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- PDB-5w69: HLA-C*06:02 presenting ARFNDLRFV -

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Basic information

Entry
Database: PDB / ID: 5w69
TitleHLA-C*06:02 presenting ARFNDLRFV
Components
  • ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL
  • Beta-2-microglobulinBeta-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


peripheral nervous system neuron development / RUNX3 regulates RUNX1-mediated transcription / core-binding factor complex / positive regulation of CD8-positive, alpha-beta T cell differentiation / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates BCL2L11 (BIM) transcription / RUNX3 regulates WNT signaling / response to transforming growth factor beta / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX3 regulates YAP1-mediated transcription ...peripheral nervous system neuron development / RUNX3 regulates RUNX1-mediated transcription / core-binding factor complex / positive regulation of CD8-positive, alpha-beta T cell differentiation / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates BCL2L11 (BIM) transcription / RUNX3 regulates WNT signaling / response to transforming growth factor beta / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX3 regulates YAP1-mediated transcription / chromatin => GO:0000785 / RUNX3 Regulates Immune Response and Cell Migration / RUNX3 regulates NOTCH signaling / RUNX3 regulates CDKN1A transcription / regulation of cell differentiation / hemopoiesis / RUNX3 regulates p14-ARF / negative regulation of cell cycle / TAP binding / chondrocyte differentiation / ossification / 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 / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of RUNX3 expression and activity / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sequence-specific double-stranded DNA binding / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / Amyloid fiber formation / DNA-binding transcription factor activity / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / protein phosphorylation / signaling receptor binding
Similarity search - Function
Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / MHC class I, alpha chain, C-terminal ...Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / Runt-related transcription factor 3 / 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: 2.8 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

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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: HLA class I histocompatibility antigen, Cw-6 alpha chain
D: Beta-2-microglobulin
E: HLA class I histocompatibility antigen, Cw-6 alpha chain
F: Beta-2-microglobulin
G: HLA class I histocompatibility antigen, Cw-6 alpha chain
H: Beta-2-microglobulin
I: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL
J: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL
K: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL
L: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Theoretical massNumber of molelcules
Total (without water)180,42312
Polymers180,42312
Non-polymers00
Water13,872770
1
A: HLA class I histocompatibility antigen, Cw-6 alpha chain
B: Beta-2-microglobulin
I: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Theoretical massNumber of molelcules
Total (without water)45,1063
Polymers45,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-15 kcal/mol
Surface area18500 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, Cw-6 alpha chain
D: Beta-2-microglobulin
J: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Theoretical massNumber of molelcules
Total (without water)45,1063
Polymers45,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-14 kcal/mol
Surface area18420 Å2
MethodPISA
3
E: HLA class I histocompatibility antigen, Cw-6 alpha chain
F: Beta-2-microglobulin
K: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Theoretical massNumber of molelcules
Total (without water)45,1063
Polymers45,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-17 kcal/mol
Surface area18600 Å2
MethodPISA
4
G: HLA class I histocompatibility antigen, Cw-6 alpha chain
H: Beta-2-microglobulin
L: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Theoretical massNumber of molelcules
Total (without water)45,1063
Polymers45,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-14 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.182, 182.137, 222.736
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.: 4
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 / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 4
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-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Mass: 1139.307 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q13761*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M Na acetate and 20 % PEG 3350

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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: 2.8→74.34 Å / Num. obs: 52631 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 51.22 Å2 / Rpim(I) all: 0.11 / Net I/σ(I): 11.8
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 9.2 % / Num. unique obs: 4512 / Rpim(I) all: 0.51 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NT6

4nt6


Resolution: 2.8→40.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / Rfactor Rfree error: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.317
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2671 5.08 %RANDOM
Rwork0.164 ---
obs0.167 52539 100 %-
Displacement parametersBiso mean: 34.86 Å2
Baniso -1Baniso -2Baniso -3
1--7.5189 Å20 Å20 Å2
2--5.8439 Å20 Å2
3---1.675 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.8→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12458 0 0 795 13253
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112831HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1117458HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4355SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes364HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1876HARMONIC5
X-RAY DIFFRACTIONt_it12831HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion18.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1571SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14305SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 183 4.76 %
Rwork0.211 3665 -
all0.216 3848 -
obs--100 %
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)
11.2874-0.296-0.23271.2875-0.03782.8525-0.0270.1044-0.0512-0.2094-0.0487-0.12510.391-0.02910.0757-0.0671-0.040.0448-0.1123-0.0189-0.04579.9448-56.8992-22.032
23.37171.318-1.43173.6046-0.83822.73710.0184-0.05740.06660.06040.0021-0.0975-0.02010.2102-0.0206-0.09990.00680.0240.07090.003-0.154116.4536-32.0175-47.7354
31.0038-0.84240.71931.7429-2.04714.0285-0.0682-0.02270.09780.09730.17770.1351-0.5434-0.5401-0.1095-0.05530.05150.03440.00920.0171-0.0591-0.7206-34.5311-33.6411
41.04050.39580.06983.3803-1.26753.47520.1683-0.1368-0.1729-0.04420.06990.47610.52970.0896-0.2382-0.12380.027-0.0648-0.214-0.04170.0542-6.0751-56.2223-89.5292
53.5212-1.1102-0.8423.90460.75452.4939-0.01570.12870.0146-0.033-0.00190.1206-0.0837-0.08690.0176-0.0978-0.01970.01390.04640.048-0.1436-11.7641-31.4653-63.4878
61.45260.57181.5491.65581.93284.4589-0.05760.0692-0.0401-0.0250.0251-0.076-0.18830.50410.0324-0.1093-0.02470.02710.0258-0.0052-0.03175.5093-34.5094-77.467
71.24440.06070.5043.15950.2651.2057-0.0201-0.04250.046-0.11060.2439-0.5442-0.15730.1686-0.2238-0.0747-0.0660.1233-0.1428-0.1136-0.0137-7.098.1527-95.1786
82.93991.29640.70095.07792.52463.9554-0.09270.17220.0696-0.27710.1463-0.0201-0.19540.1226-0.0537-0.09090.03810.037-0.09910.0095-0.0444-4.7636-25.9382-107.131
91.1153-0.4723-0.76724.79380.05012.5632-0.13390.0031-0.49560.12890.34420.54420.2551-0.1483-0.2102-0.1405-0.05330.0467-0.1623-0.02040.1253-20.6168-15.3856-94.7704
104.44561.12190.84414.75750.98471.30390.133-0.0708-0.1306-0.30920.07610.2306-0.0135-0.2238-0.20910.0325-0.1309-0.1395-0.25410.1288-0.15544.96957.7815-15.8773
112.61410.14631.20122.9452-1.15931.9012-0.2735-0.24550.35870.07980.00270.1324-0.5441-0.16980.2708-0.0280.0652-0.0931-0.086-0.0925-0.04616.4854-26.9568-3.2035
121.93211.0444-0.47370.8230.21022.26620.0139-0.0234-0.1939-0.1834-0.0514-0.2227-0.48730.45560.03750.0301-0.152-0.152-0.1240.0949-0.024720.8948-14.0806-15.0741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION2{ A|181 - A|274 }A181 - 274
2X-RAY DIFFRACTION3{ B|0 - B|99 }B0 - 99
3X-RAY DIFFRACTION5{ C|181 - C|274 }C181 - 274
4X-RAY DIFFRACTION6{ D|0 - D|99 }D0 - 99
5X-RAY DIFFRACTION8{ E|181 - E|274 }E181 - 274
6X-RAY DIFFRACTION9{ F|0 - F|99 }F0 - 99
7X-RAY DIFFRACTION11{ G|181 - G|274 }G181 - 274
8X-RAY DIFFRACTION12{ H|0 - H|99 }H0 - 99

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