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- PDB-7bh8: 3H4-Fab HLA-E-VL9 co-complex -

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Basic information

Entry
Database: PDB / ID: 7bh8
Title3H4-Fab HLA-E-VL9 co-complex
Components
  • 3H4 Fab heavy chain
  • 3H4 Fab light chain
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain E
  • VL9 leader peptide
KeywordsIMMUNE SYSTEM / Antibody Fab Fragment MHC class I molecule Human leukocyte antigen E
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / beta-2-microglobulin binding / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / negative regulation of T cell proliferation / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / MHC class II protein complex / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / innate immune response
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWalters, L.C. / Rozbesky, D.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1133649 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/M019837/1 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5UM1AI12661905 United Kingdom
CitationJournal: Commun Biol / Year: 2022
Title: Mouse and human antibodies bind HLA-E-leader peptide complexes and enhance NK cell cytotoxicity.
Authors: Li, D. / Brackenridge, S. / Walters, L.C. / Swanson, O. / Harlos, K. / Rozbesky, D. / Cain, D.W. / Wiehe, K. / Scearce, R.M. / Barr, M. / Mu, Z. / Parks, R. / Quastel, M. / Edwards, R.J. / ...Authors: Li, D. / Brackenridge, S. / Walters, L.C. / Swanson, O. / Harlos, K. / Rozbesky, D. / Cain, D.W. / Wiehe, K. / Scearce, R.M. / Barr, M. / Mu, Z. / Parks, R. / Quastel, M. / Edwards, R.J. / Wang, Y. / Rountree, W. / Saunders, K.O. / Ferrari, G. / Borrow, P. / Jones, E.Y. / Alam, S.M. / Azoitei, M.L. / Gillespie, G.M. / McMichael, A.J. / Haynes, B.F.
History
DepositionJan 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, alpha chain E
D: Beta-2-microglobulin
G: 3H4 Fab heavy chain
H: 3H4 Fab light chain
E: 3H4 Fab heavy chain
F: 3H4 Fab light chain
P: VL9 leader peptide
Q: VL9 leader peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,89021
Polymers192,92910
Non-polymers96111
Water21,1141172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23370 Å2
ΔGint-124 kcal/mol
Surface area72980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.433, 73.695, 159.727
Angle α, β, γ (deg.)90.000, 101.632, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E


Mass: 31824.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules PQ

#5: Protein/peptide VL9 leader peptide


Mass: 1000.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Antibody , 2 types, 4 molecules GEHF

#3: Antibody 3H4 Fab heavy chain


Mass: 26090.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Antibody 3H4 Fab light chain


Mass: 25670.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 1183 molecules

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


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1172 / 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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 8000, 0.1 M NA HEPES

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Data collection

DiffractionMean temperature: 293.5 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→54.74 Å / Num. obs: 196943 / % possible obs: 98.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 36.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 1.289 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 9653 / CC1/2: 0.724

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
DIALSdata scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GH4, 6HGU

6gh4

6hgu


Resolution: 1.8→54.74 Å / SU ML: 0.302 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2392
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2321 9845 5 %
Rwork0.1954 186976 -
obs0.1972 196821 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→54.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12839 0 61 1172 14072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004513220
X-RAY DIFFRACTIONf_angle_d0.683217946
X-RAY DIFFRACTIONf_chiral_restr0.04861929
X-RAY DIFFRACTIONf_plane_restr0.00472308
X-RAY DIFFRACTIONf_dihedral_angle_d15.88324801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.48863160.45366076X-RAY DIFFRACTION96.53
1.82-1.840.40143120.41876161X-RAY DIFFRACTION96.97
1.84-1.860.40312910.38026109X-RAY DIFFRACTION96.82
1.86-1.890.39393110.35676190X-RAY DIFFRACTION96.94
1.89-1.910.3333510.31956019X-RAY DIFFRACTION97.04
1.91-1.940.343280.29366223X-RAY DIFFRACTION97.18
1.94-1.970.31563410.27176088X-RAY DIFFRACTION97.36
1.97-20.30063010.25626256X-RAY DIFFRACTION97.4
2-2.030.26843420.24396096X-RAY DIFFRACTION97.4
2.03-2.060.29983430.24386120X-RAY DIFFRACTION97.57
2.06-2.10.28833340.23836201X-RAY DIFFRACTION97.64
2.1-2.130.25873260.22476200X-RAY DIFFRACTION97.71
2.13-2.180.25023160.22826210X-RAY DIFFRACTION97.83
2.18-2.220.26553150.21816226X-RAY DIFFRACTION97.93
2.22-2.270.25983360.21226174X-RAY DIFFRACTION97.98
2.27-2.320.25723590.20826210X-RAY DIFFRACTION98.03
2.32-2.380.27143000.21056265X-RAY DIFFRACTION98.25
2.38-2.440.25853110.20756213X-RAY DIFFRACTION98.27
2.44-2.510.27893110.21016255X-RAY DIFFRACTION98.38
2.51-2.60.24783320.20526242X-RAY DIFFRACTION98.44
2.6-2.690.2573520.20696257X-RAY DIFFRACTION98.64
2.69-2.80.253220.2056262X-RAY DIFFRACTION98.64
2.8-2.920.24493420.20156327X-RAY DIFFRACTION98.76
2.92-3.080.23313410.19826273X-RAY DIFFRACTION98.88
3.08-3.270.25563470.19376255X-RAY DIFFRACTION99.01
3.27-3.520.22993070.19036407X-RAY DIFFRACTION99.1
3.52-3.880.20233560.17476314X-RAY DIFFRACTION99.26
3.88-4.440.17783380.15926377X-RAY DIFFRACTION99.36
4.44-5.590.16393320.14146411X-RAY DIFFRACTION99.47
5.59-54.740.21913320.18096559X-RAY DIFFRACTION99.24

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