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- PDB-4mvb: 42F3 pCPB7/H-2Ld Complex -

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Basic information

Entry
Database: PDB / ID: 4mvb
Title42F3 pCPB7/H-2Ld Complex
Components
  • 42F3 alpha VmCh
  • 42F3 beta VmCh
  • H-2 class I histocompatibility antigen, L-D alpha chain
  • pCPB7
KeywordsIMMUNE SYSTEM / Ig / TCR / MHC
Function / homology
Function and homology information


MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / T cell receptor complex / TAP complex binding / Golgi medial cisterna / CD8 receptor binding / beta-2-microglobulin binding ...MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / T cell receptor complex / TAP complex binding / Golgi medial cisterna / CD8 receptor binding / beta-2-microglobulin binding / endoplasmic reticulum exit site / MHC class I protein binding / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I peptide loading complex / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / phagocytic vesicle membrane / protein-folding chaperone binding / early endosome membrane / adaptive immune response / early endosome / cell surface receptor signaling pathway / immune response / receptor ligand activity / Golgi membrane / signaling receptor binding / external side of plasma membrane / lysosomal membrane / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / : / identical protein binding / plasma membrane
Similarity search - Function
: / Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / : ...: / Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
T cell receptor beta, variable 13-1 / T-cell receptor alpha chain V region PHDS58 / H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.088 Å
AuthorsBirnbaum, M.E. / Adams, J.J. / Garcia, K.C.
CitationJournal: Nat. Immunol. / Year: 2016
Title: Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.
Authors: Adams, J.J. / Narayanan, S. / Birnbaum, M.E. / Sidhu, S.S. / Blevins, S.J. / Gee, M.H. / Sibener, L.V. / Baker, B.M. / Kranz, D.M. / Garcia, K.C.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 42F3 alpha VmCh
D: 42F3 beta VmCh
A: H-2 class I histocompatibility antigen, L-D alpha chain
B: pCPB7


Theoretical massNumber of molelcules
Total (without water)72,6934
Polymers72,6934
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.799, 60.402, 69.652
Angle α, β, γ (deg.)90.00, 97.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 42F3 alpha VmCh


Mass: 23383.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: UniProt: P01738*PLUS
#2: Protein 42F3 beta VmCh


Mass: 27248.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: UniProt: A0A075B5I3*PLUS
#3: Protein H-2 class I histocompatibility antigen, L-D alpha chain


Mass: 21115.303 Da / Num. of mol.: 1 / Fragment: UNP residues 25-203 / Mutation: F8Y, V12T, P15R, I23T, N30D, A49V, K131R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Escherichia coli (E. coli) / References: UniProt: P01897
#4: Protein/peptide pCPB7


Mass: 946.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 100mM BIS-TRIS pH 5.5 and 200mM ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 13152 / Num. obs: 11969 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5
Reflection shellResolution: 3.1→3.15 Å / % possible all: 80.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.088→34.489 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 35.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 587 4.91 %random
Rwork0.231 ---
all0.2334 13304 --
obs0.2334 11956 89.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.088→34.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 0 0 4920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025055
X-RAY DIFFRACTIONf_angle_d0.6256860
X-RAY DIFFRACTIONf_dihedral_angle_d12.8981806
X-RAY DIFFRACTIONf_chiral_restr0.047714
X-RAY DIFFRACTIONf_plane_restr0.002899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.088-3.39850.37041260.30952554X-RAY DIFFRACTION81
3.3985-3.88960.28641430.26622880X-RAY DIFFRACTION92
3.8896-4.89830.26421660.21592918X-RAY DIFFRACTION93
4.8983-34.49120.26171520.20583017X-RAY DIFFRACTION93
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)
15.65940.3708-0.636.16020.8195.42140.48730.32660.18060.28670.10520.8708-0.5315-0.4089-0.43820.61770.07-0.01860.56680.09010.579244.1222-16.493710.2627
20.93710.30980.5270.11510.19080.5375-0.32350.0251-0.56891.4268-0.0347-0.47170.37241.14140.35881.2068-0.20270.18550.8068-0.03690.628156.1479-19.990612.2567
38.7018-2.5505-4.21985.1828-1.64573.9253-0.26360.9792-0.6080.86240.0940.49491.9565-1.2613-0.06530.9644-0.2702-0.0190.7257-0.21320.586451.1426-25.08810.0596
45.0034-0.2698-2.08794.01581.53493.91350.00420.1065-0.4311-0.062-0.3-0.52840.3507-0.20460.24250.5693-0.0201-0.0340.5105-0.04980.638946.6345-16.126611.944
53.27213.5685-3.95823.7768-4.22434.49450.2799-2.23380.9509-0.3703-0.18451.77191.53521.3570.30911.0195-0.12770.34181.007-0.06331.138927.0221-21.875524.4904
62.89074.85721.25318.73360.10859.2898-1.0138-0.38060.33940.5710.30152.11730.8166-1.75530.95830.8914-0.07460.23541.04740.0181.083812.9961-4.764333.2221
73.68821.0452-1.39688.9637-4.96586.3085-0.75840.7622-0.9757-0.7667-0.4389-1.3519-1.061-0.61881.23081.959-0.1754-0.05591.23630.06320.690717.0757-12.593118.8246
84.9996-2.0509-0.8147.85235.15863.42860.3183-0.05760.7846-0.1530.2785-1.20840.36431.3791-0.87360.8027-0.12160.18390.9467-0.08440.868225.5978-12.686428.8066
94.6287-2.90313.25635.5898-5.95988.64431.68640.7082-0.9058-0.7721-0.79351.36980.6090.676-0.83241.1398-0.1544-0.09391.1181-0.12810.654320.7486-11.297327.7575
104.2584-3.1981-1.9952.44670.54548.68330.23850.70920.0429-0.6229-0.70461.13881.3231-1.90810.57210.7821-0.1305-0.10571.303-0.06741.20078.4401-11.184623.8892
115.6645-5.54060.87575.3174-1.11071.66440.5835-1.19562.11440.01740.8748-1.6413-1.1236-0.0404-0.89591.47030.08460.23930.7662-0.01440.845847.79368.933919.9632
123.4113-5.26422.30359.1498-1.77925.2177-0.2990.01660.2762-1.2956-0.0228-0.9574-0.16970.72570.31020.9793-0.15490.21620.69260.00590.658453.46041.282210.0409
137.0092-4.7308-2.52035.99481.49772.63340.36090.36570.5248-0.3266-0.1965-0.2229-0.48610.3197-0.11640.9889-0.18980.04580.6058-0.09430.501746.94126.328115.6334
144.53952.3475-1.53325.7334-1.03455.04740.06580.15970.0710.05930.36460.1860.0945-0.3393-0.43930.59220.03-0.01320.5846-0.05160.520824.4969-2.998430.6049
155.72933.9458-4.2353.8959-5.32219.22550.6320.22460.44771.96020.14420.6066-1.7215-0.066-0.75810.820.1383-0.01340.5792-0.08740.602327.77319.037134.2638
168.380.9515-3.92577.385-0.08533.70690.97381.13561.082-0.4627-0.8564-0.9233-1.3102-0.4487-0.22870.9767-0.0977-0.03081.40180.43060.86681.0304-5.90574.141
177.1073-0.6968-4.55851.10652.13125.5383-0.1464-0.4019-0.0089-0.39221.92250.1138-1.15581.5569-1.69050.75540.05020.13261.80010.57231.475981.8119-7.2402-4.9726
184.12-1.7989-3.86753.1201-0.52295.70990.51631.32970.9838-0.4677-0.66970.2501-1.2745-0.8740.3151.03460.22340.08611.74670.57151.387376.99090.1843-7.7958
196.3542-1.03960.09588.991.35999.47850.0476-0.61131.38910.87380.0076-0.1659-0.42490.4388-0.09150.5976-0.1011-0.02381.1757-0.00620.853875.3811-4.57879.6829
205.40730.5677-1.80364.7753-3.79583.49380.2381-1.32930.50870.52540.13880.76020.67530.6544-0.43380.58150.10320.1910.87660.07391.16378.7608-19.62697.4207
211.96911.21081.787.98994.08432.794-0.7058-0.7527-1.0019-0.38231.1451-0.6713-0.21291.4479-0.32641.15690.1633-0.00661.54170.12090.602175.3849-24.062814.687
225.7208-0.2845-3.28215.54094.30677.1611-0.25520.21050.37730.38970.25340.33721.03340.67920.17060.6302-0.07990.14051.26130.0290.810970.6102-17.5626.2294
232.5717-2.52860.95794.218-0.15160.71230.4153-1.46292.2871-1.7819-0.56210.034-0.5528-0.4087-0.01481.105-0.21190.15631.0302-0.3171.126669.2767-9.28818.4816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 2 through 43 )
2X-RAY DIFFRACTION2chain 'C' and (resid 44 through 54 )
3X-RAY DIFFRACTION3chain 'C' and (resid 55 through 71 )
4X-RAY DIFFRACTION4chain 'C' and (resid 72 through 106 )
5X-RAY DIFFRACTION5chain 'C' and (resid 107 through 120 )
6X-RAY DIFFRACTION6chain 'C' and (resid 121 through 139 )
7X-RAY DIFFRACTION7chain 'C' and (resid 140 through 154 )
8X-RAY DIFFRACTION8chain 'C' and (resid 155 through 169 )
9X-RAY DIFFRACTION9chain 'C' and (resid 170 through 179 )
10X-RAY DIFFRACTION10chain 'C' and (resid 180 through 200 )
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 25 )
12X-RAY DIFFRACTION12chain 'D' and (resid 26 through 64 )
13X-RAY DIFFRACTION13chain 'D' and (resid 65 through 120 )
14X-RAY DIFFRACTION14chain 'D' and (resid 121 through 198 )
15X-RAY DIFFRACTION15chain 'D' and (resid 199 through 241 )
16X-RAY DIFFRACTION16chain 'A' and (resid 2 through 28 )
17X-RAY DIFFRACTION17chain 'A' and (resid 29 through 37 )
18X-RAY DIFFRACTION18chain 'A' and (resid 38 through 56 )
19X-RAY DIFFRACTION19chain 'A' and (resid 57 through 103 )
20X-RAY DIFFRACTION20chain 'A' and (resid 104 through 126 )
21X-RAY DIFFRACTION21chain 'A' and (resid 127 through 137 )
22X-RAY DIFFRACTION22chain 'A' and (resid 138 through 175 )
23X-RAY DIFFRACTION23chain 'B' and (resid 1 through 9 )

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