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- PDB-3l3k: Crystal structure of HLA-B*4402 in complex with the R5A/F7A doubl... -

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Basic information

Entry
Database: PDB / ID: 3l3k
TitleCrystal structure of HLA-B*4402 in complex with the R5A/F7A double mutant of a self-peptide derived from DPA*0201
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-44 alpha chain
  • peptide from HLA-DPA1 protein
KeywordsIMMUNE SYSTEM / Immunoglobulin domain / Immune response / Major Histocompatibility Complex Class I / MHC-I peptide complex / altered peptide ligand
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium ...antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / 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 / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 ...MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / HLA class II histocompatibility antigen DP alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTheodossis, A. / Ely, L.K. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Constraints within major histocompatibility complex class I restricted peptides: presentation and consequences for T-cell recognition
Authors: Theodossis, A. / Guillonneau, C. / Welland, A. / Ely, L.K. / Clements, C.S. / Williamson, N.A. / Webb, A.I. / Wilce, J.A. / Mulder, R.J. / Dunstone, M.A. / Doherty, P.C. / McCluskey, J. / ...Authors: Theodossis, A. / Guillonneau, C. / Welland, A. / Ely, L.K. / Clements, C.S. / Williamson, N.A. / Webb, A.I. / Wilce, J.A. / Mulder, R.J. / Dunstone, M.A. / Doherty, P.C. / McCluskey, J. / Purcell, A.W. / Turner, S.J. / Rossjohn, J.
History
DepositionDec 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-44 alpha chain
B: Beta-2-microglobulin
C: peptide from HLA-DPA1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7484
Polymers44,6563
Non-polymers921
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-18 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.581, 82.084, 109.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-44 alpha chain / MHC class I antigen B*44 / Bw-44 / HLA-B*4402


Mass: 31980.258 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P30481, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide peptide from HLA-DPA1 protein / HLA-DPA*0201 peptide


Mass: 927.953 Da / Num. of mol.: 1 / Mutation: R5A,F7A / Source method: obtained synthetically / Details: automated Fmoc-peptide synthesis / References: UniProt: Q95HB9
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→65.6 Å / Num. all: 15875 / Num. obs: 15875 / % possible obs: 93.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3 / % possible all: 71.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M6O

1m6o


Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.878 / SU B: 26.516 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: isotropic atomic temperature factors with TLS
Cross valid method: THROUGHOUT / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27528 1430 10.1 %RANDOM
Rwork0.21075 ---
all0.21734 12715 --
obs0.21734 12715 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.712 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0 Å20 Å2
2---3.46 Å20 Å2
3---3.82 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 6 142 3269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0213213
X-RAY DIFFRACTIONr_angle_refined_deg0.8611.9364372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7615381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04323.371175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32615502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5561530
X-RAY DIFFRACTIONr_chiral_restr0.0590.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212557
X-RAY DIFFRACTIONr_mcbond_it0.1341.51919
X-RAY DIFFRACTIONr_mcangle_it0.26123098
X-RAY DIFFRACTIONr_scbond_it0.38231294
X-RAY DIFFRACTIONr_scangle_it0.6854.51274
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 108 -
Rwork0.231 805 -
obs--86.95 %
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)
12.9358-0.27210.44530.97780.04780.41650.04310.2281-0.0557-0.1857-0.0255-0.01950.0131-0.0061-0.01760.0728-0.01470.00430.0556-0.00220.001921.033712.566223.7743
21.2634-0.4153-0.83250.77781.21469.2618-0.1712-0.23630.01490.26080.07050.0613-0.0860.11750.10070.12380.03710.01490.0730.00970.1010.212615.613452.9717
34.14392.1162-1.72815.15-1.89822.26220.0205-0.2947-0.21770.1745-0.0450.2240.167-0.03930.02450.11790.03270.01390.0840.0030.077310.3055-2.469743.8771
40.5233-0.1776-0.16640.30550.03260.16240.0165-0.0214-0.06570.0313-0.02460.05120.0170.04140.00810.0858-0.0172-0.01490.1033-0.02230.021414.91358.92735.0381
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A182 - 276
4X-RAY DIFFRACTION3B1 - 99
5X-RAY DIFFRACTION4A277 - 381
6X-RAY DIFFRACTION4B101 - 345
7X-RAY DIFFRACTION4C10 - 133

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