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- PDB-3tbw: CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY ... -

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Basic information

Entry
Database: PDB / ID: 3tbw
TitleCRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH THE LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (A2G, V3P, Y4S)
Components
  • Beta-2-microglobulin
  • GLYCOPROTEIN GPC
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsImmune system/agonist / Murine MHC / LCMV / receptor binding / Beta2-microglobulin / Immune system / T cell recognition / antigen presentation / altered peptide ligand / agonism / antagonism / T cell receptor / CD8 / Cell Surface / Immune system-agonist complex
Function / homology
Function and homology information


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 / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...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 / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / receptor-mediated endocytosis of virus by host cell / learning or memory / host cell endoplasmic reticulum membrane / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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 ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDuru, A.D. / Allerbring, E.B. / Uchtenhagen, H. / Mazumdar, P.A. / Badia-Martinez, D. / Madhurantakam, C. / Sandalova, T. / Nygren, P. / Achour, A.
CitationJournal: To be Published
Title: Conversion of a T cell viral antagonist into an agonist through higher stabilization and conserved molecular mimicry: Implications for TCR recognition
Authors: Duru, A.D. / Allerbring, E.B. / Uchtenhagen, H. / Mazumdar, P.A. / Badia-Martinez, D. / Madhurantakam, C. / Sandalova, T. / Nygren, P. / Achour, A.
History
DepositionAug 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / 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

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: GLYCOPROTEIN GPC
J: GLYCOPROTEIN GPC
K: GLYCOPROTEIN GPC
L: GLYCOPROTEIN GPC


Theoretical massNumber of molelcules
Total (without water)178,98112
Polymers178,98112
Non-polymers00
Water10,341574
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
I: GLYCOPROTEIN GPC


Theoretical massNumber of molelcules
Total (without water)44,7453
Polymers44,7453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-19 kcal/mol
Surface area19610 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
J: GLYCOPROTEIN GPC


Theoretical massNumber of molelcules
Total (without water)44,7453
Polymers44,7453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-20 kcal/mol
Surface area19700 Å2
MethodPISA
3
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
K: GLYCOPROTEIN GPC


Theoretical massNumber of molelcules
Total (without water)44,7453
Polymers44,7453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-19 kcal/mol
Surface area19910 Å2
MethodPISA
4
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
L: GLYCOPROTEIN GPC


Theoretical massNumber of molelcules
Total (without water)44,7453
Polymers44,7453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-18 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.399, 124.277, 99.887
Angle α, β, γ (deg.)90.00, 103.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 1:175 or resseq 182:274 ) and (not element H) and (not element D)A0
211chain 'C' and (resseq 1:175 or resseq 182:274 ) and (not element H) and (not element D)C0
311chain 'E' and (resseq 1:175 or resseq 182:274 ) and (not element H) and (not element D)E0
411chain 'G' and (resseq 1:175 or resseq 182:274 ) and (not element H) and (not element D)G0
112chain 'B' and (resseq 1:99 ) and (not element H) and (not element D)B0
212chain 'D' and (resseq 1:99 ) and (not element H) and (not element D)D0
312chain 'F' and (resseq 1:99 ) and (not element H) and (not element D)F0
412chain 'H' and (resseq 1:99 ) and (not element H) and (not element D)H0

NCS ensembles :
ID
1
2

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Components

#1: Protein
H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32087.703 Da / Num. of mol.: 4 / Fragment: RESIDUES 25-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1, H2-DB / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 4 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide
GLYCOPROTEIN GPC


Mass: 953.094 Da / Num. of mol.: 4 / Fragment: RESIDUES 33-41 / Mutation: A34G, V35P, Y36S / Source method: obtained synthetically
Details: LYMPHOCYTIC CHORIOMENINGITIS VIRUS PROTEIN GPC, residues 33-41
Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: P07399
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O

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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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization ...Details: Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: Bruker AXS/Roentec X-Flash XRF detector / Detector: X-Flash XRF detector / Date: Sep 9, 2009
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.15→96.7 Å / Num. all: 116037 / Num. obs: 116037 / % possible obs: 98.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 55.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.8
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.5 / Num. unique all: 17142 / % possible all: 99.7

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Processing

Software
NameVersionClassification
APEXdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7U

1s7u


Resolution: 2.15→47.482 Å / SU ML: 0.39 / σ(F): 1.03 / Phase error: 31.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 10791 5.01 %Random
Rwork0.2324 ---
all0.2349 215594 --
obs0.2349 -92.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.582 Å2 / ksol: 0.412 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5824 Å20 Å23.3843 Å2
2--6.5528 Å2-0 Å2
3----5.9704 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12480 0 0 574 13054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0212933
X-RAY DIFFRACTIONf_angle_d1.65617532
X-RAY DIFFRACTIONf_dihedral_angle_d19.8164712
X-RAY DIFFRACTIONf_chiral_restr0.1081766
X-RAY DIFFRACTIONf_plane_restr0.0092284
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2201X-RAY DIFFRACTIONPOSITIONAL0.111
12C2201X-RAY DIFFRACTIONPOSITIONAL0.111
13E2201X-RAY DIFFRACTIONPOSITIONAL0.09
14G2201X-RAY DIFFRACTIONPOSITIONAL0.124
21B820X-RAY DIFFRACTIONPOSITIONAL0.112
22D820X-RAY DIFFRACTIONPOSITIONAL0.112
23F820X-RAY DIFFRACTIONPOSITIONAL0.099
24H820X-RAY DIFFRACTIONPOSITIONAL0.128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.22680.336811230.288820535X-RAY DIFFRACTION93
2.2268-2.3160.358110220.29320709X-RAY DIFFRACTION93
2.316-2.42140.350710210.27920649X-RAY DIFFRACTION93
2.4214-2.54910.324111080.25820508X-RAY DIFFRACTION93
2.5491-2.70880.325811370.253820562X-RAY DIFFRACTION93
2.7088-2.91790.303310900.247120531X-RAY DIFFRACTION93
2.9179-3.21140.31611210.240320470X-RAY DIFFRACTION93
3.2114-3.6760.277211010.220820472X-RAY DIFFRACTION93
3.676-4.63080.21510570.18120431X-RAY DIFFRACTION92
4.6308-47.49320.233610110.199119936X-RAY DIFFRACTION90
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)
10.9605-0.2794-0.04091.14420.3011.64350.03960.1733-0.1771-0.2382-0.0160.0108-0.05190.0242-0.00880.11350.0510.04630.13850.01380.1381-7.56260.721915.8712
20.85160.73380.03572.02470.26450.94620.03340.216-0.12140.46930.2925-0.07330.12260.2773-0.26650.28840.062-0.0580.1504-0.02520.18073.1204-10.877849.3589
30.90110.0447-0.0850.41440.61321.96350.2478-0.3121-0.0150.11210.1507-0.0601-0.32750.4604-0.18570.1513-0.06060.02880.2888-0.0870.0941-0.661110.411841.5376
40.980.2156-0.18320.65140.44490.625-0.2407-0.3758-0.1460.1740.23630.03130.21620.23040.09560.21730.1733-0.01920.25090.01730.1359-9.5327-39.955535.0854
52.81440.6378-0.7952.6627-0.43040.2992-0.16220.74550.3096-0.95550.3569-0.10.0762-0.322-0.15420.5520.0760.01650.32070.00590.36335.4354-29.11652.9626
61.4324-0.1072-0.96680.61720.4750.703-0.35290.3392-0.16330.10220.16820.10170.23-0.18950.18890.29860.01520.07780.2088-0.0330.1325-0.1378-50.293710.5592
72.16251.3479-0.9260.7464-0.06090.45380.1187-0.28190.06320.1774-0.23340.1777-0.0664-0.13260.13360.22680.1380.04080.4074-0.03670.230843.37581.53333.4985
81.33641.260.09682.8843-0.93361.5978-0.45910.1759-0.3197-0.92940.6411-0.47990.5404-0.3307-0.13080.5024-0.0870.00750.2028-0.05950.27530.368-9.42721.1773
90.30.18850.23040.3432-0.43472.9342-0.05130.24250.03940.14710.3161-0.0247-1.0148-0.3625-0.10670.35670.2002-0.00180.33030.05730.10736.015911.42537.7079
100.5306-0.06680.31460.7077-0.06261.4338-0.09590.12970.0653-0.05290.01370.06280.1105-0.18070.06760.1745-0.0538-0.04120.1528-0.00660.231642.7516-39.092213.2716
112.16460.09290.05621.86450.08110.38690.3407-1.37740.20670.76510.14860.3787-0.173-0.4098-0.43120.48970.02230.25830.8423-0.00870.49528.4041-28.596445.7975
122.6774-0.0188-0.81611.0565-0.60261.2291-0.4262-0.70750.24310.06550.52370.0870.6218-0.2132-0.2041-0.1009-0.19270.06640.27520.11260.036133.2197-49.856837.5169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:181)
2X-RAY DIFFRACTION2(chain A and resid 182:277)
3X-RAY DIFFRACTION3(chain B and resid 1:99)
4X-RAY DIFFRACTION4(chain C and resid 1:181)
5X-RAY DIFFRACTION5(chain C and resid 182:274)
6X-RAY DIFFRACTION6(chain D and resid 1:99)
7X-RAY DIFFRACTION7(chain E and resid 1:174)
8X-RAY DIFFRACTION8(chain E and resid 175:276)
9X-RAY DIFFRACTION9(chain F and resid 1:99)
10X-RAY DIFFRACTION10(chain G and resid 1:181)
11X-RAY DIFFRACTION11(chain G and resid 182:274)
12X-RAY DIFFRACTION12(chain H and resid 1:99)

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