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- PDB-6l9k: H2-Ld a1a2 complexed with A5 peptide -

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Basic information

Entry
Database: PDB / ID: 6l9k
TitleH2-Ld a1a2 complexed with A5 peptide
Components
  • H2-Ld a1a2
  • SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / 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 / positive regulation of interleukin-4 production / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / 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 / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of tumor necrosis factor production / protein-folding chaperone binding / antibacterial humoral response / adaptive immune response / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / plasma membrane
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 / 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 ...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 / 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
H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWei, P.C. / Yin, L.
Funding support China, United States, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China3187072 China
National Natural Science Foundation of China31470738 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_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_conn / 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_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_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_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 2.1Jun 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 2.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H2-Ld a1a2
Q: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)21,6562
Polymers21,6562
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-8 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.730, 76.730, 73.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

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Components

#1: Protein H2-Ld a1a2


Mass: 20555.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: P01897*PLUS
#2: Protein/peptide SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Mass: 1100.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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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: 57.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 1.1 M ammonium tartrate dibasic pH 7.0

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→30.3 Å / Num. obs: 23063 / % possible obs: 98 % / Redundancy: 2 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 2310 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TJH

3tjh


Resolution: 1.8→30.263 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.78
RfactorNum. reflection% reflection
Rfree0.2309 1991 8.63 %
Rwork0.1943 --
obs0.1975 23063 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 46.443 Å2 / ksol: 0.411 e/Å3
Displacement parametersBiso max: 93.27 Å2 / Biso mean: 31.23 Å2 / Biso min: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.2536 Å20 Å20 Å2
2---0.2536 Å20 Å2
3---0.5073 Å2
Refinement stepCycle: final / Resolution: 1.8→30.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 0 198 1726
Biso mean---41.49 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081604
X-RAY DIFFRACTIONf_angle_d1.1322176
X-RAY DIFFRACTIONf_chiral_restr0.084204
X-RAY DIFFRACTIONf_plane_restr0.004291
X-RAY DIFFRACTIONf_dihedral_angle_d16.466596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8002-1.86450.28762010.25122109100
1.8645-1.93910.32012010.27972104100
1.9391-2.02740.23782030.20392119100
2.0274-2.13420.23882040.21222127100
2.1342-2.26790.29442000.20422140100
2.2679-2.4430.22522020.1912126100
2.443-2.68870.22242030.18692124100
2.6887-3.07740.222030.18452176100
3.0774-3.87590.19611970.1669215699
3.8759-30.2630.22211770.1939189183
Refinement TLS params.Method: refined / Origin x: 23.461 Å / Origin y: 17.211 Å / Origin z: 1.3196 Å
111213212223313233
T0.112 Å2-0.0147 Å2-0.0258 Å2-0.139 Å2-0.0293 Å2--0.1327 Å2
L2.7547 °2-0.825 °2-0.8977 °2-2.2349 °21.5811 °2--2.9496 °2
S-0.0293 Å °-0.3768 Å °0.1785 Å °0.0893 Å °0.1023 Å °-0.1199 Å °-0.0914 Å °0.1518 Å °-0.0547 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 176
2X-RAY DIFFRACTION1allQ1 - 9
3X-RAY DIFFRACTION1allS1 - 198

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