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- PDB-2q6w: The structure of HLA-DRA, DRB3*0101 (DR52a) with bound platelet i... -

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Basic information

Entry
Database: PDB / ID: 2q6w
TitleThe structure of HLA-DRA, DRB3*0101 (DR52a) with bound platelet integrin peptide associated with fetal and neonatal alloimmune thrombocytopenia
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB3-1 beta chain
  • Integrin beta-3
KeywordsIMMUNE SYSTEM / DRB3 / peptide-class II MHC complex / fetal-maternal alloimmune thrombocytopenia / thrombocytopenia purpura / myasthenia gravis / beta 11 arginine / autoimmunity
Function / homology
Function and homology information


myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / autolysosome membrane / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of T-helper cell differentiation ...myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / autolysosome membrane / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of T-helper cell differentiation / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / MHC class II receptor activity / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / positive regulation of CD4-positive, alpha-beta T cell activation / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / glycinergic synapse / alphav-beta3 integrin-PKCalpha complex / positive regulation of T cell mediated immune response to tumor cell / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of memory T cell differentiation / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / angiogenesis involved in wound healing / platelet-derived growth factor receptor binding / alphav-beta3 integrin-IGF-1-IGF1R complex / filopodium membrane / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of fibroblast migration / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / positive regulation of cell adhesion mediated by integrin / apoptotic cell clearance / activation of protein kinase activity / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / Molecules associated with elastic fibres / smooth muscle cell migration / positive regulation of cell-matrix adhesion / cell adhesion mediated by integrin / negative chemotaxis / Syndecan interactions / cellular response to insulin-like growth factor stimulus / microvillus membrane / transport vesicle membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / Translocation of ZAP-70 to Immunological synapse / cell-substrate adhesion / Phosphorylation of CD3 and TCR zeta chains / positive regulation of osteoblast proliferation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / polysaccharide binding / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / Generation of second messenger molecules / negative regulation of lipid storage / immunological synapse / Co-inhibition by PD-1 / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / T cell receptor binding / coreceptor activity / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / MHC class II antigen presentation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / substrate adhesion-dependent cell spreading / protein kinase C binding / trans-Golgi network membrane / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells
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 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrins beta chain EGF (I-EGF) domain profile. / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / 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 / EGF-like domain, extracellular / EGF-like domain / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 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 / Integrin beta-3 / HLA class II histocompatibility antigen, DR beta 3 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsParry, C.S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystallographic Structure of the Human Leukocyte Antigen DRA, DRB3*0101: Models of a Directional Alloimmune Response and Autoimmunity
Authors: Parry, C.S. / Gorski, J. / Stern, L.J.
History
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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, DRB3-1 beta chain
C: Integrin beta-3
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB3-1 beta chain
F: Integrin beta-3


Theoretical massNumber of molelcules
Total (without water)89,1226
Polymers89,1226
Non-polymers00
Water8,773487
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB3-1 beta chain
C: Integrin beta-3


Theoretical massNumber of molelcules
Total (without water)44,5613
Polymers44,5613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-31 kcal/mol
Surface area16220 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB3-1 beta chain
F: Integrin beta-3


Theoretical massNumber of molelcules
Total (without water)44,5613
Polymers44,5613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-35 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.169, 92.169, 248.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 21155.904 Da / Num. of mol.: 2 / Fragment: sequence database residues 26-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): S2 / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB3-1 beta chain


Mass: 22102.637 Da / Num. of mol.: 2 / Fragment: sequence database residues 30-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB3 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): S2 / References: UniProt: P79483
#3: Protein/peptide Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa / CD61 antigen


Mass: 1302.414 Da / Num. of mol.: 2 / Fragment: sequence database residues 50-61 / Mutation: C26R / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05106
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 10-20% PEG 8000, 0.1M sodium acetate, 10% (v/v) glycerol, 0.01M Cd2+, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 51116 / Num. obs: 48049 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.8 % / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.12
Reflection shellResolution: 2.25→2.308 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.04 / % possible all: 55.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DLH

1dlh


Resolution: 2.25→20.05 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.91 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.295 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26543 3684 7.6 %RANDOM
Rwork0.20984 ---
obs0.214 44561 93.27 %-
all-47777 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.241 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2--0.82 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6043 0 0 487 6530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0226214
X-RAY DIFFRACTIONr_angle_refined_deg2.4781.9348463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2665751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67123.257307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.37515945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2681546
X-RAY DIFFRACTIONr_chiral_restr0.1590.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024857
X-RAY DIFFRACTIONr_nbd_refined0.2780.24017
X-RAY DIFFRACTIONr_nbtor_refined0.340.24312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2730
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.28
X-RAY DIFFRACTIONr_mcbond_it1.6771.53823
X-RAY DIFFRACTIONr_mcangle_it2.55126107
X-RAY DIFFRACTIONr_scbond_it3.83432697
X-RAY DIFFRACTIONr_scangle_it5.6414.52356
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 146 -
Rwork0.264 1757 -
obs--51.29 %

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