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- PDB-4g9d: Crystal Structure of HLA B2705-KK10 -

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Basic information

Entry
Database: PDB / ID: 4g9d
TitleCrystal Structure of HLA B2705-KK10
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-27 alpha chain
  • P24
KeywordsIMMUNE SYSTEM / TCR / T cell / HLA B*2705 / KK10 / KK10-L6M / HIV / immune escape
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / viral process / detection of bacterium ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / viral process / detection of bacterium / negative regulation of receptor binding / secretory granule membrane / 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 / HIV-1 retropepsin / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / exoribonuclease H / cellular response to iron(III) ion / exoribonuclease H activity / 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 / defense response / 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 / DNA integration / 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 / viral genome integration into host DNA / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / specific granule lumen / viral penetration into host nucleus / host multivesicular body / phagocytic vesicle membrane / RNA-directed DNA polymerase activity / recycling endosome membrane / Interferon gamma signaling / RNA-DNA hybrid ribonuclease activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / viral capsid / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / host cell / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / protein homotetramerization / amyloid fibril formation / DNA-directed DNA polymerase / adaptive immune response / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / DNA-directed DNA polymerase activity / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / signaling receptor binding / viral translational frameshifting
Similarity search - Function
gag protein p24 N-terminal domain / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin ...gag protein p24 N-terminal domain / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / Reverse transcriptase thumb / Reverse transcriptase thumb domain / : / MHC class I-like antigen recognition-like / Integrase Zinc binding domain / Zinc finger integrase-type profile. / MHC class I-like antigen recognition-like superfamily / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Gag-Pol polyprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / p24
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsGras, S. / Wilmann, P.G. / Rossjohn, J.
CitationJournal: Immunity / Year: 2013
Title: A Molecular Basis for the Control of Preimmune Escape Variants by HIV-Specific CD8(+) T Cells.
Authors: Ladell, K. / Hashimoto, M. / Iglesias, M.C. / Wilmann, P.G. / McLaren, J.E. / Gras, S. / Chikata, T. / Kuse, N. / Fastenackels, S. / Gostick, E. / Bridgeman, J.S. / Venturi, V. / Arkoub, Z.A. ...Authors: Ladell, K. / Hashimoto, M. / Iglesias, M.C. / Wilmann, P.G. / McLaren, J.E. / Gras, S. / Chikata, T. / Kuse, N. / Fastenackels, S. / Gostick, E. / Bridgeman, J.S. / Venturi, V. / Arkoub, Z.A. / Agut, H. / van Bockel, D.J. / Almeida, J.R. / Douek, D.C. / Meyer, L. / Venet, A. / Takiguchi, M. / Rossjohn, J. / Price, D.A. / Appay, V.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 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, B-27 alpha chain
B: Beta-2-microglobulin
C: P24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0124
Polymers44,9203
Non-polymers921
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-14 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.207, 82.350, 109.244
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, B-27 alpha chain / MHC class I antigen B*27


Mass: 31928.160 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03989, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide P24


Mass: 1243.564 Da / Num. of mol.: 1 / Fragment: UNP residues 99-108 / Source method: obtained synthetically / Details: GL peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YXW1, UniProt: P03366*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% PEG 3350 and 0.3M Na2SO4, pH 8, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 61797 / % possible obs: 100 % / Redundancy: 7.1 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
Blu-Iceicedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ogt

1ogt


Resolution: 1.6→46.366 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.17 / σ(F): 1.35 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 3129 5.07 %
Rwork0.1945 --
obs0.1965 61718 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.3221 Å2
Baniso -1Baniso -2Baniso -3
1--2.6959 Å2-0 Å20 Å2
2---4.077 Å2-0 Å2
3---6.7728 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 6 507 3682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063377
X-RAY DIFFRACTIONf_angle_d1.0514601
X-RAY DIFFRACTIONf_dihedral_angle_d14.0451265
X-RAY DIFFRACTIONf_chiral_restr0.075471
X-RAY DIFFRACTIONf_plane_restr0.004611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6250.27481440.24592614X-RAY DIFFRACTION100
1.625-1.65170.28121440.24152633X-RAY DIFFRACTION100
1.6517-1.68010.2951560.23682596X-RAY DIFFRACTION100
1.6801-1.71070.28421270.23442666X-RAY DIFFRACTION100
1.7107-1.74360.2561420.22412598X-RAY DIFFRACTION100
1.7436-1.77920.25341370.22672656X-RAY DIFFRACTION100
1.7792-1.81790.26861470.21312623X-RAY DIFFRACTION100
1.8179-1.86020.24391310.21582615X-RAY DIFFRACTION100
1.8602-1.90670.2611330.21252670X-RAY DIFFRACTION100
1.9067-1.95820.25061180.21592668X-RAY DIFFRACTION100
1.9582-2.01590.28591370.21062631X-RAY DIFFRACTION100
2.0159-2.08090.24231500.20542642X-RAY DIFFRACTION100
2.0809-2.15530.25971220.20942689X-RAY DIFFRACTION100
2.1553-2.24160.23661560.22629X-RAY DIFFRACTION100
2.2416-2.34360.23421540.20572649X-RAY DIFFRACTION100
2.3436-2.46720.22251370.19782651X-RAY DIFFRACTION100
2.4672-2.62170.26441550.2022671X-RAY DIFFRACTION100
2.6217-2.82410.24321620.19742655X-RAY DIFFRACTION100
2.8241-3.10830.23071430.19192705X-RAY DIFFRACTION100
3.1083-3.55790.2181360.17812714X-RAY DIFFRACTION100
3.5579-4.4820.19111480.15912732X-RAY DIFFRACTION100
4.482-46.38570.20411500.17992882X-RAY DIFFRACTION100

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