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

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Basic information

Entry
Database: PDB / ID: 8tnj
TitleCryo-EM structure of HLA-B*73:01 bound to a 9mer peptide and two Fabs
Components
  • 9mer peptide,Beta-2-microglobulin,MHC class I antigen chimera
  • B.1 Fab heavy chain
  • B.1 Fab light chain
  • B.8 Fab heavy chain
  • B.8 Fab light chain
KeywordsIMMUNE SYSTEM / HLA / MHC / FAB
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRoss, P. / Adams, E.J. / Lodwick, J. / Zhao, M. / Slezak, T. / Kossiakoff, A.
Funding support United States, 1items
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, E.J.
History
DepositionAug 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 9mer peptide,Beta-2-microglobulin,MHC class I antigen chimera
C: B.8 Fab light chain
D: B.8 Fab heavy chain
E: B.1 Fab heavy chain
F: B.1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)146,1365
Polymers146,1365
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 49165.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, HLA-B / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61771, UniProt: A0A583ZBV1
#2: Antibody B.8 Fab light chain


Mass: 23523.064 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)
#3: Antibody B.8 Fab heavy chain


Mass: 24684.623 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)
#4: Antibody B.1 Fab heavy chain


Mass: 25284.029 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)
#5: Antibody B.1 Fab light chain


Mass: 23478.066 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)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of B.1 and B.8 Fabs with single-chain P2R-B2M-HLA-B*73:01
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2 / Details: 10 mM HEPES 150 mM NaCl 0.02% sodium azide pH 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESHEPES1
2150 mMSodium chlorideNaCl1
30.02 PercentSodium azideNaN31
41
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono-disperse
Specimen supportDetails: 10 seconds at 20 watts using Solarus 950 Plasma Cleaner System (Gatan)
Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
7UCSF ChimeraX1.5model fitting
13PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 502247 / Details: Masked / Symmetry type: POINT
Atomic model buildingB value: 86.65 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: EMRinger
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18TMU

8tmu

18TMU1PDBexperimental model
21AlphaFoldin silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038284
ELECTRON MICROSCOPYf_angle_d0.48511282
ELECTRON MICROSCOPYf_dihedral_angle_d4.5851138
ELECTRON MICROSCOPYf_chiral_restr0.0421222
ELECTRON MICROSCOPYf_plane_restr0.0041452

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