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- PDB-5w6a: HLA-C*06:02 presenting ARTELYRSL -

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Basic information

Entry
Database: PDB / ID: 5w6a
TitleHLA-C*06:02 presenting ARTELYRSL
Components
  • ALA-ARG-THR-GLU-LEU-TYR-ARG-SER-LEU
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, Cw-6 alpha chain
KeywordsIMMUNE SYSTEM / HLA / Antigen presentation / Human Leukocyte Antigen
Function / homology
Function and homology information


leucine zipper domain binding / negative regulation of amyloid precursor protein biosynthetic process / embryonic cleavage / NRAGE signals death through JNK / TAP binding / negative regulation of apoptotic signaling pathway / 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 / regulation of mitotic cell cycle / secretory granule membrane ...leucine zipper domain binding / negative regulation of amyloid precursor protein biosynthetic process / embryonic cleavage / NRAGE signals death through JNK / TAP binding / negative regulation of apoptotic signaling pathway / 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 / regulation of mitotic cell cycle / 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 / small-subunit processome / 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 / 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 / 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 / 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 / ribosomal small subunit biogenesis / protein refolding / early endosome membrane / protein homotetramerization / transcription regulator complex / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / cell adhesion / 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 / Neutrophil degranulation / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Protein AATF/Bfr2 / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis antagonizing transcription factor / 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 ...Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Protein AATF/Bfr2 / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis antagonizing transcription factor / 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 / Protein AATF
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, Cw-6 alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, Cw-6 alpha chain
D: Beta-2-microglobulin
E: ALA-ARG-THR-GLU-LEU-TYR-ARG-SER-LEU
F: ALA-ARG-THR-GLU-LEU-TYR-ARG-SER-LEU


Theoretical massNumber of molelcules
Total (without water)90,1546
Polymers90,1546
Non-polymers00
Water14,142785
1
A: HLA class I histocompatibility antigen, Cw-6 alpha chain
B: Beta-2-microglobulin
E: ALA-ARG-THR-GLU-LEU-TYR-ARG-SER-LEU


Theoretical massNumber of molelcules
Total (without water)45,0773
Polymers45,0773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-14 kcal/mol
Surface area18420 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, Cw-6 alpha chain
D: Beta-2-microglobulin
F: ALA-ARG-THR-GLU-LEU-TYR-ARG-SER-LEU


Theoretical massNumber of molelcules
Total (without water)45,0773
Polymers45,0773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-14 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.191, 136.950, 70.961
Angle α, β, γ (deg.)90.00, 107.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTRPTRPAA2 - 2742 - 274
21SERSERTRPTRPCC2 - 2742 - 274
12METMETMETMETBB0 - 991 - 100
22METMETMETMETDD0 - 991 - 100

NCS ensembles :
ID
2
1

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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.: 2
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.: 2
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 ALA-ARG-THR-GLU-LEU-TYR-ARG-SER-LEU


Mass: 1110.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q9NY61*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris propane pH 7.0, 0.1 M Na fluoride and 20 % PEG 8000

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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: 1.74→68.47 Å / Num. obs: 86176 / % possible obs: 99.6 % / Redundancy: 8.7 % / Rpim(I) all: 0.03 / Net I/σ(I): 18.8
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4252 / Rpim(I) all: 0.32 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NT6

4nt6


Resolution: 1.74→68.47 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.702 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20074 4391 5.1 %RANDOM
Rwork0.1605 ---
obs0.16259 81743 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å2-0.15 Å2
2---0.65 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.74→68.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6248 0 0 787 7035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0196428
X-RAY DIFFRACTIONr_bond_other_d0.0020.025552
X-RAY DIFFRACTIONr_angle_refined_deg2.3131.9268738
X-RAY DIFFRACTIONr_angle_other_deg1.163312836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66822.975353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.552151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.641566
X-RAY DIFFRACTIONr_chiral_restr0.1510.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0217272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021470
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_it1.1361.1353050
X-RAY DIFFRACTIONr_mcbond_other1.1361.1353049
X-RAY DIFFRACTIONr_mcangle_it1.6741.6963802
X-RAY DIFFRACTIONr_mcangle_other1.6741.6963803
X-RAY DIFFRACTIONr_scbond_it1.8761.3783378
X-RAY DIFFRACTIONr_scbond_other1.8761.3783378
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8921.9824936
X-RAY DIFFRACTIONr_long_range_B_refined5.67814.8237474
X-RAY DIFFRACTIONr_long_range_B_other5.59113.8677269
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A173280.11
12C173280.11
21B61660.09
22D61660.09
LS refinement shellResolution: 1.737→1.782 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 296 -
Rwork0.236 5729 -
obs--94.63 %
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)
11.27110.22360.54311.44830.06493.38130.0261-0.0485-0.04070.06420.0109-0.01950.0814-0.1466-0.03690.0079-0.00140.00870.00790.00760.0367-17.54921.6804-31.1334
23.9941.33671.00182.83891.27192.8001-0.10240.09070.3578-0.12710.1361-0.2646-0.26270.4349-0.03370.0493-0.04520.03060.07750.00570.1572-0.406722.342-33.8533
31.1325-0.3880.24616.1791-0.27451.385-0.08960.02390.0884-0.0977-0.04790.3498-0.2798-0.16870.13750.12020.0161-0.07280.0489-0.04970.1497-13.924236.9813-23.3932
42.9963-0.46871.75061.923-0.69873.0924-0.0592-0.02490.1507-0.0498-0.0221-0.0972-0.15040.150.08130.0194-0.01220.01770.0146-0.00880.046711.515751.4561-3.7773
52.1346-0.33-1.15823.4268-1.89663.6907-0.0981-0.212-0.33310.1220.15570.46020.1509-0.2683-0.05760.0258-0.01580.04450.10440.05440.1879-3.289931.33666.4797
61.55090.466-0.09565.4886-0.05850.7909-0.05050.1599-0.1005-0.30920.118-0.20910.1580.0224-0.06740.0748-0.01340.01870.12130.0380.073312.648615.65155.0567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 180
2X-RAY DIFFRACTION1E1 - 9
3X-RAY DIFFRACTION2B0 - 99
4X-RAY DIFFRACTION3A181 - 274
5X-RAY DIFFRACTION4C2 - 180
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D0 - 99
8X-RAY DIFFRACTION6C181 - 274

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