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- PDB-8ek5: Engineered scFv 10LH bound to PHOX2B/HLA-A24:02 -

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Basic information

Entry
Database: PDB / ID: 8ek5
TitleEngineered scFv 10LH bound to PHOX2B/HLA-A24:02
Components
  • 10LH single chain fragment variable (scFv)
  • Beta-2-microglobulin
  • MHC class I antigen
  • Paired mesoderm homeobox protein 2B peptide
KeywordsANTITUMOR PROTEIN / Neuroblastoma / PHOX2B
Function / homology
Function and homology information


medullary reticular formation development / parasympathetic nervous system development / efferent axon development in a lateral line nerve / retrotrapezoid nucleus neuron differentiation / negative regulation of type B pancreatic cell proliferation / cell differentiation in hindbrain / noradrenergic neuron development / respiratory system development / autonomic nervous system development / hindbrain tangential cell migration ...medullary reticular formation development / parasympathetic nervous system development / efferent axon development in a lateral line nerve / retrotrapezoid nucleus neuron differentiation / negative regulation of type B pancreatic cell proliferation / cell differentiation in hindbrain / noradrenergic neuron development / respiratory system development / autonomic nervous system development / hindbrain tangential cell migration / noradrenergic neuron differentiation / cellular response to carbon dioxide / brainstem development / motor neuron migration / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / enteric nervous system development / regulation of respiratory gaseous exchange by nervous system process / sympathetic nervous system development / glial cell differentiation / cellular response to BMP stimulus / dopaminergic neuron differentiation / type B pancreatic cell proliferation / negative regulation of neuron differentiation / antigen processing and presentation of peptide antigen via MHC class I / inner ear development / skeletal muscle cell differentiation / membrane depolarization / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of neuron differentiation / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / response to activity / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / neuron migration / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / positive regulation of cold-induced thermogenesis / ER-Phagosome pathway / regulation of gene expression / protein refolding / DNA-binding transcription activator activity, RNA polymerase II-specific / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / learning or memory / RNA polymerase II cis-regulatory region sequence-specific DNA binding / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane
Similarity search - Function
: / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...: / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Homeobox-like domain superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
NITRATE ION / MHC class I antigen / Beta-2-microglobulin / Paired mesoderm homeobox protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsGarfinkle, S.E. / Florio, T.J. / Sgourakis, N.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI143997 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM125034 United States
Citation
Journal: Sci Immunol / Year: 2023
Title: Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion.
Authors: Sun, Y. / Florio, T.J. / Gupta, S. / Young, M.C. / Marshall, Q.F. / Garfinkle, S.E. / Papadaki, G.F. / Truong, H.V. / Mycek, E. / Li, P. / Farrel, A. / Church, N.L. / Jabar, S. / Beasley, M. ...Authors: Sun, Y. / Florio, T.J. / Gupta, S. / Young, M.C. / Marshall, Q.F. / Garfinkle, S.E. / Papadaki, G.F. / Truong, H.V. / Mycek, E. / Li, P. / Farrel, A. / Church, N.L. / Jabar, S. / Beasley, M.D. / Kiefel, B.R. / Yarmarkovich, M. / Mallik, L. / Maris, J.M. / Sgourakis, N.G.
#1: Journal: Sci Immunol / Year: 2023
Title: The chilling origin of germinal centers.
Authors: Boehm, T.
History
DepositionSep 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 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: MHC class I antigen
B: Beta-2-microglobulin
C: Paired mesoderm homeobox protein 2B peptide
E: 10LH single chain fragment variable (scFv)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1368
Polymers94,8274
Non-polymers3084
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: See https://www.nature.com/articles/s41586-021-04061-6 for evidence of complex formation necessary for CAR-T cell killing data.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-22 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.087, 174.562, 47.193
Angle α, β, γ (deg.)90.00, 118.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31909.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F6IR24
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769

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Protein/peptide / Antibody , 2 types, 2 molecules CE

#3: Protein/peptide Paired mesoderm homeobox protein 2B peptide / Neuroblastoma Phox / NBPhox / PHOX2B homeodomain protein / Paired-like homeobox 2B


Mass: 1140.268 Da / Num. of mol.: 1 / Fragment: Residues 43-51 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99453
#4: Antibody 10LH single chain fragment variable (scFv)


Mass: 49898.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 310 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Sodium Nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.108→43.68 Å / Num. obs: 37369 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.057 / Rrim(I) all: 0.111 / Net I/σ(I): 4.5
Reflection shellResolution: 2.108→2.115 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 377 / CC1/2: 0.817 / Rpim(I) all: 0.389 / Rrim(I) all: 0.776 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSJan 10,2022data reduction
Aimless0.7.7data scaling
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MJA

7mja


Resolution: 2.11→43.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.01 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21245 2006 5.4 %RANDOM
Rwork0.18149 ---
obs0.18319 35362 97.37 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.173 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å20 Å20.44 Å2
2---2.16 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.11→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4857 0 20 306 5183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0175036
X-RAY DIFFRACTIONr_bond_other_d0.0010.0194495
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.8396829
X-RAY DIFFRACTIONr_angle_other_deg1.0262.63410367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.39221.707287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62515807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4641538
X-RAY DIFFRACTIONr_chiral_restr0.0810.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021235
X-RAY DIFFRACTIONr_mcbond_it0.9742.3032454
X-RAY DIFFRACTIONr_mcbond_other0.9742.3022453
X-RAY DIFFRACTIONr_mcangle_it1.6073.4493061
X-RAY DIFFRACTIONr_mcangle_other1.6073.4493062
X-RAY DIFFRACTIONr_scbond_it1.1862.4492582
X-RAY DIFFRACTIONr_scbond_other1.1742.4422577
X-RAY DIFFRACTIONr_scangle_other1.9013.5993762
X-RAY DIFFRACTIONr_long_range_B_refined4.46526.75550
X-RAY DIFFRACTIONr_long_range_B_other4.31426.295485
LS refinement shellResolution: 2.11→2.163 Å
RfactorNum. reflection% reflection
Rfree0.274 223 -
Rwork0.248 2509 -
obs--96.16 %
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)
10.50830.33560.06851.5623-0.11040.47490.03170.0450.02620.03810.03670.0658-0.0235-0.0221-0.06840.00650.01160.010.08510.00350.0214-6.087-3.05311.357
22.08391.221-0.04433.83280.71141.6871-0.03260.0305-0.0237-0.15810.0261-0.5039-0.10630.23380.00650.03860.01870.03920.08820.02940.11511.0914.7057.354
34.7925-0.3116-1.83155.53542.4852.4159-0.02260.305-0.13870.7094-0.26470.34440.328-0.23690.28740.1791-0.08470.03610.1463-0.08650.1452-9.152-22.258.588
41.7826-0.716-0.74522.15990.23671.31240.02330.1509-0.1634-0.1917-0.04750.02030.0171-0.05620.02430.069-0.0040.0040.0441-0.00430.0371-12.248-41.54816.624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 277
2X-RAY DIFFRACTION2B2 - 100
3X-RAY DIFFRACTION3C1 - 9
4X-RAY DIFFRACTION4E113 - 359

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