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- PDB-3bp7: The high resolution crystal structure of HLA-B*2709 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3bp7
TitleThe high resolution crystal structure of HLA-B*2709 in complex with a Cathepsin A signal sequence peptide, pCatA
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-27 alpha chain
  • nonameric peptide from Lysosomal protective protein
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex / MHC / Human Leukocyte Antigen / HLA / HLA-B*2709 / HLA-B2709 / beta-2-microglobulin / b2m / Cathepsin A signal sequence / pCatA / Ankylosing Spondylitis / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Carboxypeptidase / Hydrolase / Lysosome / Protease / Zymogen
Function / homology
Function and homology information


carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / Sialic acid metabolism / regulation of chaperone-mediated autophagy / Glycosphingolipid catabolism / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production ...carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / Sialic acid metabolism / regulation of chaperone-mediated autophagy / Glycosphingolipid catabolism / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / negative regulation of chaperone-mediated autophagy / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / carboxypeptidase activity / MHC class II antigen presentation / lysosomal lumen / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / intracellular protein transport / enzyme activator activity / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / regulation of protein stability / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / azurophil granule lumen / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / lysosome / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum
Similarity search - Function
Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Alpha/Beta hydrolase fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Lysosomal protective protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Homo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKumar, P. / Vahedi-Faridi, A. / Saenger, W. / Uchanska-Ziegler, B. / Ziegler, A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens
Authors: Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Merino, E. / Lopez de Castro, J.A. / Uchanska-Ziegler, B. / Ziegler, A.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 22, 2015Group: Source and taxonomy
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 1, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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, B-27 alpha chain
B: Beta-2-microglobulin
C: nonameric peptide from Lysosomal protective protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9054
Polymers44,8133
Non-polymers921
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-21 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.195, 83.002, 110.779
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-27 alpha chain / MHC class I antigen B*27 / Leukocyte Antigen (HLA) B*2709


Mass: 31951.219 Da / Num. of mol.: 1
Fragment: HLA-B*2709 extracellular domain, UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03989, UniProt: P01889*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) / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P61769
#3: Protein/peptide nonameric peptide from Lysosomal protective protein / Cathepsin A / Carboxypeptidase C / Protective protein for beta-galactosidase


Mass: 982.198 Da / Num. of mol.: 1 / Fragment: Cathepsin A signal sequence, UNP residues 2-10 / Source method: obtained synthetically
Details: Cathepsin A signal sequence peptide, pCatA, chemically synthesized, This sequence occurs naturally in humans.
Source: (synth.) Homo Sapiens (human) / References: UniProt: P10619
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE 140TH RESIDUE IS HIS IN ALLELE B*2709.

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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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23.5% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95373 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 18, 2006 / Details: Mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 41600 / % possible obs: 93.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.057 / Χ2: 0.796 / Net I/σ(I): 19.4
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.07 / Num. unique all: 3694 / Χ2: 0.684 / % possible all: 84.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.47 / Cor.coef. Fo:Fc: 0.463
Highest resolutionLowest resolution
Rotation3 Å46.07 Å
Translation3 Å46.07 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JGE

1jge


Resolution: 1.8→46.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.24 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2090 5 %RANDOM
Rwork0.167 ---
obs0.169 41552 92.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 6 513 3680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213274
X-RAY DIFFRACTIONr_bond_other_d0.0020.022822
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9244453
X-RAY DIFFRACTIONr_angle_other_deg1.12836573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20623.315178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65315531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7171532
X-RAY DIFFRACTIONr_chiral_restr0.1070.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
X-RAY DIFFRACTIONr_nbd_refined0.2150.2534
X-RAY DIFFRACTIONr_nbd_other0.2040.22801
X-RAY DIFFRACTIONr_nbtor_other0.0860.21850
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2333
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.232
X-RAY DIFFRACTIONr_mcbond_it1.5061.52504
X-RAY DIFFRACTIONr_mcbond_other0.3051.5775
X-RAY DIFFRACTIONr_mcangle_it1.62823131
X-RAY DIFFRACTIONr_scbond_it2.81531602
X-RAY DIFFRACTIONr_scangle_it3.8874.51320
LS refinement shellResolution: 1.797→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.26 -
Rwork0.217 2336
all-2453
obs-2336

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