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- PDB-9gwt: crystal structure of 23ME-00610 Fab in complex with human CD200R1 -

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Basic information

Entry
Database: PDB / ID: 9gwt
Titlecrystal structure of 23ME-00610 Fab in complex with human CD200R1
Components
  • (23ME-00610 Fab ...) x 2
  • Isoform 1 of Cell surface glycoprotein CD200 receptor 1
KeywordsANTITUMOR PROTEIN / 23ME-00610 / human CD200R1 / immune checkpoint inhibitor / immuno-oncology
Function / homology
Function and homology information


immunoglobulin receptor activity / glycosylated region protein binding / negative regulation of T cell migration / negative regulation of macrophage migration / negative regulation of neuroinflammatory response / regulation of neuroinflammatory response / heterotypic cell-cell adhesion / negative regulation of interleukin-6 production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity ...immunoglobulin receptor activity / glycosylated region protein binding / negative regulation of T cell migration / negative regulation of macrophage migration / negative regulation of neuroinflammatory response / regulation of neuroinflammatory response / heterotypic cell-cell adhesion / negative regulation of interleukin-6 production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / receptor complex / intracellular signal transduction / external side of plasma membrane / cell surface / signal transduction / extracellular region / plasma membrane
Similarity search - Function
Cell surface glycoprotein CD200 receptor / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Cell surface glycoprotein CD200 receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsHuang, Y.M. / Ganichkin, O.M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Mabs / Year: 2024
Title: CD200R1 immune checkpoint blockade by the first-in-human anti-CD200R1 antibody 23ME-00610: molecular mechanism and engineering of a surrogate antibody.
Authors: Melero, C. / Budiardjo, S.J. / Daruwalla, A. / Larrabee, L. / Ganichkin, O. / Heiler, A.J. / Fenaux, J. / Chung, B. / Fuh, G. / Huang, Y.M.
History
DepositionSep 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 23ME-00610 Fab (heavy)
L: 23ME-00610 Fab (light)
P: Isoform 1 of Cell surface glycoprotein CD200 receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2629
Polymers78,7503
Non-polymers3,5116
Water45025
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint13 kcal/mol
Surface area31660 Å2
Unit cell
Length a, b, c (Å)98.654, 98.654, 279.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules P

#3: Protein Isoform 1 of Cell surface glycoprotein CD200 receptor 1 / CD200 cell surface glycoprotein receptor / Cell surface glycoprotein OX2 receptor 1


Mass: 29882.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD200R1, CD200R, CRTR2, MOX2R, OX2R, UNQ2522/PRO6015 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q8TD46

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Antibody , 2 types, 2 molecules HL

#1: Antibody 23ME-00610 Fab (heavy) / 23ME-00610 Fab


Mass: 24980.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab Heavy chain / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody 23ME-00610 Fab (light) / 23ME-00610 Fab


Mass: 23887.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab light chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 4 types, 5 molecules

#4: 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
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 26 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.32 Å3/Da / Density % sol: 71.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sodium Cacodylate 0.1M, Glycerol 10% (v/v), NaCl 1M, PEG 600 30.0% (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.887→93.031 Å / Num. obs: 27539 / % possible obs: 94.3 % / Redundancy: 25.1 % / CC1/2: 0.998 / Net I/σ(I): 16.3
Reflection shellResolution: 2.887→3.077 Å / Num. unique obs: 1377 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→93.03 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 28.716 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.57 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1362 4.9 %RANDOM
Rwork0.2018 ---
obs0.2036 26177 86.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 224.29 Å2 / Biso mean: 108.553 Å2 / Biso min: 59.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å2-0 Å2-0 Å2
2--0.82 Å2-0 Å2
3----1.64 Å2
Refinement stepCycle: final / Resolution: 2.89→93.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4845 0 234 25 5104
Biso mean--165.19 76.91 -
Num. residues----632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125151
X-RAY DIFFRACTIONr_bond_other_d0.0210.0164511
X-RAY DIFFRACTIONr_angle_refined_deg0.9511.677071
X-RAY DIFFRACTIONr_angle_other_deg0.5771.55810577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1715634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.955517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.810717
X-RAY DIFFRACTIONr_chiral_restr0.0450.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025615
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02934
X-RAY DIFFRACTIONr_mcbond_it1.8677.0232539
X-RAY DIFFRACTIONr_mcbond_other1.8667.0232539
X-RAY DIFFRACTIONr_mcangle_it3.11910.5263172
LS refinement shellResolution: 2.89→2.962 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.258 4 -
Rwork0.338 141 -
obs--6.32 %
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)
12.77360.5870.14763.07010.99243.4428-0.0753-0.2357-0.0565-0.1050.04660.19420.0189-0.05310.02880.0327-0.0022-0.01920.29490.06520.2494-12.07430.1815.854
24.88080.4576-3.30591.7125-0.17056.7089-0.17790.2674-0.7355-0.5045-0.0767-0.12540.593-0.16920.25470.4934-0.0491-0.11120.1516-0.02560.4208-7.99919.244-20.272
34.88950.1459-2.03842.98050.72785.81750.1196-0.38550.5901-0.0517-0.0182-0.0788-0.58410.4098-0.10130.2006-0.1245-0.0890.34240.02940.27213.39744.9869.33
46.5371.05320.87213.3743-0.41173.6154-0.02310.24750.0281-0.4894-0.08870.27450.0872-0.16540.11180.3441-0.0481-0.07090.09370.00140.1704-6.93435.579-18.523
54.1823-1.2496-2.81822.56772.02173.2112-0.11920.3551-0.0641-0.1060.04480.268-0.06630.05220.07440.23130.0477-0.10440.4355-0.07830.4182-10.16749.30742.168
69.2019-1.2535-0.85112.0402-0.12192.999-0.0272-0.18050.04660.0509-0.01470.34890.0022-0.32090.04190.44390.0168-0.02590.2265-0.05980.4593-36.84657.21754.732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 111
2X-RAY DIFFRACTION2L112 - 255
3X-RAY DIFFRACTION3H1 - 119
4X-RAY DIFFRACTION4H120 - 300
5X-RAY DIFFRACTION5P1 - 151
6X-RAY DIFFRACTION6P152 - 400

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