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- PDB-1t5w: HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) -

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Basic information

Entry
Database: PDB / ID: 1t5w
TitleHLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR)
Components
  • 15-mer peptide fragment of Regulatory protein MIG1
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
KeywordsIMMUNE SYSTEM / MHC class II / najor histocompatibility complex protein / HLA-DR1 / antigen / peptide
Function / homology
Function and homology information


positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / 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 / 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 ...positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / 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 / 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 T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / nuclear envelope lumen / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of T cell activation / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / positive regulation of protein phosphorylation / early endosome membrane / adaptive immune response / sequence-specific DNA binding / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Golgi membrane / external side of plasma membrane / lysosomal membrane / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / zinc ion binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / 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 ...: / 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 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 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 / Regulatory protein MIG1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZavala-Ruiz, Z. / Strug, I. / Anderson, M.W. / Gorski, J. / Stern, L.J.
CitationJournal: Chem.Biol. / Year: 2004
Title: A Polymorphic Pocket at the P10 Position Contributes to Peptide Binding Specificity in Class II MHC Proteins
Authors: Zavala-Ruiz, Z. / Strug, I. / Anderson, M.W. / Gorski, J. / Stern, L.J.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 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 II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: 15-mer peptide fragment of Regulatory protein MIG1
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: 15-mer peptide fragment of Regulatory protein MIG1


Theoretical massNumber of molelcules
Total (without water)89,3126
Polymers89,3126
Non-polymers00
Water2,666148
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: 15-mer peptide fragment of Regulatory protein MIG1


Theoretical massNumber of molelcules
Total (without water)44,6563
Polymers44,6563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-38 kcal/mol
Surface area17930 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: 15-mer peptide fragment of Regulatory protein MIG1


Theoretical massNumber of molelcules
Total (without water)44,6563
Polymers44,6563
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-38 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.554, 112.646, 206.976
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsTow molecules in the asymteric unit are related by an approximate 2-fold axis

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Components

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


Mass: 20971.670 Da / Num. of mol.: 2 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA / Plasmid: pRMAHA-3 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class I antigen DRB1*1 / DR-1 / DR1


Mass: 22080.664 Da / Num. of mol.: 2 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pRMHA-3 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide 15-mer peptide fragment of Regulatory protein MIG1 / Regulatory protein CAT4


Mass: 1603.795 Da / Num. of mol.: 2 / Fragment: Synthetic peptide / Source method: obtained synthetically
Details: Synthetic peptide desinged to study the P10 side chain specificity of HLA-DR1
References: UniProt: P27705
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.21 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 6000, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2001 / Details: Cylindrical platinum-coated silicon mirror
RadiationMonochromator: Cylindrical platinum-coated silicon mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→23.9 Å / Num. all: 46428 / Num. obs: 44505 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.065 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 5 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4384 / Rsym value: 0.378 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AQD

1aqd


Resolution: 2.4→23.9 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3143 -Random
Rwork0.231 ---
all0.232 46428 --
obs0.2311 44322 99.8 %-
Displacement parametersBiso mean: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1--10.81 Å20 Å20 Å2
2--20.61 Å20 Å2
3----9.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→23.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6259 0 0 148 6407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.344 532 -
Rwork0.302 --
obs-6770 99.9 %

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