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- PDB-3cvh: How TCR-like antibody recognizes MHC-bound peptide -

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Basic information

Entry
Database: PDB / ID: 3cvh
TitleHow TCR-like antibody recognizes MHC-bound peptide
Components
  • 25-D1.16 heavy chain
  • 25-D1.16 light chain
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • Ovalbumin
KeywordsIMMUNE SYSTEM / MHC / TCR / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Allergen / Phosphoprotein / Secreted / Immunoglobulin domain
Function / homology
Function and homology information


intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / embryo development ending in birth or egg hatching / DAP12 signaling ...intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / embryo development ending in birth or egg hatching / DAP12 signaling / response to steroid hormone / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to corticosterone / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / monoatomic ion transport / phagocytic vesicle / Neutrophil degranulation / early endosome lumen / response to progesterone / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / 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 / MHC class I protein complex / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / response to estrogen / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protease binding / protein homotetramerization / vesicle / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / intracellular membrane-bounded organelle / calcium ion binding / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / cytosol
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / MHC class I, alpha chain, C-terminal ...Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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
Ovalbumin / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsMareeva, T. / Martinez-Hackert, E. / Sykulev, Y.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: How a T cell receptor-like antibody recognizes major histocompatibility complex-bound peptide
Authors: Mareeva, T. / Martinez-Hackert, E. / Sykulev, Y.
History
DepositionApr 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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, K-B alpha chain
B: Beta-2-microglobulin
C: Ovalbumin
H: 25-D1.16 heavy chain
L: 25-D1.16 light chain
M: H-2 class I histocompatibility antigen, K-B alpha chain
N: Beta-2-microglobulin
O: Ovalbumin
Q: 25-D1.16 heavy chain
R: 25-D1.16 light chain


Theoretical massNumber of molelcules
Total (without water)181,90610
Polymers181,90610
Non-polymers00
Water3,171176
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: Ovalbumin
H: 25-D1.16 heavy chain
L: 25-D1.16 light chain


Theoretical massNumber of molelcules
Total (without water)90,9535
Polymers90,9535
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: H-2 class I histocompatibility antigen, K-B alpha chain
N: Beta-2-microglobulin
O: Ovalbumin
Q: 25-D1.16 heavy chain
R: 25-D1.16 light chain


Theoretical massNumber of molelcules
Total (without water)90,9535
Polymers90,9535
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.570, 111.345, 219.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules AMBN

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H- 2KB


Mass: 31648.322 Da / Num. of mol.: 2 / Fragment: sequence database residues 21-295 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01887

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Antibody , 2 types, 4 molecules HQLR

#4: Antibody 25-D1.16 heavy chain


Mass: 23534.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: Antibody 25-D1.16 light chain


Mass: 23101.502 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Protein/peptide / Non-polymers , 2 types, 178 molecules CO

#3: Protein/peptide Ovalbumin / Egg albumin / Plakalbumin / Allergen Gal d 2 / Allergen Gal d II


Mass: 964.137 Da / Num. of mol.: 2 / Fragment: sequence database residues 258-265 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P01012
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / pH: 4.6
Details: 0.2 M (NH4)2SO4, 0.1 M NaOAc, pH 4.6 containing 25% w/v polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97925
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 48272 / % possible obs: 97.6 %
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.429 / % possible all: 95

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.9 Å49.63 Å
Translation2.9 Å49.63 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3CVI AND 2VAA

3cvi

2vaa


Resolution: 2.9→19.98 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.84 / SU B: 39.639 / SU ML: 0.38 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.487 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2203 5.1 %RANDOM
Rwork0.219 ---
obs0.223 41343 100 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 42.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12710 0 0 176 12886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02213062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.94717789
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56951591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45523.986582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.148152122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3651568
X-RAY DIFFRACTIONr_chiral_restr0.0710.21926
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.25487
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.28622
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2476
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3531.58204
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.617212989
X-RAY DIFFRACTIONr_scbond_it0.7735677
X-RAY DIFFRACTIONr_scangle_it1.3264.54800
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 158 -
Rwork0.287 2948 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5757-0.12860.6141.99350.00480.7464-0.0221-0.0264-0.0071-0.02930.00630.0421-0.09480.00970.0158-0.04740.00620.0063-0.0162-0.03150.0119-11.175-30.98921.497
21.85060.3039-0.99141.3143-0.80662.62870.11430.0028-0.0462-0.1292-0.01650.0088-0.0718-0.3234-0.0978-0.07260.0337-0.02410.1081-0.0992-0.0965-24.025-10.15164.425
30.467-0.745-0.07111.2362-0.12651.2127-0.0585-0.08130.0866-0.08740.05060.06740.15590.08340.00790.0051-0.01180.0012-0.0066-0.0207-0.0221-4.665-57.37615.041
42.0598-0.0806-0.88483.0456-0.30222.59060.032-0.11750.2852-0.1403-0.00370.0125-0.512-0.1714-0.0283-0.01880.2785-0.01630.3133-0.1503-0.0642-33.24115.49469.953
50.5151-0.3629-0.22380.6030.27371.1729-0.0913-0.0286-0.10490.02690.0521-0.0665-0.1097-0.04510.0392-0.02230.05450.00930.0169-0.0109-0.013520.149-81.584.016
62.71521.0662-0.81633.87281.7557.21270.14150.11610.3231-0.4527-0.04260.2766-0.2430.4683-0.09890.54250.13640.14170.354-0.12140.521-26.35546.30685.391
72.7324-1.24410.42464.1449-0.85937.1419-0.0734-0.24970.1560.23030.15580.2943-1.1142-0.7602-0.08240.19430.1287-0.0078-0.0012-0.0912-0.0434-18.0344.23533.477
82.76740.4272-0.67555.90722.05796.4026-0.2413-0.0556-0.21290.0464-0.16690.30481.1832-0.21360.40810.23910.01050.08630.0513-0.0787-0.1865-7.85-43.13653.562
91.18520.60560.52955.1903-0.8030.6178-0.02890.1161-0.0843-0.09620.10990.1152-0.08510.2024-0.0810.03510.02330.0033-0.0438-0.017-0.0614-13.679-3.64112.425
103.3744-1.60930.86442.6282-0.81072.81540.12420.034-0.04450.1458-0.20280.21690.53650.07730.07860.1507-0.06750.0152-0.0095-0.0846-0.1975-14.756-35.72174.451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1801 - 180
2X-RAY DIFFRACTION1CC1 - 81 - 8
3X-RAY DIFFRACTION2MF1 - 1791 - 179
4X-RAY DIFFRACTION2OH1 - 81 - 8
5X-RAY DIFFRACTION3HD1 - 1191 - 119
6X-RAY DIFFRACTION3LE1 - 1071 - 107
7X-RAY DIFFRACTION4QI1 - 1191 - 119
8X-RAY DIFFRACTION4RJ1 - 1071 - 107
9X-RAY DIFFRACTION5HD120 - 213120 - 213
10X-RAY DIFFRACTION5LE108 - 209108 - 209
11X-RAY DIFFRACTION6QI120 - 213120 - 213
12X-RAY DIFFRACTION6RJ108 - 209108 - 209
13X-RAY DIFFRACTION7AA181 - 274181 - 274
14X-RAY DIFFRACTION8MF181 - 274181 - 274
15X-RAY DIFFRACTION9BB1 - 991 - 99
16X-RAY DIFFRACTION10NG1 - 991 - 99

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