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- PDB-5w67: HLA-C*06:02 presenting VRSRR(ABA)LRL -

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Basic information

Entry
Database: PDB / ID: 5w67
TitleHLA-C*06:02 presenting VRSRR(ABA)LRL
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, Cw-6 alpha chain
  • VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
KeywordsIMMUNE SYSTEM / HLA / Antigen presentation / Human Leukocyte Antigen
Function / homology
Function and homology information


TAP binding / 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 / 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 ...TAP binding / 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 / 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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / MHC class II protein complex / 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 / 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 / peptide antigen binding / positive regulation of T cell activation / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / 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 / 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 / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / innate immune response / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 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 / 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, C alpha chain / Beta-2-microglobulin / HLA class I histocompatibility antigen, C alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMobbs, J.I. / Vivian, J.P. / Rossjohn, J.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule.
Authors: Mobbs, J.I. / Illing, P.T. / Dudek, N.L. / Brooks, A.G. / Baker, D.G. / Purcell, A.W. / Rossjohn, J. / Vivian, J.P.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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, Cw-6 alpha chain
B: Beta-2-microglobulin
C: VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4839
Polymers45,1113
Non-polymers3726
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint2 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.065, 81.575, 116.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, Cw-6 alpha chain / MHC class I antigen Cw*6


Mass: 32087.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C, HLAC / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q29963, UniProt: P10321*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, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU


Mass: 1144.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M Na acetate pH 4.5 and 1.8 M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→41.2 Å / Num. obs: 19189 / % possible obs: 99.7 % / Redundancy: 4 % / Rpim(I) all: 0.09 / Net I/σ(I): 7.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 6072 / Rpim(I) all: 0.42 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NT6

4nt6


Resolution: 2.3→41.197 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 23.66
RfactorNum. reflection% reflection
Rfree0.2347 956 5.02 %
Rwork0.1883 --
obs0.1907 19163 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 24 223 3327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023187
X-RAY DIFFRACTIONf_angle_d0.5054327
X-RAY DIFFRACTIONf_dihedral_angle_d9.6481866
X-RAY DIFFRACTIONf_chiral_restr0.039441
X-RAY DIFFRACTIONf_plane_restr0.003570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.36780.2631490.24212704X-RAY DIFFRACTION95
2.3678-2.44420.28491540.23162776X-RAY DIFFRACTION97
2.4442-2.53150.22221480.21432722X-RAY DIFFRACTION97
2.5315-2.63290.30031260.21892796X-RAY DIFFRACTION97
2.6329-2.75270.24681590.21862760X-RAY DIFFRACTION98
2.7527-2.89780.27651500.20752742X-RAY DIFFRACTION97
2.8978-3.07930.27111480.19362762X-RAY DIFFRACTION98
3.0793-3.31690.26291400.18482776X-RAY DIFFRACTION97
3.3169-3.65060.21311410.16642828X-RAY DIFFRACTION99
3.6506-4.17840.19431570.15382728X-RAY DIFFRACTION97
4.1784-5.26260.16921300.1552715X-RAY DIFFRACTION95
5.2626-41.2040.2721470.20692768X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.05740.4897-0.37542.18970.05641.78410.0217-0.12170.03120.1911-0.02710.05050.0966-0.107-0.00630.1314-0.0036-0.00050.171-0.02090.108513.49245.7706-3.6449
20.8370.2006-0.33851.44420.75691.5440.03240.01240.02530.1469-0.0014-0.05260.14420.1472-0.01020.18480.019-0.03190.16750.00160.21110.3134-22.4505-24.7216
30.9810.22510.42341.54650.08951.6601-0.00480.0498-0.0601-0.093-0.03090.2810.0917-0.20110.02210.1507-0.006-0.0130.1841-0.02290.2675-2.702-4.6143-22.9474
42.9861.4597-0.90411.6259-1.92562.68640.0844-0.13960.18490.5584-0.0229-0.2465-0.17960.1892-0.060.2662-0.0545-0.04370.1682-0.05170.160514.97479.85551.2787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 274 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 99 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 9 )

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