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- PDB-4i48: Structure of HLA-A68 complexed with an HIV Env derived peptide -

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Basic information

Entry
Database: PDB / ID: 4i48
TitleStructure of HLA-A68 complexed with an HIV Env derived peptide
Components
  • 9-mer peptide from Envelope glycoprotein gp160
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-68 alpha chain
KeywordsIMMUNE SYSTEM / Monomer / Peptide presentation
Function / homology
Function and homology information


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 / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I ...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 / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome 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 / 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 / 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 / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / viral protein processing / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1 lw12.3 isolate
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 Å
AuthorsNiu, L. / Cheng, H. / Zhang, S. / Tan, S. / Zhang, Y. / Qi, J. / Liu, J. / Gao, G.F.
CitationJournal: Mol.Immunol. / Year: 2013
Title: Structural basis for the differential classification of HLA-A*6802 and HLA-A*6801 into the A2 and A3 supertypes
Authors: Niu, L. / Cheng, H. / Zhang, S. / Tan, S. / Zhang, Y. / Qi, J. / Liu, J. / Gao, G.F.
History
DepositionNov 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-68 alpha chain
B: Beta-2-microglobulin
C: 9-mer peptide from Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)44,4513
Polymers44,4513
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-17 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.853, 68.194, 72.795
Angle α, β, γ (deg.)90.00, 100.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31778.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: P01891, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide 9-mer peptide from Envelope glycoprotein gp160


Mass: 925.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide derived from HIV
Source: (synth.) Human immunodeficiency virus type 1 lw12.3 isolate
References: UniProt: Q70626
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE CONFLICTS IN CHAIN A ARE NATURAL VARIANT, ALLELE A*68:02.

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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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M ammonium acetate, 0.1M Bis-Tris, 17%(w/v) PEG10000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 8, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.799→50 Å / Num. obs: 11512 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 73.62 Å2
Reflection shellResolution: 2.799→2.9 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.799→32.517 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7279 / SU ML: 0.39 / σ(F): 1.36 / Phase error: 33.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2813 538 4.74 %RANDOM
Rwork0.2176 ---
all0.2813 ---
obs0.2205 11355 96.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.16 Å2 / Biso mean: 79.2755 Å2 / Biso min: 26.66 Å2
Refinement stepCycle: LAST / Resolution: 2.799→32.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 0 3 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033221
X-RAY DIFFRACTIONf_angle_d0.7564368
X-RAY DIFFRACTIONf_chiral_restr0.052447
X-RAY DIFFRACTIONf_plane_restr0.003572
X-RAY DIFFRACTIONf_dihedral_angle_d13.2891179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.799-3.08050.34481310.29362649278095
3.0805-3.52580.33861370.26872761289899
3.5258-4.44040.26351440.22722710285498
4.4404-32.51960.25861260.18172697282395
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)
11.8004-0.36940.30542.77331.3663.0961-0.12320.4576-0.3584-1.0614-0.005-0.3063-0.0780.5326-0.00430.74490.05560.09770.7286-0.0490.4816-9.2557-19.658-28.8351
20.591-0.2123-0.92371.20920.57421.46230.0564-0.1424-0.0005-0.09820.0904-0.4759-0.02080.40640.01240.3243-0.0203-0.0890.39290.08410.4874-10.14963.1189-1.7459
30.39390.2256-0.02970.12460.00110.1236-0.11920.2496-0.2878-0.39010.1843-0.1736-0.27330.2686-00.37380.086-0.02580.368-0.01330.3813-16.7503-16.8529-6.3442
41.33690.24631.03440.11810.17680.8054-0.13970.64380.7695-0.4303-0.5810.6945-0.5339-0.2035-0.06660.49030.00760.04810.3795-0.02130.9419-28.91883.8053-7.4817
50.1920.11650.05560.12660.31311.1642-0.29360.0015-0.1863-0.61160.10330.21990.217-0.2297-0.00130.42210.0321-0.01110.3888-0.03130.5242-23.9469-14.5335-10.5048
60.11590.48890.18342.08990.76420.28260.3970.6545-0.00310.473-0.81040.28040.9214-0.1915-0.03570.27630.0457-0.06740.590.01220.4721-37.708-14.277-4.3435
70.12790.1201-0.24520.4264-0.05680.5401-0.317-0.76350.3324-0.38150.22930.0159-0.16850.164200.49320.0138-0.02070.68940.04210.3905-19.5915-15.5772-17.2191
80.40480.6208-0.31431.0169-0.54510.30520.1227-0.343-0.6269-0.2029-0.40930.8045-0.4496-0.3196-00.49550.1022-0.05240.5385-0.02750.66-29.1403-7.1024-9.3737
90.42310.1637-0.31980.3315-0.36430.43770.3644-0.1237-0.9466-0.3917-0.65230.16810.25570.1146-0.00520.32960.064-0.04130.3204-0.03740.6425-25.6455-20.6147-4.0449
103.2853-0.38621.71450.89210.05520.97760.3448-0.6594-0.14080.2646-0.13670.10780.062-0.46640.38820.4286-0.06090.07510.3341-0.1860.2733-26.2194-7.79780.6006
110.0849-0.0597-0.00490.0507-0.00110.00210.6649-0.31910.58440.40480.2241-0.4486-0.20580.261201.53250.25290.20561.61430.00550.7652-8.3573-23.0537-35.8498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:179 )A1 - 179
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 180:274 )A180 - 274
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 2:12 )B2 - 12
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 13:20 )B13 - 20
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 21:42 )B21 - 42
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 43:47 )B43 - 47
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 48:62 )B48 - 62
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 63:78 )B63 - 78
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 79:91 )B79 - 91
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 92:100 )B92 - 100
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 1:9 )C1 - 9

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