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- PDB-4is6: Crystal structure of HLA-DR4 bound to GP100 peptide -

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Basic information

Entry
Database: PDB / ID: 4is6
TitleCrystal structure of HLA-DR4 bound to GP100 peptide
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-4 beta chain
  • Melanocyte protein PMEL
KeywordsIMMUNE SYSTEM / MHC class II / HLA-DR4 / Gp100
Function / homology
Function and homology information


positive regulation of melanin biosynthetic process / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / regulation of T-helper cell differentiation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / T-helper 1 type immune response ...positive regulation of melanin biosynthetic process / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / regulation of T-helper cell differentiation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / T-helper 1 type immune response / positive regulation of CD4-positive, alpha-beta T cell activation / eye development / melanosome membrane / cis-Golgi network membrane / inflammatory response to antigenic stimulus / positive regulation of T cell mediated immune response to tumor cell / positive regulation of memory T cell differentiation / multivesicular body membrane / multivesicular body, internal vesicle / melanosome organization / positive regulation of monocyte differentiation / CD4 receptor binding / intermediate filament / transport vesicle membrane / humoral immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / epidermis development / polysaccharide binding / negative regulation of type II interferon production / macrophage differentiation / Regulation of MITF-M-dependent genes involved in pigmentation / Generation of second messenger molecules / Co-inhibition by PD-1 / immunological synapse / negative regulation of T cell proliferation / detection of bacterium / T cell receptor binding / MHC class II antigen presentation / positive regulation of T cell mediated cytotoxicity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / negative regulation of inflammatory response to antigenic stimulus / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cognition / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / T cell receptor signaling pathway / positive regulation of T cell activation / Interferon gamma signaling / structural constituent of cytoskeleton / adaptive immune response / endocytic vesicle membrane / melanosome / MHC class II protein complex binding / Downstream TCR signaling / late endosome membrane / extracellular vesicle / early endosome membrane / lysosome / immune response / external side of plasma membrane / Golgi membrane / lysosomal membrane / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / cell surface / endoplasmic reticulum / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / : / PKAT, KLD domain / PMEL/NMB N-terminal domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 ...PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / : / PKAT, KLD domain / PMEL/NMB N-terminal domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / 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 / Melanocyte protein PMEL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, Y.
CitationJournal: J.Immunol. / Year: 2013
Title: Structure-Based Design of Altered MHC Class II-Restricted Peptide Ligands with Heterogeneous Immunogenicity.
Authors: Chen, S. / Li, Y. / Depontieu, F.R. / McMiller, T.L. / English, A.M. / Shabanowitz, J. / Kos, F. / Sidney, J. / Sette, A. / Rosenberg, S.A. / Hunt, D.F. / Mariuzza, R.A. / Topalian, S.L.
History
DepositionJan 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Nov 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-4 beta chain
C: Melanocyte protein PMEL


Theoretical massNumber of molelcules
Total (without water)45,7833
Polymers45,7833
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-34 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.290, 117.590, 41.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / HLA-DR4A / MHC class II antigen DRA


Mass: 21155.904 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 / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-4 beta chain / HLA-DR4B / MHC class II antigen DRB1*4 / DR-4 / DR4


Mass: 22520.021 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 / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13760, UniProt: P01911*PLUS
#3: Protein/peptide Melanocyte protein PMEL / ME20-M / ME20M / Melanocyte protein Pmel 17 / Melanocytes lineage-specific antigen GP100 / Melanoma- ...ME20-M / ME20M / Melanocyte protein Pmel 17 / Melanocytes lineage-specific antigen GP100 / Melanoma-associated ME20 antigen / P1 / P100 / Premelanosome protein / Silver locus protein homolog


Mass: 2107.284 Da / Num. of mol.: 1 / Fragment: UNP residues 44-59 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40967
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG8000, magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.502 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2010 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 14968 / % possible obs: 93 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.079 / Χ2: 1.01 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5410.60.3375510.945171.2
2.54-2.5910.30.2865700.969172.9
2.59-2.6410.40.2896040.999176.6
2.64-2.6910.30.2796510.937181.2
2.69-2.7510.10.2356570.971183.8
2.75-2.829.80.1956950.972187.5
2.82-2.899.60.1757390.991195.4
2.89-2.969.40.1657871.039198.3
2.96-3.059.70.1537611.04198.4
3.05-3.159.60.1388141.1199.5
3.15-3.269.60.1097871.067199.7
3.26-3.399.60.0937891.08199.9
3.39-3.559.70.0768111.012199.8
3.55-3.739.60.0688021.018199.9
3.73-3.979.60.0677991.062199.8
3.97-4.279.50.068131.098199.8
4.27-4.79.40.0558191.023199.8
4.7-5.389.40.058150.869199
5.38-6.7690.0518260.948198.2
6.76-309.20.0398781.007196.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.727 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.298 1470 9.1 %
Rwork0.265 --
obs-14952 93 %
Solvent computationBsol: 14.0886 Å2
Displacement parametersBiso max: 109.3 Å2 / Biso mean: 64.7056 Å2 / Biso min: 31.04 Å2
Baniso -1Baniso -2Baniso -3
1--28.931 Å20 Å20 Å2
2---30.529 Å20 Å2
3---59.46 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 11 3149
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.530.5279300.3985336366
2.53-2.560.3618350.3776373408
2.56-2.590.429400.3859350390
2.59-2.630.4635370.4258394431
2.63-2.660.4611380.4347382420
2.66-2.70.4455560.4382385441
2.7-2.740.4211460.4271412458
2.74-2.780.4156540.395414468
2.78-2.830.3654460.3879447493
2.83-2.880.4911400.4341463503
2.88-2.930.3872520.4446501553
2.93-2.990.3431420.4296497539
2.99-3.050.3924430.37487530
3.05-3.110.3522500.3642495545
3.11-3.190.3742580.3458498556
3.19-3.270.354550.3271490545
3.27-3.350.4053590.2764492551
3.35-3.450.2799480.276504552
3.45-3.560.2585480.2718507555
3.56-3.690.3349440.263502546
3.69-3.840.3386570.2461505562
3.84-4.010.3155590.2357482541
4.01-4.220.2128670.2087503570
4.22-4.490.2248590.172496555
4.49-4.830.2057600.1477494554
4.83-5.320.2163610.1904523584
5.32-6.080.2612610.247500561
6.08-7.640.3844560.2389511567
7.64-300.216690.18539608
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3gol.param

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