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- EMDB-41418: Cryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs -

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Basic information

Entry
Database: EMDB / ID: EMD-41418
TitleCryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs
Map data
Sample
  • Complex: Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA-B*73:01
    • Protein or peptide: 9mer peptide,Beta-2-microglobulin,MHC class I antigen chimera
    • Protein or peptide: B.8 Fab light chain
    • Protein or peptide: B.8 Fab heavy chain
    • Protein or peptide: B.1 Fab heavy chain
    • Protein or peptide: B.1 Fab light chain
KeywordsHLA / MHC / FAB / IMMUNE SYSTEM
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / 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 / iron ion transport / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex ...antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / 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 / iron ion transport / 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 / phagocytic vesicle membrane / recycling endosome membrane / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / structural molecule activity / cell surface / Golgi apparatus / protein homodimerization activity / extracellular region / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / MHC classes I/II-like antigen recognition protein / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / 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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRoss P / Adams EJ / Lodwick J / Zhao M / Slezak T / Kossiakoff A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs
Authors: Ross P / Adams EJ
History
DepositionAug 2, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41418.png

Downloads & links

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Map

FileDownload / File: emd_41418.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 272.64 Å		1.07 Å/pix.
x 256 pix.
= 272.64 Å		1.07 Å/pix.
x 256 pix.
= 272.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0980219 - 0.17654131
Average (Standard dev.)0.00012115361 (±0.0025173498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41418_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41418_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41418_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA...

EntireName: Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA-B*73:01
Components
  • Complex: Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA-B*73:01
    • Protein or peptide: 9mer peptide,Beta-2-microglobulin,MHC class I antigen chimera
    • Protein or peptide: B.8 Fab light chain
    • Protein or peptide: B.8 Fab heavy chain
    • Protein or peptide: B.1 Fab heavy chain
    • Protein or peptide: B.1 Fab light chain

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Supramolecule #1: Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA...

SupramoleculeName: Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA-B*73:01
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 9mer peptide,Beta-2-microglobulin,MHC class I antigen chimera

MacromoleculeName: 9mer peptide,Beta-2-microglobulin,MHC class I antigen chimera
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.165848 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: NRFLGDYVVG GGGSGGGGSG GGGSIQRTPK IQVYSRHPAE NGKSNFLNCY VSGFHPSDIE VDLLKNGERI EKVEHSDLSF SKDWSFYLL YYTEFTPTEK DEYACRVNHV TLSQPKIVKW DRDMGGGGSG GGGSGGGGSG GGGSGSHSMR YFHTSVSRPG R GEPRFITV ...String:
NRFLGDYVVG GGGSGGGGSG GGGSIQRTPK IQVYSRHPAE NGKSNFLNCY VSGFHPSDIE VDLLKNGERI EKVEHSDLSF SKDWSFYLL YYTEFTPTEK DEYACRVNHV TLSQPKIVKW DRDMGGGGSG GGGSGGGGSG GGGSGSHSMR YFHTSVSRPG R GEPRFITV GYVDDTQFVR FDSDAASPRE EPRAPWIEQE GPEYWDRNTQ ICKAKAQTDR VGLRNLRGYY NQSEDGSHTW QT MYGCDMG PDGRLLRGYN QFAYDGKDYI ALNEDLRSWT AADTAAQITQ RKWEAARVAE QLRAYLEGEC VEWLRRHLEN GKE TLQRAD PPKTHVTHHP ISDHEATLRC WALGFYPAEI TLTWQRDGED QTQDTELVET RPAGDGTFQK WAAVVVPSGQ EQRY TCHVQ HEGLQEPLTL RWKPGGSGLE VLFQGPHHHH HHHH

UniProtKB: Beta-2-microglobulin, MHC class I antigen

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Macromolecule #2: B.8 Fab light chain

MacromoleculeName: B.8 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.523064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSWSAYPFT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSWSAYPFT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #3: B.8 Fab heavy chain

MacromoleculeName: B.8 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.684623 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSYSIHWV RQAPGKGLEW VASISPYSGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARLIFYMWSS AMDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSSYSIHWV RQAPGKGLEW VASISPYSGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARLIFYMWSS AMDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD KTHT

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Macromolecule #4: B.1 Fab heavy chain

MacromoleculeName: B.1 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.284029 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSYYSIHWV RQAPGKGLEW VASISPYSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYSYGNSWS YDPYYGAMDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSYYSIHWV RQAPGKGLEW VASISPYSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYSYGNSWS YDPYYGAMDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTHT

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Macromolecule #5: B.1 Fab light chain

MacromoleculeName: B.1 Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.478066 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYYWAPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYYWAPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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

Concentration0.6 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
10.0 mMHEPESHEPES
150.0 mMNaClSodium chloride
0.02 PercentNaN3Sodium azide

Details: 10 mM HEPES 150 mM NaCl 0.02% sodium azide pH 7.2
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
Details: 10 seconds at 20 watts using Solarus 950 Plasma Cleaner System (Gatan)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was mono-disperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Masked / Number images used: 502247
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8tmu

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 86.65 / Target criteria: EMRinger
Output model

PDB-8tnj:
Cryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs

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