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- PDB-1uxw: CRYSTAL STRUCTURE OF HLA-B*2709 COMPLEXED WITH THE LATENT MEMBRAN... -

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Basic information

Entry
Database: PDB / ID: 1uxw
TitleCRYSTAL STRUCTURE OF HLA-B*2709 COMPLEXED WITH THE LATENT MEMBRANE PROTEIN 2 PEPTIDE (LMP2) OF EPSTEIN-BARR VIRUS
Components
  • BETA-2-MICROGLOBULIN
  • GENE TERMINAL PROTEIN (MEMBRANE PROTEIN LMP-2A/LMP-2B)
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN B-27 ALPHA CHAIN
KeywordsIMMUNE SYSTEM/PEPTIDE / IMMUNE SYSTEM-PEPTIDE COMPLEX / COMPLEX (ANTIGEN-PEPTIDE) / IMMUNE SYSTEM / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA- B*2709
Function / homology
Function and homology information


: / : / : / : / : / negative regulation of receptor binding / viral latency / host cell endomembrane system / regulation of interleukin-12 production / regulation of dendritic cell differentiation ...: / : / : / : / : / negative regulation of receptor binding / viral latency / host cell endomembrane system / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / positive regulation of protein binding / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of membrane depolarization / protection from natural killer cell mediated cytotoxicity / TAP binding / T cell differentiation in thymus / detection of bacterium / 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 / beta-2-microglobulin binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / positive regulation of T cell mediated cytotoxicity / DAP12 interactions / secretory granule membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of neuron projection development / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / iron ion transport / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / defense response / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / protein refolding / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of immune response / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / cellular response to lipopolysaccharide / protein-folding chaperone binding / ER-Phagosome pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / early endosome membrane / antibacterial humoral response / defense response to Gram-negative bacterium / amyloid fibril formation / protein homotetramerization / symbiont-mediated perturbation of host ubiquitin-like protein modification / adaptive immune response / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / host cell perinuclear region of cytoplasm / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / focal adhesion / lysosomal membrane
Similarity search - Function
Gammaherpesvirus latent membrane protein 2 / Gammaherpesvirus latent membrane protein (LMP2) protein / 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 / : ...Gammaherpesvirus latent membrane protein 2 / Gammaherpesvirus latent membrane protein (LMP2) protein / 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
Beta-2-microglobulin / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Latent membrane protein 2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN HERPESVIRUS 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsHulsmeyer, M. / Kozerski, C. / Fiorillo, M.T. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Allele-Dependent Similarity between Viral and Self-Peptide Presentation by Hla-B27 Subtypes
Authors: Fiorillo, M.T. / Ruckert, C. / Hulsmeyer, M. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
#1: Journal: J.Exp.Med. / Year: 2004
Title: Dual, Hla-B27 Subtype-Dependent Conformation of a Self-Peptide
Authors: Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
History
DepositionMar 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 1, 2025Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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 B-27 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: GENE TERMINAL PROTEIN (MEMBRANE PROTEIN LMP-2A/LMP-2B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5958
Polymers45,1343
Non-polymers4605
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.920, 82.595, 62.790
Angle α, β, γ (deg.)90.00, 104.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN B-27 ALPHA CHAIN / MHC CLASS I ANTIGEN B*27


Mass: 31951.219 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03989, UniProt: P01889*PLUS
#2: Protein BETA-2-MICROGLOBULIN / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN DOMAIN, RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01884, UniProt: P61769*PLUS
#3: Protein/peptide GENE TERMINAL PROTEIN (MEMBRANE PROTEIN LMP-2A/LMP-2B) / LATENT MEMBRANE PROTEIN 2 (LMP2)


Mass: 1303.586 Da / Num. of mol.: 1 / Fragment: TRANSMEMBRANE DOMAIN, RESIDUES 236-244 / Source method: obtained synthetically / Source: (synth.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) / References: UniProt: P13285
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.9 Å3/Da / Density % sol: 56.9 %
Crystal growpH: 8.5 / Details: 0.1M TRIS, PH 8.5, 21% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8856
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.72→60 Å / Num. obs: 53353 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 4 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K5N

1k5n


Resolution: 1.71→60.86 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.609 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2703 5.1 %RANDOM
Rwork0.154 ---
obs0.156 50633 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å2-0.12 Å2
2--0.08 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.71→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 30 596 3809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213369
X-RAY DIFFRACTIONr_bond_other_d0.0030.022926
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9324567
X-RAY DIFFRACTIONr_angle_other_deg0.90236820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023724
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02738
X-RAY DIFFRACTIONr_nbd_refined0.2040.2574
X-RAY DIFFRACTIONr_nbd_other0.260.23511
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21979
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2397
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0790.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3360.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9651.51944
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71523155
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.69531425
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3714.51410
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.76 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.224 186
Rwork0.183 3319
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)
10.353-0.01250.01340.1343-0.05080.0920.00870.0527-0.0125-0.0215-0.00260.00430.002-0.0033-0.00610.0243-0.00230.00090.0224-0.00090.01544.3725-5.2955-7.5417
20.16780.0231-0.00780.1254-0.01460.03580.00090.0085-0.00130.00840.0085-0.0055-0.0027-0.0003-0.00940.02550.00150.00370.02090.0020.0274.6205-2.17490.055
30.0186-0.03240.31950.20530.00720.77540.0039-0.00740.00970.0224-0.015-0.02640.0104-0.03120.01110.0206-0.0011-0.00670.03670.00120.010227.3117-4.360425.156
40.36430.20620.06520.55640.11370.2817-0.0135-0.03610.02290.01170.0276-0.0115-0.0351-0.0044-0.01410.02440.0018-0.00770.0173-0.01620.016615.139212.431815.9969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 85
2X-RAY DIFFRACTION1A138 - 180
3X-RAY DIFFRACTION1C1 - 9
4X-RAY DIFFRACTION2A1 - 49
5X-RAY DIFFRACTION2A86 - 137
6X-RAY DIFFRACTION3A181 - 276
7X-RAY DIFFRACTION4B1 - 99

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