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- PDB-6ei2: Crystal Structure of HLA-A68 presenting a C-terminally extended p... -

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Basic information

Entry
Database: PDB / ID: 6ei2
TitleCrystal Structure of HLA-A68 presenting a C-terminally extended peptide
Components
  • Beta-2-microglobulin
  • G1/S-specific cyclin-D2
  • HLA class I histocompatibility antigen, A-68 alpha chain
KeywordsIMMUNE SYSTEM / C-terminally extended peptide / HLA
Function / homology
Function and homology information


mitotic cell cycle phase transition / Regulation of RUNX1 Expression and Activity / cyclin-dependent protein serine/threonine kinase regulator activity / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / regulation of cyclin-dependent protein serine/threonine kinase activity ...mitotic cell cycle phase transition / Regulation of RUNX1 Expression and Activity / cyclin-dependent protein serine/threonine kinase regulator activity / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of cyclin-dependent protein serine/threonine kinase activity / TAP binding / protection from natural killer cell mediated cytotoxicity / cyclin-dependent protein kinase holoenzyme complex / positive regulation of G1/S transition of mitotic cell cycle / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / Cyclin D associated events in G1 / 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 / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / nuclear membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / positive regulation of protein phosphorylation / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / cell division
Similarity search - Function
Cyclin D / Cyclin, C-terminal domain / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma ...Cyclin D / Cyclin, C-terminal domain / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / NICKEL (II) ION / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / G1/S-specific cyclin-D2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsPicaud, S. / Guillaume, P. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gfeller, D. / Filippakopoulos, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust095751/Z/11/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal Structure of HLA-A68 presenting a C-terminally extended peptide
Authors: Picaud, S. / Guillaume, P. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gfeller, D. / Filippakopoulos, P.
History
DepositionSep 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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, A-68 alpha chain
B: Beta-2-microglobulin
C: G1/S-specific cyclin-D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,77015
Polymers44,9383
Non-polymers83212
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Complex (HLA-A*68 : B2M : peptide)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-46 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.061, 80.247, 110.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A-68 alpha chain / Aw-68 / HLA class I histocompatibility antigen / A-28 alpha chain / MHC class I antigen A*68


Mass: 31969.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET24(+) Vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: P01891, UniProt: P04439*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: pHN1 Vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide G1/S-specific cyclin-D2


Mass: 1089.216 Da / Num. of mol.: 1 / Fragment: UNP residues 114-123 / Source method: obtained synthetically / Details: C-terminally extended peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P30279

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Non-polymers , 5 types, 454 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#7: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% PEG3350 0.005M cobalt chloride 0.005M cadmium chloride 0.005M nickel chloride 0.005M magnesium chloride 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 1.61→29.531 Å / Num. all: 68846 / Num. obs: 68846 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Rsym value: 0.094 / Net I/av σ(I): 5.4 / Net I/σ(I): 11.3 / Num. measured all: 454107
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.61-1.76.60.6021.398730.2530.6540.60299.5
1.7-1.86.70.4211.894080.1760.4570.421100
1.8-1.926.60.2842.688520.1190.3080.284100
1.92-2.086.60.184482650.0770.20.184100
2.08-2.286.60.1345.376320.0560.1450.134100
2.28-2.556.70.116.369340.0460.1190.11100
2.55-2.946.70.0867.661390.0360.0940.086100
2.94-3.66.60.0649.352440.0270.070.064100
3.6-5.096.40.05610.741260.0240.060.056100
5.09-29.5315.90.0579.823730.0250.0620.05799.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å29.53 Å
Translation3.5 Å29.53 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
SCALA3.3.22data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 4HWZ, 5T6X, 4RMU, 4HWZ

4hwz

5t6x

4rmu

4hwz


Resolution: 1.61→29.53 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.37 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0678 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 1917 2.8 %RANDOM
Rwork0.1579 ---
obs0.1586 66856 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.77 Å2 / Biso mean: 20.343 Å2 / Biso min: 9.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0 Å2
2--0.09 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.61→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 29 442 3602
Biso mean--34.11 30.46 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193273
X-RAY DIFFRACTIONr_bond_other_d0.0020.022864
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9264437
X-RAY DIFFRACTIONr_angle_other_deg1.03536638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83723.295173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9631529
X-RAY DIFFRACTIONr_chiral_restr0.1160.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
LS refinement shellResolution: 1.61→1.652 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 117 -
Rwork0.219 4822 -
all-4939 -
obs--98.66 %
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)
10.17510.0252-0.04750.1375-0.11720.1337-0.0206-0.0158-0.002-0.0217-0.0206-0.04260.0199-0.02550.04120.0050.00540.00460.0659-0.00640.022848.362743.564620.9237
20.3794-0.20950.58390.7278-0.70991.1605-0.04430.00660.02330.10510.0090.0167-0.1177-0.00040.03530.02150.00550.00220.03950.00980.026950.668344.674239.9641
30.8649-0.6855-0.48220.76320.31260.3119-0.0142-0.04320.0324-0.10390.0388-0.01760.02510.0197-0.02460.0633-0.0075-0.00870.05470.00290.023753.446158.6249.1478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 299
2X-RAY DIFFRACTION2B20 - 119
3X-RAY DIFFRACTION3C10 - 19

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