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- PDB-3lv3: Crystal structure of HLA-B*2705 complexed with a peptide derived ... -

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Basic information

Entry
Database: PDB / ID: 3lv3
TitleCrystal structure of HLA-B*2705 complexed with a peptide derived from the human voltage-dependent calcium channel alpha1 subunit (residues 513-521)
Components
  • 9-meric peptide from Voltage-dependent L-type calcium channel subunit alpha-1D
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-27 alpha chain
KeywordsIMMUNE SYSTEM / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA-B*2705 / Disulfide bond / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Amyloid / Amyloidosis / Disease mutation / Glycation / Immunoglobulin domain / Secreted / Calcium channel / Voltage-gated channel
Function / homology
Function and homology information


voltage-gated calcium channel activity involved SA node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / positive regulation of adenylate cyclase activity / membrane depolarization during SA node cell action potential / regulation of atrial cardiac muscle cell membrane repolarization / L-type voltage-gated calcium channel complex / membrane depolarization during cardiac muscle cell action potential / regulation of interleukin-12 production / regulation of dendritic cell differentiation / NCAM1 interactions ...voltage-gated calcium channel activity involved SA node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / positive regulation of adenylate cyclase activity / membrane depolarization during SA node cell action potential / regulation of atrial cardiac muscle cell membrane repolarization / L-type voltage-gated calcium channel complex / membrane depolarization during cardiac muscle cell action potential / regulation of interleukin-12 production / regulation of dendritic cell differentiation / NCAM1 interactions / calcium ion import / positive regulation of calcium ion transport / cardiac muscle cell action potential involved in contraction / regulation of T cell anergy / regulation of potassium ion transmembrane transport / regulation of interleukin-6 production / ankyrin binding / Sensory processing of sound by inner hair cells of the cochlea / voltage-gated calcium channel complex / regulation of heart rate by cardiac conduction / protection from natural killer cell mediated cytotoxicity / calcium ion import across plasma membrane / alpha-actinin binding / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / voltage-gated calcium channel activity / secretory granule membrane / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Regulation of insulin secretion / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / defense response / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / sensory perception of sound / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / calcium ion transmembrane transport / calcium channel activity / recycling endosome membrane / Z disc / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / tertiary granule lumen / calcium ion transport / positive regulation of cellular senescence / MHC class II protein complex binding / Adrenaline,noradrenaline inhibits insulin secretion / T cell differentiation in thymus / DAP12 signaling / late endosome membrane / negative regulation of neuron projection development / protein refolding / protein-folding chaperone binding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / immune response / endoplasmic reticulum lumen
Similarity search - Function
Voltage-dependent calcium channel, L-type, alpha-1D subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / : / Voltage-dependent L-type calcium channel, IQ-associated domain ...Voltage-dependent calcium channel, L-type, alpha-1D subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / : / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage-dependent channel domain superfamily / 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 / : / Ion transport domain / Ion transport 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 / 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 / Beta-2-microglobulin / Voltage-dependent L-type calcium channel subunit alpha-1D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLoll, B. / Rueckert, C. / Saenger, W. / Uchanska-Ziegler, B. / Ziegler, A.
CitationJournal: Protein Sci. / Year: 2011
Title: Loss of recognition by cross-reactive T cells and its relation to a C-terminus-induced conformational reorientation of an HLA-B*2705-bound peptide.
Authors: Loll, B. / Ruckert, C. / Hee, C.S. / Saenger, W. / Uchanska-Ziegler, B. / Ziegler, A.
History
DepositionFeb 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Nov 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 1.4Oct 9, 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 I histocompatibility antigen, B-27 alpha chain
B: Beta-2-microglobulin
C: 9-meric peptide from Voltage-dependent L-type calcium channel subunit alpha-1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4616
Polymers45,1853
Non-polymers2763
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-11 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.290, 54.614, 69.834
Angle α, β, γ (deg.)90.00, 99.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, B-27 alpha chain / MHC class I antigen B*27


Mass: 31928.160 Da / Num. of mol.: 1 / Fragment: 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 / Beta-2-microglobulin form pI 5.3


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): BL21 / References: UniProt: P61769
#3: Protein/peptide 9-meric peptide from Voltage-dependent L-type calcium channel subunit alpha-1D


Mass: 1377.584 Da / Num. of mol.: 1 / Fragment: UNP residues 502-510 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01668
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20%(w/v) PEG 8000, 150mM NaCl, 20mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2004
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.94→20 Å / Num. all: 18393 / Num. obs: 31104 / Rsym value: 0.113 / Net I/σ(I): 16.2
Reflection shellResolution: 1.94→1.97 Å / Mean I/σ(I) obs: 4.8 / Num. unique all: 1529 / Rsym value: 0.36

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Processing

Software
NameVersionClassification
DNAdata collection
EPMRphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A83

2a83


Resolution: 1.94→19.46 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.895 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22435 1544 5.1 %RANDOM
Rwork0.17553 ---
obs0.17802 28960 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.115 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.37 Å2
2---0.06 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 18 312 3517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213415
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9354644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01522.923195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9815583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5651540
X-RAY DIFFRACTIONr_chiral_restr0.0930.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212689
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6421.51958
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22423196
X-RAY DIFFRACTIONr_scbond_it1.91531457
X-RAY DIFFRACTIONr_scangle_it3.2084.51442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 98 -
Rwork0.191 2000 -
obs--94.12 %
Refinement TLS params.Method: refined / Origin x: 38.7121 Å / Origin y: 9.6363 Å / Origin z: 18.7124 Å
111213212223313233
T0.0472 Å2-0.0041 Å2-0.0127 Å2-0.0658 Å2-0.0002 Å2--0.0705 Å2
L0.5983 °2-0.0308 °2-0.2251 °2-0.9151 °20.2845 °2--1.5196 °2
S0.0113 Å °-0.1411 Å °0.0044 Å °0.1609 Å °-0.0484 Å °0.0898 Å °-0.0429 Å °-0.1559 Å °0.0371 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 183
2X-RAY DIFFRACTION1A184 - 276
3X-RAY DIFFRACTION1B0 - 99
4X-RAY DIFFRACTION1C1 - 9

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