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- EMDB-43499: Engineered peptide-specific binder in complex with HLA-DR1/CLIP -

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Entry
Database: EMDB / ID: EMD-43499
TitleEngineered peptide-specific binder in complex with HLA-DR1/CLIP
Map data
Sample
  • Complex: Engineered peptide-specific binder in complex with HLA-DR1/CLIP
    • Protein or peptide: HLA class II histocompatibility antigen, DR alpha chain
    • Protein or peptide: HLA class II histocompatibility antigen DR beta chain
    • Protein or peptide: Superantigen
    • Protein or peptide: c44H10 Fab heavy chain
    • Protein or peptide: c44H10 Fab light chain
    • Protein or peptide: Class-II-associated invariant chain peptide
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscomplex / engineered protein / IMMUNE SYSTEM
Function / homology
Function and homology information


negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization ...negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / T cell activation involved in immune response / autolysosome membrane / positive regulation of prostaglandin biosynthetic process / regulation of T-helper cell differentiation / T cell selection / positive regulation of type 2 immune response / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / host-mediated suppression of symbiont invasion / MHC class II receptor activity / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell activation / MHC class II protein binding / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of mature B cell apoptotic process / positive regulation of kinase activity / positive regulation of memory T cell differentiation / CD4 receptor binding / positive regulation of monocyte differentiation / positive thymic T cell selection / vacuole / cytokine receptor activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / positive regulation of T cell differentiation / regulation of macrophage activation / nitric-oxide synthase binding / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / antigen processing and presentation / Translocation of ZAP-70 to Immunological synapse / cytokine binding / Phosphorylation of CD3 and TCR zeta chains / negative regulation of DNA damage response, signal transduction by p53 class mediator / polysaccharide binding / immunoglobulin mediated immune response / : / Generation of second messenger molecules / immunological synapse / response to type II interferon / Co-inhibition by PD-1 / T cell receptor binding / positive regulation of chemokine production / positive regulation of B cell proliferation / multivesicular body / protein folding chaperone / MHC class II antigen presentation / lysosomal lumen / negative regulation of cell migration / trans-Golgi network membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / intracellular protein transport / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / positive regulation of interleukin-6 production / positive regulation of T cell activation / cognition / positive regulation of fibroblast proliferation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / late endosome / Downstream TCR signaling / amyloid-beta binding / positive regulation of protein phosphorylation / protein-containing complex assembly / early endosome membrane / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / protein stabilization / endosome membrane / immune response
Similarity search - Function
Mycoplasma arthritidis-derived mitogen / Superantigen MAM / Mycoplasma arthritidis-derived mitogen, C-terminal / Mycoplasma arthritidis-derived mitogen / MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain ...Mycoplasma arthritidis-derived mitogen / Superantigen MAM / Mycoplasma arthritidis-derived mitogen, C-terminal / Mycoplasma arthritidis-derived mitogen / MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
HLA class II histocompatibility antigen DR beta chain / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen gamma chain / Superantigen
Similarity search - Component
Biological speciesHomo sapiens (human) / Metamycoplasma arthritidis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsJude KM / Yang X / Du H / Kassardjian A / Julien J-P / Huang P / Garcia KC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)r01gm147893 United States
CitationJournal: Nat Biotechnol / Year: 2024
Title: A general system for targeting MHC class II-antigen complex via a single adaptable loop.
Authors: Haotian Du / Jingjia Liu / Kevin M Jude / Xinbo Yang / Ying Li / Braxton Bell / Hongli Yang / Audrey Kassardjian / Wyatt Blackson / Ali Mobedi / Udit Parekh / R Andres Parra Sperberg / Jean- ...Authors: Haotian Du / Jingjia Liu / Kevin M Jude / Xinbo Yang / Ying Li / Braxton Bell / Hongli Yang / Audrey Kassardjian / Wyatt Blackson / Ali Mobedi / Udit Parekh / R Andres Parra Sperberg / Jean-Philippe Julien / Elizabeth D Mellins / K Christopher Garcia / Po-Ssu Huang /
Abstract: Major histocompatibility complex class II (MHCII) bound to a peptide antigen mediates interactions between CD4 T cells and antigen-presenting cells. Targeting peptide-MHCII with T cell antigen ...Major histocompatibility complex class II (MHCII) bound to a peptide antigen mediates interactions between CD4 T cells and antigen-presenting cells. Targeting peptide-MHCII with T cell antigen receptors (TCRs) and TCR-like antibodies has shown promise for autoimmune diseases and microbiome tolerance. To develop a general targeting approach, we introduce targeted recognition of antigen-MHC complex reporter for MHCII (TRACeR-II) for the rapid development of peptide-specific MHCII binders. TRACeR-II binders have a small helical bundle scaffold and use a single loop to recognize peptide-MHCII, which offers versatility and enables structural modeling of the interactions to target MHCII antigens. We demonstrate rapid generation of TRACeR-II binders to multiple molecules with affinities in the low-nanomolar to low-micromolar range, comparable to best-in-class TCRs and antibodies. Through computational protein design, we created specific binding sequences in silico from only the sequence of a severe acute respiratory syndrome coronavirus 2 peptide. TRACeR-II provides a straightforward approach to target antigen-MHCII without relying on combinatorial selection on complementarity-determining region loops.
History
DepositionJan 24, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43499.png

Downloads & links

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Map

FileDownload / File: emd_43499.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 320 pix.
= 237.76 Å		0.74 Å/pix.
x 320 pix.
= 237.76 Å		0.74 Å/pix.
x 320 pix.
= 237.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0767
Minimum - Maximum-0.28634056 - 0.5309422
Average (Standard dev.)-0.0003951363 (±0.009823044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 237.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43499_msk_1.map
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Additional map: DeepEMHancer sharpened map used for interactive rebuilding of model

Fileemd_43499_additional_1.map
AnnotationDeepEMHancer sharpened map used for interactive rebuilding of model
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Additional map: phenix autosharpened map used in real space refinement of model

Fileemd_43499_additional_2.map
Annotationphenix autosharpened map used in real space refinement of model
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Half map: #1

Fileemd_43499_half_map_1.map
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Half map: #2

Fileemd_43499_half_map_2.map
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Sample components

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Entire : Engineered peptide-specific binder in complex with HLA-DR1/CLIP

EntireName: Engineered peptide-specific binder in complex with HLA-DR1/CLIP
Components
  • Complex: Engineered peptide-specific binder in complex with HLA-DR1/CLIP
    • Protein or peptide: HLA class II histocompatibility antigen, DR alpha chain
    • Protein or peptide: HLA class II histocompatibility antigen DR beta chain
    • Protein or peptide: Superantigen
    • Protein or peptide: c44H10 Fab heavy chain
    • Protein or peptide: c44H10 Fab light chain
    • Protein or peptide: Class-II-associated invariant chain peptide
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Engineered peptide-specific binder in complex with HLA-DR1/CLIP

SupramoleculeName: Engineered peptide-specific binder in complex with HLA-DR1/CLIP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: HLA class II histocompatibility antigen, DR alpha chain

MacromoleculeName: HLA class II histocompatibility antigen, DR alpha chain
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.400178 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IKEEHVIIQA EFYLNPDQSG EFMFDFDGDE IFHVDMAKKE TVWRLEEFGR FASFEAQGAL ANIAVDKANL EIMTKRSNYT PITNVPPEV TVLTNSPVEL REPNVLICFI DKFTPPVVNV TWLRNGKPVT TGVSETVFLP REDHLFRKFH YLPFLPSTED V YDCRVEHW GLDEPLLKHW EFDASR

UniProtKB: HLA class II histocompatibility antigen, DR alpha chain

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Macromolecule #2: HLA class II histocompatibility antigen DR beta chain

MacromoleculeName: HLA class II histocompatibility antigen DR beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.324938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDTRPRFLWQ LKFECHFFNG TERVRLLERC IYNQEESVRF DSDVGEYRAV TELGRPDAEY WNSQKDLLEQ RRAAVDTYCR HNYGVGESF TVQRRVEPKV TVYPSKTQPL QHHNLLVCSV SGFYPGSIEV RWFRNGQEEK AGVVSTGLIQ NGDWTFQTLV M LETVPRSG ...String:
GDTRPRFLWQ LKFECHFFNG TERVRLLERC IYNQEESVRF DSDVGEYRAV TELGRPDAEY WNSQKDLLEQ RRAAVDTYCR HNYGVGESF TVQRRVEPKV TVYPSKTQPL QHHNLLVCSV SGFYPGSIEV RWFRNGQEEK AGVVSTGLIQ NGDWTFQTLV M LETVPRSG EVYTCQVEHP SVTSPLTVEW RASR

UniProtKB: HLA class II histocompatibility antigen DR beta chain

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Macromolecule #3: Superantigen

MacromoleculeName: Superantigen / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Metamycoplasma arthritidis (bacteria)
Molecular weightTheoretical: 15.544818 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKLRCENPKK ASIYLAQNLN NVVFTNKELE DIYDLSNKEE TKEVLKKFKE KVNQFYRHAF DIINKYGDKE VFNMMFLKLS VVFDIQRKE ANNVEQIKRN IATLDEIMAK ADNDLCYFIS QWLEHHHHHH

UniProtKB: Superantigen

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Macromolecule #4: c44H10 Fab heavy chain

MacromoleculeName: c44H10 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.668643 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLKESGPG LVAPSQSLSI TCTVSGFSLT SYGVHWVRQP PGKGLEWLGV IWAGGSINYN SALMSRLSIS KDNFKSQVFL KMSSLQTDD TAMYYCARAY GDYVHYAMDY WGQGTSVTAS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
QVQLKESGPG LVAPSQSLSI TCTVSGFSLT SYGVHWVRQP PGKGLEWLGV IWAGGSINYN SALMSRLSIS KDNFKSQVFL KMSSLQTDD TAMYYCARAY GDYVHYAMDY WGQGTSVTAS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSC

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Macromolecule #5: c44H10 Fab light chain

MacromoleculeName: c44H10 Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.505068 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASLGQRVS LTCRASQEIS GYLTWLQQKP DGTIKRLVYA ASTLDSGVPK RFSGSRSGSD YSLTISSLES EDFADYYCL QYTNYPLTFG AGTKLELKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASLGQRVS LTCRASQEIS GYLTWLQQKP DGTIKRLVYA ASTLDSGVPK RFSGSRSGSD YSLTISSLES EDFADYYCL QYTNYPLTFG AGTKLELKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #6: Class-II-associated invariant chain peptide

MacromoleculeName: Class-II-associated invariant chain peptide / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.676118 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PVSKMRMATP LLMQA

UniProtKB: HLA class II histocompatibility antigen gamma chain

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
0.15 MNaClsodium chloride
0.01 MHEPES
0.01 %fluorinated octylmaltoside
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00039000000000000005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 21332 / Average electron dose: 60.0 e/Å2 / Details: eer images
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 18639350 / Details: template based picks
Startup modelType of model: OTHER / Details: ab initio model calculated in cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3706646
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 2
FSC plot (resolution estimation)

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