  • (Prezalumab Fab ...) x 2
  • ICOS ligand
  • VNAR
KeywordsIMMUNE SYSTEM / Immune checkpoint / receptor ligand / glycoprotein / antibody / B cell
Function / homology
Function and homology information


hyperosmotic response / Costimulation by the CD28 family / B cell activation / positive regulation of activated T cell proliferation / regulation of cytokine production / T cell activation / defense response / cytoplasmic ribonucleoprotein granule / T cell receptor signaling pathway / adaptive immune response ...hyperosmotic response / Costimulation by the CD28 family / B cell activation / positive regulation of activated T cell proliferation / regulation of cytokine production / T cell activation / defense response / cytoplasmic ribonucleoprotein granule / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / signaling receptor binding / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
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
Biological speciesHomo sapiens (human)
Orectolobus maculatus (spotted wobbegong)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ICOS ligand
B: Prezalumab Fab Heavy chain
C: ICOS ligand
D: Prezalumab Fab Heavy chain
E: Prezalumab Fab Light chain
F: Prezalumab Fab Light chain
G: VNAR
N: VNAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,45821
Polymers176,4348
Non-polymers3,02413
Water00
1
A: ICOS ligand
D: Prezalumab Fab Heavy chain
F: Prezalumab Fab Light chain
G: VNAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,93212
Polymers88,2174
Non-polymers1,7158
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-16 kcal/mol
Surface area35530 Å2
MethodPISA
2
B: Prezalumab Fab Heavy chain
C: ICOS ligand
E: Prezalumab Fab Light chain
N: VNAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5269
Polymers88,2174
Non-polymers1,3095
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-18 kcal/mol
Surface area35420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.508, 151.984, 86.675
Angle α, β, γ (deg.)90.000, 104.101, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 20 through 147 or resid 154 through 231 or resid 1002 through 1007))A20 - 147
121(chain 'A' and (resid 20 through 147 or resid 154 through 231 or resid 1002 through 1007))A154 - 231
131(chain 'A' and (resid 20 through 147 or resid 154 through 231 or resid 1002 through 1007))A1002 - 1007
211(chain 'C' and (resid 20 through 231 or resid 1000 through 1006))C20 - 147
221(chain 'C' and (resid 20 through 231 or resid 1000 through 1006))C154 - 231
231(chain 'C' and (resid 20 through 231 or resid 1000 through 1006))C1000 - 1001
241(chain 'C' and (resid 20 through 231 or resid 1000 through 1006))C1003 - 1006
112(chain 'B' and resid 1 through 215)B1 - 215
212chain 'D'D1 - 100
222chain 'D'D105 - 219
113(chain 'E' and resid 1 through 212)E1 - 211
213chain 'F'F1 - 211
114(chain 'G' and (resid 1 through 12 or resid 20 through 52 or resid 56 through 115))G1 - 12
124(chain 'G' and (resid 1 through 12 or resid 20 through 52 or resid 56 through 115))G20 - 52
134(chain 'G' and (resid 1 through 12 or resid 20 through 52 or resid 56 through 115))G56 - 115
214(chain 'N' and (resid 1 through 44 or (resid 45...N1 - 12
224(chain 'N' and (resid 1 through 44 or (resid 45...N20 - 52
234(chain 'N' and (resid 1 through 44 or (resid 45...N56 - 115

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules ACGN

#1: 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.: 2
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
#4: Protein VNAR


Mass: 13987.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orectolobus maculatus (spotted wobbegong)
Production host: Homo sapiens (human)

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Antibody , 2 types, 4 molecules BDEF

#2: Antibody Prezalumab Fab Heavy chain


Mass: 24000.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Prezalumab Fab Light chain


Mass: 23456.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 11 molecules

#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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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.: 9
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 , 1 types, 2 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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Details

Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-ammonium tartrate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033158 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033158 Å / Relative weight: 1
ReflectionResolution: 3.15→40 Å / Num. obs: 29746 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 76.67 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.068 / Net I/σ(I): 9.4
Reflection shellResolution: 3.15→3.25 Å / Redundancy: 7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1378 / CC1/2: 0.76 / Rpim(I) all: 0.27 / % possible all: 100

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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, internal database

1i8l

4i0k

1t6v


Resolution: 3.15→38.88 Å / SU ML: 0.4902 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2819
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2562 1483 4.99 %
Rwork0.2006 28223 -
obs0.2035 29706 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.32 Å2
Refinement stepCycle: LAST / Resolution: 3.15→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11580 0 194 0 11774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003712011
X-RAY DIFFRACTIONf_angle_d0.807516320
X-RAY DIFFRACTIONf_chiral_restr0.05551887
X-RAY DIFFRACTIONf_plane_restr0.00512082
X-RAY DIFFRACTIONf_dihedral_angle_d20.11474333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.250.43751350.34192563X-RAY DIFFRACTION99.82
3.25-3.370.37191340.29152524X-RAY DIFFRACTION99.63
3.37-3.50.32691340.25842566X-RAY DIFFRACTION99.85
3.5-3.660.33141360.24352553X-RAY DIFFRACTION99.81
3.66-3.850.32691350.23092565X-RAY DIFFRACTION99.85
3.86-4.10.24651350.19792569X-RAY DIFFRACTION99.93
4.1-4.410.24251340.17322539X-RAY DIFFRACTION99.93
4.41-4.850.18871370.15522595X-RAY DIFFRACTION99.93
4.86-5.560.21331320.17082554X-RAY DIFFRACTION99.89
5.56-6.990.26341370.22590X-RAY DIFFRACTION99.96
6.99-38.880.19831340.17372605X-RAY DIFFRACTION99.49

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