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- PDB-3ws6: Crystal Structure of H-2D in complex with a mimotopic peptide -

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Basic information

Entry
Database: PDB / ID: 3ws6
TitleCrystal Structure of H-2D in complex with a mimotopic peptide
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Mimotope 9-mer peptide
KeywordsIMMUNE SYSTEM / Class I MHC / Major histocompatibility complex / mimotope / H-2D / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane ...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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / 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 / 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 / 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 / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
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
IMIDAZOLE / Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsKumar, P.R. / Mukherjee, G. / Samanta, D. / DiLorenzo, T.P. / Almo, S.C. / Immune Function Network / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: J. Immunol. / Year: 2014
Title: Compensatory mechanisms allow undersized anchor-deficient class I MHC ligands to mediate pathogenic autoreactive T cell responses
Authors: Lamont, D. / Mukherjee, G. / Kumar, P.R. / Samanta, D. / McPhee, C.G. / Kay, T.W.H. / Almo, S.C. / DiLorenzo, T.P. / Serreze, D.V.
History
DepositionFeb 28, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author
Revision 1.2Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation
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 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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-B alpha chain
D: Beta-2-microglobulin
B: H-2 class I histocompatibility antigen, D-B alpha chain
C: Beta-2-microglobulin
E: Mimotope 9-mer peptide
F: Mimotope 9-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,32023
Polymers89,9876
Non-polymers1,33317
Water11,530640
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: Mimotope 9-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,52010
Polymers44,9933
Non-polymers5267
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-77 kcal/mol
Surface area19180 Å2
MethodPISA
2
B: H-2 class I histocompatibility antigen, D-B alpha chain
C: Beta-2-microglobulin
F: Mimotope 9-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,80013
Polymers44,9933
Non-polymers80610
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-95 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.723, 69.265, 73.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-680-

HOH

21F-101-

HOH

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Components

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Protein , 2 types, 4 molecules ABDC

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


Mass: 32030.648 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H-2Db, H2-D1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 2
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

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Mimotope 9-mer peptide


Mass: 1127.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide based on a peptide library

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Non-polymers , 5 types, 657 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS SEQUENCE CORRESPONDS TO A NATURAL VARIANT, ALLELE A WHICH HAS A A->D MUTATION.

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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: 2.31 Å3/Da / Density % sol: 46.74 % / Mosaicity: 0.588 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M Sodium Chloride, 10% PEG 3000, 0.1M Phosphate/Citrate buffer, 20% Glycerol, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 18, 2012 / Details: Mirrors
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 54087 / % possible obs: 92.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 25.36 Å2 / Rmerge(I) obs: 0.113 / Χ2: 0.931 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2-2.0312.323590.86482.5
2.03-2.0712.423600.89281.90.891
2.07-2.1112.323621.03181.90.822
2.11-2.1512.423770.89483.30.686
2.15-2.212.423760.88983.10.586
2.2-2.2512.124930.92885.10.534
2.25-2.311224891.06386.60.499
2.31-2.3711.825630.90389.30.413
2.37-2.4411.626460.92192.10.358
2.44-2.5211.427230.90294.30.297
2.52-2.6111.328430.91297.30.261
2.61-2.7111.328180.9697.60.224
2.71-2.8411.528930.91999.20.173
2.84-2.9911.729070.97699.30.143
2.99-3.1711.829181.01999.90.112
3.17-3.4211.929191.09899.90.089
3.42-3.7612.229451.14299.90.07
3.76-4.311329670.8951000.052
4.31-5.4314.130110.7581000.042
5.43-5013.631180.73298.60.042

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YN6

1yn6


Resolution: 1.98→30.496 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2477 4.78 %RANDOM
Rwork0.1693 ---
obs0.172 51779 88.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.69 Å2 / Biso mean: 33.1248 Å2 / Biso min: 8.7 Å2
Refinement stepCycle: LAST / Resolution: 1.98→30.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6233 0 73 640 6946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086527
X-RAY DIFFRACTIONf_angle_d1.1118842
X-RAY DIFFRACTIONf_chiral_restr0.045884
X-RAY DIFFRACTIONf_plane_restr0.0051150
X-RAY DIFFRACTIONf_dihedral_angle_d14.7172405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9805-2.01850.2823850.22841853193861
2.0185-2.05970.31791110.21612202231371
2.0597-2.10450.25231050.2182254235973
2.1045-2.15350.26491180.20742311242975
2.1535-2.20730.271000.21382327242776
2.2073-2.2670.30061160.21662434255079
2.267-2.33360.29691250.2072495262081
2.3336-2.40890.27631250.21062650277585
2.4089-2.4950.27811290.19722778290790
2.495-2.59480.31781310.20672978310996
2.5948-2.71290.23381430.19993034317798
2.7129-2.85580.22791460.19963090323699
2.8558-3.03460.22791630.18623071323499
3.0346-3.26860.20991820.174431013283100
3.2686-3.59710.22341760.146831063282100
3.5971-4.11650.17851790.135231453324100
4.1165-5.18230.1621490.114631873336100
5.1823-30.49970.21761940.15763286348099
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)
11.4406-0.813-0.91981.75460.41562.3311-0.0284-0.1046-0.2599-0.0272-0.03340.2990.0680.11030.02880.13220.0183-0.05110.1556-0.02790.224113.246213.09315.8264
22.70450.3704-0.95333.7175-0.14611.90530.19860.30380.2845-0.3414-0.07560.4322-0.1848-0.135-0.11740.21810.0348-0.0550.20050.00530.137816.07137.97621.211
31.61020.20510.45491.67050.81693.09550.00660.11470.0846-0.01640.03160.1986-0.09870.1332-0.04740.12030.01920.03810.10130.02510.208211.608456.895157.0206
42.233-0.12160.33032.21910.35981.92660.0108-0.3213-0.72550.40750.08790.66250.1678-0.135-0.08470.2076-0.00850.06160.22790.07830.357516.09531.55651.661
53.34330.0762-0.40753.0986-0.4723.1058-0.0446-0.01110.19780.17820.13570.08310.3705-0.0223-0.0740.15030.0309-0.01760.1891-0.01760.104129.12239.32963.24
67.1238-5.1497-5.04134.26583.4474.64880.0845-0.16650.43970.01380.1407-0.1629-0.09450.2032-0.25490.1989-0.01050.030.1651-0.02070.224933.49138.01351.7
73.9912-1.8431-1.03784.45371.5482.4218-0.0907-0.21740.11890.23870.1742-0.32340.1020.2531-0.07210.14610.0072-0.00770.1895-0.00570.144133.97240.80351.627
85.44491.21361.65284.74641.03025.3699-0.06610.0065-0.0478-0.1288-0.0169-0.1231-0.23110.09010.05910.0782-0.001-0.00770.0810.02590.149229.84631.60710.18
94.2163.96014.42394.24083.68244.8745-0.0830.0635-0.16570.02240.1562-0.35440.08540.1791-0.15750.19580.035-0.0180.2222-0.02920.241233.84532.85321.776
102.7841.26121.11613.82231.24692.8089-0.08520.32960.0013-0.34860.0723-0.3686-0.25620.4109-0.03630.1621-0.01220.03310.2140.0410.186834.52330.21721.955
112.5456-2.8257-3.27244.61514.96295.4624-0.0084-0.0996-0.47620.2109-0.08950.55220.8015-0.11780.08160.2179-0.0128-0.08670.1829-0.03940.477310.00996.404713.9311
126.54251.92995.05394.00052.91324.92320.13540.08450.3704-0.0518-0.06850.4632-0.819-0.3434-0.08150.22380.02510.12020.19960.04420.37788.163763.620158.8764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 26:174 )A26 - 174
2X-RAY DIFFRACTION2(CHAIN A AND RESSEQ 175:276 )A175 - 276
3X-RAY DIFFRACTION3(CHAIN B AND RESSEQ 26:174 )B26 - 174
4X-RAY DIFFRACTION4(CHAIN B AND RESSEQ 175:278 )B175 - 278
5X-RAY DIFFRACTION5(CHAIN C AND RESSEQ 23:28 )C23 - 28
6X-RAY DIFFRACTION6(CHAIN C AND RESSEQ 29:61 )C29 - 61
7X-RAY DIFFRACTION7(CHAIN C AND RESSEQ 62:99 )C62 - 99
8X-RAY DIFFRACTION8(CHAIN D AND RESSEQ 23:28 )D23 - 28
9X-RAY DIFFRACTION9(CHAIN D AND RESSEQ 29:61 )D29 - 61
10X-RAY DIFFRACTION10(CHAIN D AND RESSEQ 62:99 )D62 - 99
11X-RAY DIFFRACTION11(CHAIN E AND RESSEQ 1:9 )E1 - 9
12X-RAY DIFFRACTION12(CHAIN F AND RESSEQ 1:9 )F1 - 9

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