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- PDB-8tq8: Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd) -

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Basic information

Entry
Database: PDB / ID: 8tq8
TitleCrystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd)
Components
  • Beta-2-microglobulin
  • Fab.34.5.8 Heavy chain
  • Fab.34.5.8 Light chain
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Transmembrane protein gp41
KeywordsIMMUNE SYSTEM / histocompatibility complex class I / MHC-I / immune response / immune system Fab / antibody / anti-MHC antibody / cancer tumor
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Binding and entry of HIV virion / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / Neutrophil degranulation / actin filament organization / host cell endosome membrane / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / Assembly Of The HIV Virion / 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 / Budding and maturation of HIV virion / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / 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 / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsJiang, J. / Boyd, L.F. / Natarajan, K. / Margulies, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J Immunol. / Year: 2024
Title: Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction.
Authors: Boyd, L.F. / Jiang, J. / Ahmad, J. / Natarajan, K. / Margulies, D.H.
History
DepositionAug 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 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: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
P: Transmembrane protein gp41
H: Fab.34.5.8 Heavy chain
L: Fab.34.5.8 Light chain
C: H-2 class I histocompatibility antigen, D-D alpha chain
D: Beta-2-microglobulin
E: Transmembrane protein gp41
F: Fab.34.5.8 Heavy chain
G: Fab.34.5.8 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,91018
Polymers184,26410
Non-polymers6478
Water2,216123
1
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
P: Transmembrane protein gp41
H: Fab.34.5.8 Heavy chain
L: Fab.34.5.8 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4709
Polymers92,1325
Non-polymers3384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: H-2 class I histocompatibility antigen, D-D alpha chain
D: Beta-2-microglobulin
E: Transmembrane protein gp41
F: Fab.34.5.8 Heavy chain
G: Fab.34.5.8 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4409
Polymers92,1325
Non-polymers3084
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.087, 50.892, 224.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein H-2 class I histocompatibility antigen, D-D alpha chain / MHC-I H2-Dd A chain


Mass: 31819.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01900
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2 / Mutation: A85D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Gene: B2m / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887

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Protein/peptide , 1 types, 2 molecules PE

#3: Protein/peptide Transmembrane protein gp41 / TM / Glycoprotein 41 / gp41


Mass: 1075.265 Da / Num. of mol.: 2 / Fragment: HV1: HIV-1 P18-I10 (UNP residues 311-320) / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578

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Antibody , 2 types, 4 molecules HFLG

#4: Antibody Fab.34.5.8 Heavy chain


Mass: 23325.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): 34.5.8 / Production host: Mus musculus (house mouse)
#5: Antibody Fab.34.5.8 Light chain


Mass: 24207.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): 34.5.8 / Production host: Mus musculus (house mouse)

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Non-polymers , 3 types, 131 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18% PEG4000, 0.1 M MES, pH 6.0, 0.12 M calcium acetate

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→87.09 Å / Num. obs: 54120 / % possible obs: 97.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 57.76 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.085 / Net I/σ(I): 7.6
Reflection shellResolution: 2.69→2.8 Å / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5458 / CC1/2: 0.565 / CC star: 0.85 / Rpim(I) all: 0.455 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WEU

5weu


Resolution: 2.69→87.09 Å / Cross valid method: FREE R-VALUE / σ(F): 154.07 / Phase error: 23.426
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2425 2738 5.06 %
Rwork0.2009 51382 -
obs0.2085 54120 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.4 Å2
Refinement stepCycle: LAST / Resolution: 2.69→87.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12393 0 42 123 12558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004512760
X-RAY DIFFRACTIONf_angle_d0.755917359
X-RAY DIFFRACTIONf_chiral_restr0.04791856
X-RAY DIFFRACTIONf_plane_restr0.0062255
X-RAY DIFFRACTIONf_dihedral_angle_d18.4294543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.740.34351320.30282480X-RAY DIFFRACTION86.05
2.74-2.790.36431430.28452753X-RAY DIFFRACTION94.18
2.79-2.850.31661390.28332634X-RAY DIFFRACTION92.55
2.85-2.910.2621410.26412730X-RAY DIFFRACTION94.07
2.91-2.980.28871440.26112728X-RAY DIFFRACTION93.49
2.98-3.060.35151320.26072501X-RAY DIFFRACTION86.99
3.06-3.140.30081440.24912728X-RAY DIFFRACTION94.13
3.14-3.230.29191450.24172708X-RAY DIFFRACTION93.54
3.23-3.340.26371440.23222735X-RAY DIFFRACTION94.51
3.34-3.450.23611430.21842720X-RAY DIFFRACTION93.6
3.46-3.590.26311450.20742769X-RAY DIFFRACTION94.51
3.59-3.760.24711420.19632695X-RAY DIFFRACTION93.54
3.76-3.950.23651440.18872769X-RAY DIFFRACTION93.39
3.95-4.20.20211460.17822733X-RAY DIFFRACTION93.44
4.2-4.530.2181340.16592568X-RAY DIFFRACTION88.37
4.53-4.980.21911450.16692752X-RAY DIFFRACTION93.83
4.98-5.70.24131460.1752790X-RAY DIFFRACTION93.62
5.7-7.180.25621490.21222814X-RAY DIFFRACTION94.08
7.19-87.090.21361480.21142807X-RAY DIFFRACTION90.61

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