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- PDB-1jge: HLA-B*2705 bound to nona-peptide m9 -

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Basic information

Entry
Database: PDB / ID: 1jge
TitleHLA-B*2705 bound to nona-peptide m9
Components
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-27 B*2705 ALPHA CHAIN
  • peptide m9
KeywordsIMMUNE SYSTEM / MHC (Major Histocompatibility Complex) / HLA (Human Leukocyte Antigen)
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 I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / secretory granule membrane ...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 I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / secretory granule membrane / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / 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 / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / 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 / 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 / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 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
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHulsmeyer, M. / Hillig, R.C. / Volz, A. / Ruhl, M. / Schroder, W. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: HLA-B27 subtypes differentially associated with disease exhibit subtle structural alterations
Authors: Hulsmeyer, M. / Hillig, R.C. / Volz, A. / Ruhl, M. / Schroder, W. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
#1: Journal: Nature / Year: 1991
Title: The Structure of HLA-B27 Reveals Nonamer Self-peptides Bound in an Extended Conformation
Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: The Three-dimensional Structure of HLA-B27 at 2.1 A Resolution Suggests a General Mechanism for Tight Peptide Binding to MHC
Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
History
DepositionJun 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 B*2705 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: peptide m9


Theoretical massNumber of molelcules
Total (without water)44,7143
Polymers44,7143
Non-polymers00
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-15 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.3, 83.2, 110.4
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a heterotrimeric complex consisting of one HLA-B*2705 (heavy) chain, one beta-2-microglobulin (light) chain and one nonameric model peptide m9.

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-27 B*2705 ALPHA CHAIN


Mass: 31928.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B or HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P03989, UniProt: P01889*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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide peptide m9


Mass: 906.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide was chemically synthesized.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.7 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Tris-HCl, NaCl; PEG 400 as cryo protectant, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: used streak-seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMTris1droppH7.5
3150 mM1dropNaCl
428 %PEG80001reservoir
5100 mMTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.07→19.7 Å / Num. all: 26918 / Num. obs: 26918 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 30.7
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 6.5 / % possible all: 50.4
Reflection
*PLUS
Num. obs: 26964 / % possible obs: 91.3 %
Reflection shell
*PLUS
Lowest resolution: 2.14 Å / % possible obs: 67.1 % / Redundancy: 3 % / Num. unique obs: 1931 / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 7.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1hsa

1hsa


Resolution: 2.1→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1369 5.1 %RANDOM
Rwork0.1917 ---
all0.1945 26887 --
obs0.1945 26887 91.2 %-
Displacement parametersBiso mean: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---1.5 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 0 462 3647
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.021
X-RAY DIFFRACTIONp_mcbond_it0.7661.5
X-RAY DIFFRACTIONp_mcangle_it1.2822
X-RAY DIFFRACTIONp_scbond_it2.2633
X-RAY DIFFRACTIONp_scangle_it3.5074.5
X-RAY DIFFRACTIONp_angle_d1.426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.1-2.150.28630.22X-RAY DIFFRACTION121159.81
2.15-2.210.3780.21X-RAY DIFFRACTION164984.08
2.21-2.280.26910.2X-RAY DIFFRACTION162584.37
2.28-2.350.25920.2X-RAY DIFFRACTION159886.09
2.35-2.430.26940.2X-RAY DIFFRACTION156286.48
2.43-2.520.31850.2X-RAY DIFFRACTION154689.22
2.52-2.610.29850.2X-RAY DIFFRACTION155591.62
2.61-2.720.33700.2X-RAY DIFFRACTION153894.53
2.72-2.840.26960.2X-RAY DIFFRACTION154197.15
2.84-2.990.3720.19X-RAY DIFFRACTION148498.48
2.99-3.150.23880.19X-RAY DIFFRACTION143399.35
3.15-3.350.27700.2X-RAY DIFFRACTION133798.81
3.35-3.580.23630.19X-RAY DIFFRACTION129699.41
3.58-3.890.27650.19X-RAY DIFFRACTION119399.6
3.89-4.30.2570.18X-RAY DIFFRACTION113399.25
4.3-4.820.19630.16X-RAY DIFFRACTION99699.53
4.82-5.680.19460.16X-RAY DIFFRACTION93399.69
5.68-7.010.29420.19X-RAY DIFFRACTION798100
7.07-11.180.23390.2X-RAY DIFFRACTION641100
11.18-19.70.2100.22X-RAY DIFFRACTION44998.92
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 19.7 Å / Num. reflection obs: 25518 / % reflection Rfree: 5 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.15 Å / Rfactor Rfree: 0.28

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