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- PDB-3bgm: Crystal Structure of PKD2 Phosphopeptide Bound to Human Class I M... -

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Basic information

Entry
Database: PDB / ID: 3bgm
TitleCrystal Structure of PKD2 Phosphopeptide Bound to Human Class I MHC HLA-A2
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • nonameric peptide from Serine/threonine-protein kinase D2
KeywordsIMMUNE SYSTEM / PHOSPHOSERINE / PHOSPHOPEPTIDE / MHC / HLA-A2 / ANCHOR RESIDUE / TUMOR ANTIGEN / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE / MHC I / POLYMORPHISM / TRANSMEMBRANE / UBL CONJUGATION / IMMUNOGLOBULIN DOMAIN / KINASE / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / positive regulation of fibroblast growth factor receptor signaling pathway / endothelial tube morphogenesis / regulation of T cell apoptotic process / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / positive regulation of vascular endothelial growth factor receptor signaling pathway ...diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / positive regulation of fibroblast growth factor receptor signaling pathway / endothelial tube morphogenesis / regulation of T cell apoptotic process / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of endothelial cell chemotaxis / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of DNA biosynthetic process / CD8 receptor binding / positive regulation of T cell receptor signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / cellular response to vascular endothelial growth factor stimulus / 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 / positive regulation of blood vessel endothelial cell migration / vascular endothelial growth factor receptor signaling pathway / detection of bacterium / T cell receptor binding / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / peptidyl-threonine phosphorylation / positive regulation of interleukin-2 production / positive regulation of cell adhesion / : / : / positive regulation of DNA-binding transcription factor activity / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / protein kinase C binding / positive regulation of interleukin-8 production / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of NF-kappaB transcription factor activity / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / peptidyl-serine phosphorylation
Similarity search - Function
Protein kinase C mu-related / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / PH domain / MHC class I, alpha chain, C-terminal ...Protein kinase C mu-related / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / PH domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / PH domain profile. / Pleckstrin homology domain. / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Pleckstrin homology domain / 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. / PH-like domain superfamily / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Serine/threonine-protein kinase D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMohammed, F. / Cobbold, M. / Zarling, A.L. / Salim, M. / Barrett-Wilt, G.A. / Shabanowitz, J. / Hunt, D.F. / Engelhard, V.H. / Willcox, B.E.
CitationJournal: Nat.Immunol. / Year: 2008
Title: Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self
Authors: Mohammed, F. / Cobbold, M. / Zarling, A.L. / Salim, M. / Barrett-Wilt, G.A. / Shabanowitz, J. / Hunt, D.F. / Engelhard, V.H. / Willcox, B.E.
History
DepositionNov 27, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: nonameric peptide from Serine/threonine-protein kinase D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8947
Polymers44,6463
Non-polymers2484
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-3 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.800, 54.800, 75.800
Angle α, β, γ (deg.)90.00, 105.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31725.088 Da / Num. of mol.: 1 / Fragment: Alpha-1, Alpha-2, Alpha-3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61769
#3: Protein/peptide nonameric peptide from Serine/threonine-protein kinase D2 / nPKC-D2


Mass: 1041.074 Da / Num. of mol.: 1 / Fragment: UNP residues 526-534 / Source method: obtained synthetically / Details: Commercial Synthesis / References: UniProt: Q9BZL6
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: SATURN / Detector: CCD / Date: Apr 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 59358 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 26.066 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.95
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.70.4413.132714835581.7
1.7-1.80.2885.636527767695
1.8-1.90.1839.132496637398.4
1.9-20.11814.227856517999.7
2-2.10.08219.924479432399.8
2.1-2.40.05827.6527909003100
2.4-2.70.04239.235752545299.9
2.7-30.03454.428567348599.9
3-40.02481.3611225469100
4-50.0298.323917197699.7
5-60.02197.11035086399.8
6-100.02196.911264957100
100.02297.7260124785.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.63 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.745 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3001 5.1 %RANDOM
Rwork0.202 ---
obs0.203 59357 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.446 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 16 400 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213231
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9244383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7555380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84823.023172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89815.029514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8911529
X-RAY DIFFRACTIONr_chiral_restr0.10.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022534
X-RAY DIFFRACTIONr_nbd_refined0.1880.21301
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.217
X-RAY DIFFRACTIONr_mcbond_it0.9161.51975
X-RAY DIFFRACTIONr_mcangle_it1.38623075
X-RAY DIFFRACTIONr_scbond_it2.22431483
X-RAY DIFFRACTIONr_scangle_it3.2864.51308
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 175 -
Rwork0.282 3206 -
all-3381 -
obs--74.6 %

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