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- PDB-7s79: STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH SYNTHETIC PHOSPHONO-MLL ... -

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Basic information

Entry
Database: PDB / ID: 7s79
TitleSTRUCTURE OF HLA-B*07:02 IN COMPLEX WITH SYNTHETIC PHOSPHONO-MLL PEPTIDE ANALOG
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-7 alpha chain
  • MLL cleavage product N320
KeywordsIMMUNE SYSTEM / HLA / MLL PEPTIDE / MHC-I / HLA-B*07:02 / HLA-B7 / IMMUNITY / PHOSPHOPEPTIDE / PHOSPHONO ANALOG / CANCER
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / definitive hemopoiesis ...negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / definitive hemopoiesis / regulation of short-term neuronal synaptic plasticity / regulation of T cell anergy / histone H3K4 methyltransferase activity / regulation of interleukin-6 production / anterior/posterior pattern specification / embryonic hemopoiesis / T-helper 2 cell differentiation / Formation of WDR5-containing histone-modifying complexes / exploration behavior / histone methyltransferase complex / minor groove of adenine-thymine-rich DNA binding / TAP binding / protection from natural killer cell mediated cytotoxicity / MLL1 complex / 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 / membrane depolarization / detection of bacterium / cellular response to transforming growth factor beta stimulus / negative regulation of fibroblast proliferation / spleen development / homeostasis of number of cells within a tissue / transcription initiation-coupled chromatin remodeling / secretory granule membrane / negative regulation of receptor binding / Transferases; Transferring one-carbon groups; Methyltransferases / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / post-embryonic development / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / circadian regulation of gene expression / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / visual learning / positive regulation of immune response / MHC class I protein complex / protein modification process / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / PKMTs methylate histone lysines / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / Transcriptional regulation of granulopoiesis / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / protein refolding / protein-containing complex assembly / fibroblast proliferation / early endosome membrane
Similarity search - Function
KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. ...KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / PHD-finger / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Zinc finger PHD-type signature. / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Zinc finger PHD-type profile. / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Zinc finger, FYVE/PHD-type / MHC classes I/II-like antigen recognition protein / : / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Zinc finger, RING/FYVE/PHD-type / 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 / Beta-2-microglobulin / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsPatskovska, L. / Patskovsky, Y. / Nyovanie, S. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. ...Patskovska, L. / Patskovsky, Y. / Nyovanie, S. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R. / Findeis, M. / Hurwitz, A. / Van Dijk, M. / Buell, J. / Underwood, D. / Krogsgaard, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM124489 United States
CitationJournal: Nat Commun / Year: 2023
Title: Molecular mechanism of phosphopeptide neoantigen immunogenicity.
Authors: Patskovsky, Y. / Natarajan, A. / Patskovska, L. / Nyovanie, S. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R.B. / Findeis, M.A. ...Authors: Patskovsky, Y. / Natarajan, A. / Patskovska, L. / Nyovanie, S. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R.B. / Findeis, M.A. / Hurwitz, A. / Van Dijk, M. / Chantzoura, E. / Yague, A.S. / Pollack Smith, D. / Buell, J.S. / Underwood, D. / Krogsgaard, M.
History
DepositionSep 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-7 alpha chain
B: Beta-2-microglobulin
E: MLL cleavage product N320
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3408
Polymers44,9493
Non-polymers3915
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-26 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.860, 65.860, 238.857
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, B-7 alpha chain / MHC class I antigen B*7


Mass: 31962.016 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: PET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01889
#2: Protein Beta-2-microglobulin


Mass: 11879.356 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: PET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules E

#3: Protein/peptide MLL cleavage product N320 / N-terminal cleavage product of 320 kDa / p320


Mass: 1107.135 Da / Num. of mol.: 1 / Fragment: PHOSPHONO-MLL(747-755) PEPTIDE / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q03164

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Non-polymers , 3 types, 572 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.88 Å3/Da / Density % sol: 57.38 % / Description: rods
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18-24% PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2019 / Details: Si(111) MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 1.53→29.45 Å / Num. obs: 80429 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.4
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5721 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RZD

7rzd


Resolution: 1.53→29.25 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.345 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 2491 3.1 %RANDOM
Rwork0.1699 ---
obs0.1707 77832 99.76 %-
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 max: 124.05 Å2 / Biso mean: 27.034 Å2 / Biso min: 9.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0 Å2-0 Å2
2--0.75 Å2-0 Å2
3----1.51 Å2
Refinement stepCycle: final / Resolution: 1.53→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 25 569 3749
Biso mean--43.23 41.66 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133448
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173005
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6644704
X-RAY DIFFRACTIONr_angle_other_deg1.4081.5836993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4465424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.79420.932236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.615565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1431539
X-RAY DIFFRACTIONr_chiral_restr0.0760.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023987
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02818
LS refinement shellResolution: 1.53→1.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 193 -
Rwork0.244 5516 -
all-5709 -
obs--97.54 %

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