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- PDB-1hsb: DIFFERENT LENGTH PEPTIDES BIND TO HLA-AW68 SIMILARLY AT THEIR END... -

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Basic information

Entry
Database: PDB / ID: 1hsb
TitleDIFFERENT LENGTH PEPTIDES BIND TO HLA-AW68 SIMILARLY AT THEIR ENDS BUT BULGE OUT IN THE MIDDLE
Components
  • BOUND PEPTIDE FRAGMENT
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HISTOCOMPATIBILITY ANTIGEN
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / 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 / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / 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 / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / T cell receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / 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 / positive regulation of type II interferon production / 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 / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / 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 / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome
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
ALANINE / ARGININE / MHC class I antigen / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsGuo, H.-C. / Strominger, J.L. / Wiley, D.C.
Citation
Journal: Nature / Year: 1992
Title: Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle.
Authors: Guo, H.C. / Jardetzky, T.S. / Garrett, T.P. / Lane, W.S. / Strominger, J.L. / Wiley, D.C.
#1: Journal: To be Published
Title: Comparison of a Specificity Pocket in Three Human Histocompatibility Antigens: Hla-Aw68, Hla-A2 and Hla-B27
Authors: Guo, H.-C. / Madden, D.R. / Strominger, J.L. / Wiley, D.C.
#2: Journal: Nature / Year: 1992
Title: Different Length Peptides Bind to Hla-Aw68 Similarly at Their Ends But Bulge Out in the Middle
Authors: Guo, H.-C. / Jardetzky, T.S. / Garrett, T.P.J. / Lane, W.S. / Strominger, J.L. / Wiley, D.C.
#3: Journal: Nature / Year: 1992
Title: Atomic Structure of a Human Mhc Molecule Presenting an Influenza Virus Peptide
Authors: Silver, M.L. / Guo, H.-C. / Strominger, J.L. / Wiley, D.C.
#4: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: The Three-Dimensional Structure of Hla-B27 at 2.1 Angstroms Resolution Suggests a General Mechanism for Tight Peptide Binding to Mhc
Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
#5: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution
Authors: Saper, M.A. / Bjorkman, P.J. / Wiley, D.C.
#6: 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.
#7: Journal: Nature / Year: 1989
Title: Specificity Pockets for the Side Chains of Peptide Antigens in Hla-Aw68
Authors: Garrett, T.P.J. / Saper, M.A. / Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C.
#8: Journal: Nature / Year: 1987
Title: Structure of the Human Class I Histocompatibility Antigen, Hla-A2
Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C.
#9: Journal: Nature / Year: 1987
Title: The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens
Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C.
#10: Journal: J.Mol.Biol. / Year: 1985
Title: Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes
Authors: Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C.
History
DepositionMar 30, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 19, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / entity_src_nat / pdbx_database_status / struct_conn / struct_ref / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE ...SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE SHEETS TWICE (DESIGNATED SHEETS SB1, SB2 AND SD1, SD2 RESPECTIVELY) WHERE THE TWO REPRESENTATIONS DIFFER IN THEIR LAST STRAND.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: BOUND PEPTIDE FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4235
Polymers43,1593
Non-polymers2642
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-12 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.430, 78.469, 111.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SIDE CHAIN ATOMS OF GLU A 58, GLU A 89, ASP A 106, ARG A 108, GLN A 115, GLU A 128, HIS A 151, ASP A 196, GLN A 255, ASP B 34, GLU B 36, LYS B 41, GLU B 44, GLU B 47, LYS B 48, LYS B 58, GLU B 69, ...1: SIDE CHAIN ATOMS OF GLU A 58, GLU A 89, ASP A 106, ARG A 108, GLN A 115, GLU A 128, HIS A 151, ASP A 196, GLN A 255, ASP B 34, GLU B 36, LYS B 41, GLU B 44, GLU B 47, LYS B 48, LYS B 58, GLU B 69, LYS B 75, GLU B 77, ASN B 83, GLN B 89, AND LYS B 94 ARE DISORDERED AND HAVE OCCUPANCIES EQUAL TO 0.01 IN THIS ENTRY.
2: RESIDUES PRO A 210 AND PRO B 32 ARE CIS PROLINES.
3: LYS A 268, PRO A 269, AND LEU A 270 ARE DISORDERED, AND HAVE OCCUPANCIES EQUAL TO 0.01 IN THIS ENTRY.
4: THESE SOLVENT MOLECULES ARE LOCATED WITHIN THE PEPTIDE-BINDING SITE OF HLA-AW68.
DetailsTHERE IS ONE COMPLEX PER ASYMMETRIC UNIT, WHICH COMPOSED OF FOUR POLYPEPTIDE CHAINS: HLA HEAVY CHAIN IDENTIFIED AS CHAIN *A* IN THIS ENTRY, BETA-2-MICROGLOBULIN IDENTIFIED AS CHAIN *B*, A MODEL OF BOUND N-TERMINAL TRI-PEPTIDE IDENTIFIED AS CHAIN *C*, A MODEL OF BOUND C-TERMINAL DI-PEPTIDE REPORTED AS RESIDUES 1001 AND 1002 IN THE ENTRY.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31151.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A6YT91, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide BOUND PEPTIDE FRAGMENT


Mass: 259.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

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Non-polymers , 3 types, 272 molecules

#4: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#5: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsSECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF THE PROCEDURE OF W. KABSCH AND C. SANDER ...SECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF THE PROCEDURE OF W. KABSCH AND C. SANDER (PROGRAM *DSSP*). THE FRAGMENT CRYSTALLIZED WAS THE EXTRACELLULAR PORTION OF THE PROTEIN CLEAVED FROM THE CELL MEMBRANE WITH PAPAIN. THE FINAL MODEL REPORTED IN THE PAPER CITED ON JRNL RECORDS ABOVE INCLUDED A MODEL OF N-TERMINAL PART OF BOUND PEPTIDES WITH SEQUENCE AVA, AND A MODEL OF C-TERMINAL PART OF BOUND PEPTIDES WITH SEQUENCE AR.
Has protein modificationY
Nonpolymer detailsTHE RESIDUES 1001 AND 1002 REPRESENT THE BOUND, C-TERMINAL DIPEPTIDE (ALA-ARG)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.06 %
Crystal grow
*PLUS
Method: vapor diffusion / Details: referred to J.Mol.Biol. 186.205-210 1985 / PH range low: 6.5 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
225 mM2-(N-morpholino)ethanesulfonic acid1dropcan be replaced with 100mM imidazole
315 %(w/v)PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.073

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.22 / Rfactor obs: 0.22 / Highest resolution: 1.9 Å
Details: LYS A 268, PRO A 269, AND LEU A 270 ARE DISORDERED, AND HAVE OCCUPANCIES EQUAL TO 0.01 IN THIS ENTRY
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 17 270 3327
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 5.5 Å / σ(F): 3 / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.1

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