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- PDB-6l9m: H2-Ld complexed with AH1 peptide -

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Basic information

Entry
Database: PDB / ID: 6l9m
TitleH2-Ld complexed with AH1 peptide
Components
  • H2-Ld
  • SER-PRO-SER-TYR-VAL-TYR-HIS-GLN-PHE
  • b2m
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / MHC class I protein complex / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWei, P.C. / Yin, L.
Funding support China, United States, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)3187072 China
National Natural Science Foundation of China (NSFC)31470738 China
National Basic Research Program of China (973 Program)2014CB910103 China
National Institutes of Health/Office of the Director1R01CA226879-01 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structures suggest an approach for converting weak self-peptide tumor antigens into superagonists for CD8 T cells in cancer.
Authors: Wei, P. / Jordan, K.R. / Buhrman, J.D. / Lei, J. / Deng, H. / Marrack, P. / Dai, S. / Kappler, J.W. / Slansky, J.E. / Yin, L.
History
DepositionNov 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 24, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 3.0Apr 7, 2021Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity_poly / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref_seq / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _entity_poly.pdbx_strand_id / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_rmsd_bond.auth_atom_id_1 / _pdbx_validate_rmsd_bond.auth_atom_id_2 / _pdbx_validate_rmsd_bond.auth_comp_id_1 / _pdbx_validate_rmsd_bond.auth_comp_id_2 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_standard_deviation / _pdbx_validate_rmsd_bond.bond_target_value / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_min / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_percent_reflns_obs / _refine.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free_error / _reflns.d_resolution_low / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.selection_details / _struct_ref_seq.pdbx_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Description: Sequence discrepancy
Details: 1. Residue numbering of chain A, D, G and J has been updated since 1-278 to 0-277. 2. Order of biological assembly has been changed.
Provider: author / Type: Coordinate replacement
Revision 3.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 3.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.3Nov 13, 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: H2-Ld
B: b2m
C: SER-PRO-SER-TYR-VAL-TYR-HIS-GLN-PHE
D: H2-Ld
E: b2m
F: SER-PRO-SER-TYR-VAL-TYR-HIS-GLN-PHE
G: H2-Ld
H: b2m
I: SER-PRO-SER-TYR-VAL-TYR-HIS-GLN-PHE
J: H2-Ld
K: b2m
L: SER-PRO-SER-TYR-VAL-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)179,83712
Polymers179,83712
Non-polymers00
Water3,801211
1
A: H2-Ld
B: b2m
C: SER-PRO-SER-TYR-VAL-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)44,9593
Polymers44,9593
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-21 kcal/mol
Surface area19570 Å2
MethodPISA
2
D: H2-Ld
E: b2m
F: SER-PRO-SER-TYR-VAL-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)44,9593
Polymers44,9593
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-21 kcal/mol
Surface area19520 Å2
MethodPISA
3
G: H2-Ld
H: b2m
I: SER-PRO-SER-TYR-VAL-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)44,9593
Polymers44,9593
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-21 kcal/mol
Surface area19530 Å2
MethodPISA
4
J: H2-Ld
K: b2m
L: SER-PRO-SER-TYR-VAL-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)44,9593
Polymers44,9593
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-21 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.865, 88.390, 105.710
Angle α, β, γ (deg.)80.97, 75.96, 88.24
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN J AND (RESSEQ 1:278 )
211CHAIN A AND (RESSEQ 1:278 )
311CHAIN D AND (RESSEQ 1:278 )
411CHAIN G AND (RESSEQ 1:278 )
112CHAIN K AND (RESSEQ 1:99 )
212CHAIN B AND (RESSEQ 1:99 )
312CHAIN E AND (RESSEQ 1:99 )
412CHAIN H AND (RESSEQ 1:99 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
H2-Ld


Mass: 32126.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01897*PLUS
#2: Protein
b2m


Mass: 11704.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01887*PLUS
#3: Protein/peptide
SER-PRO-SER-TYR-VAL-TYR-HIS-GLN-PHE


Mass: 1128.213 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium malonate pH 5.0, 15-20 % PEG 3350 and 5% 1, 6-Hexanediol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 52803 / % possible obs: 92.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.4
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 4551

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LD9

1ld9


Resolution: 2.6→19.97 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.22
RfactorNum. reflection% reflection
Rfree0.249 1866 3.53 %
Rwork0.213 --
obs0.214 52803 95.7 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 21.03 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 37.73 Å2
Baniso -1Baniso -2Baniso -3
1-9.6035 Å2-9.8845 Å28.3369 Å2
2---4.2242 Å2-4.2608 Å2
3----5.3793 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12680 0 0 211 12891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413088
X-RAY DIFFRACTIONf_angle_d1.34617792
X-RAY DIFFRACTIONf_dihedral_angle_d16.8234812
X-RAY DIFFRACTIONf_chiral_restr0.0871788
X-RAY DIFFRACTIONf_plane_restr0.0062328
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11J2268X-RAY DIFFRACTIONPOSITIONAL
12A2268X-RAY DIFFRACTIONPOSITIONAL0.135
13D2268X-RAY DIFFRACTIONPOSITIONAL0.164
14G2268X-RAY DIFFRACTIONPOSITIONAL0.124
21K821X-RAY DIFFRACTIONPOSITIONAL
22B821X-RAY DIFFRACTIONPOSITIONAL0.171
23E821X-RAY DIFFRACTIONPOSITIONAL0.172
24H821X-RAY DIFFRACTIONPOSITIONAL0.138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69270.35721700.28354381X-RAY DIFFRACTION83
2.6927-2.80030.31141910.26985183X-RAY DIFFRACTION98
2.8003-2.92730.27621830.26025208X-RAY DIFFRACTION98
2.9273-3.08110.32141940.25315231X-RAY DIFFRACTION98
3.0811-3.27340.30131850.24555262X-RAY DIFFRACTION98
3.2734-3.52490.27181950.22385198X-RAY DIFFRACTION98
3.5249-3.87730.26371790.21924823X-RAY DIFFRACTION91
3.8773-4.4330.21131910.17485245X-RAY DIFFRACTION98
4.433-5.56490.17441900.16395243X-RAY DIFFRACTION98
5.5649-19.9660.1981880.18285163X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 17.527 Å / Origin y: 90.456 Å / Origin z: 12.9298 Å
111213212223313233
T0.1338 Å20.0153 Å20.0185 Å2-0.1615 Å2-0.0278 Å2--0.1674 Å2
L0.0804 °20.1002 °2-0.0284 °2-0.2959 °2-0.1398 °2--0.228 °2
S0.0264 Å °-0.0447 Å °0.0185 Å °0.0425 Å °-0.0398 Å °-0.0044 Å °-0.0486 Å °0.0355 Å °0.0054 Å °
Refinement TLS groupSelection details: ALL

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