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- PDB-3l6f: Structure of MHC class II molecule HLA-DR1 complexed with phospho... -

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Basic information

Entry
Database: PDB / ID: 3l6f
TitleStructure of MHC class II molecule HLA-DR1 complexed with phosphopeptide MART-1
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
  • Melanoma antigen recognized by T-cells 1
KeywordsIMMUNE SYSTEM/PEPTIDE BINDING PROTEIN / MHC class II / HLA-DR1 / phosphopeptide / Disulfide bond / Glycoprotein / Immune response / Membrane / MHC II / Transmembrane / Endoplasmic reticulum / Golgi apparatus / IMMUNE SYSTEM-PEPTIDE BINDING PROTEIN complex
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / trans-Golgi network / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / melanosome / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Protein melan-A / Protein melan-A / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain ...Protein melan-A / Protein melan-A / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / 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 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 / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / Melanoma antigen recognized by T-cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, Y. / Mariuzza, R.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Basis for the Presentation of Tumor-Associated MHC Class II-Restricted Phosphopeptides to CD4(+) T Cells.
Authors: Li, Y. / Depontieu, F.R. / Sidney, J. / Salay, T.M. / Engelhard, V.H. / Hunt, D.F. / Sette, A. / Topalian, S.L. / Mariuzza, R.A.
History
DepositionDec 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: Melanoma antigen recognized by T-cells 1


Theoretical massNumber of molelcules
Total (without water)45,2683
Polymers45,2683
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-40 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.210, 135.450, 40.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21145.887 Da / Num. of mol.: 1 / Fragment: UNP residues 26-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class I antigen DRB1*1 / DR-1 / DR1


Mass: 22456.133 Da / Num. of mol.: 1 / Fragment: UNP residues 30-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide Melanoma antigen recognized by T-cells 1 / MART-1 / Melan-A protein / Antigen SK29-AA / Antigen LB39-AA


Mass: 1665.710 Da / Num. of mol.: 1 / Fragment: UNP residues 100-114 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 20% (w/v) PEG 8000 and 0.1 M sodium cacodylate, pH 6.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→43.22 Å / Num. all: 30437 / Num. obs: 30332 / % possible obs: 100 % / Redundancy: 14.2 % / Rsym value: 0.074 / Net I/σ(I): 51.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.46 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5W

1t5w


Resolution: 2.1→43.22 Å
RfactorNum. reflection% reflection
Rfree0.2494 3039 -
Rwork0.2117 --
all-30437 -
obs-30332 99.7 %
Displacement parametersBiso mean: 0.043 Å2
Baniso -1Baniso -2Baniso -3
1--1.148 Å20 Å20 Å2
2---7.947 Å20 Å2
3---9.095 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 0 196 3340
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbonds0.009665
X-RAY DIFFRACTIONangles1.58076
LS refinement shellResolution: 2.1→2.11 Å /
RfactorNum. reflection
Rfree0.3 -
Rwork0.2773 -
obs-445

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