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- PDB-6l9n: H2-Ld complexed with A5 peptide -

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Basic information

Entry
Database: PDB / ID: 6l9n
TitleH2-Ld complexed with A5 peptide
Components
  • MHC
  • SER-PRO-SER-TYR-ALA-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 / defense response / 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 / 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 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_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / 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_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_symm_contact.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 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
Revision 2.3Nov 6, 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: MHC
B: b2m
C: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE
D: MHC
E: b2m
F: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE
G: MHC
H: b2m
I: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE
J: MHC
K: b2m
L: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)179,72512
Polymers179,72512
Non-polymers00
Water3,729207
1
A: MHC
B: b2m
C: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)44,9313
Polymers44,9313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-20 kcal/mol
Surface area19530 Å2
MethodPISA
2
D: MHC
E: b2m
F: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)44,9313
Polymers44,9313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-18 kcal/mol
Surface area19470 Å2
MethodPISA
3
G: MHC
H: b2m
I: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)44,9313
Polymers44,9313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-20 kcal/mol
Surface area19530 Å2
MethodPISA
4
J: MHC
K: b2m
L: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)44,9313
Polymers44,9313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-20 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.961, 88.443, 105.805
Angle α, β, γ (deg.)80.990, 75.810, 88.340
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 1:278 )
21chain D and (resseq 1:278 )
31chain G and (resseq 1:278 )
41chain J and (resseq 1:278 )
12chain B and (resseq 1:99 )
22chain E and (resseq 1:99 )
32chain H and (resseq 1:99 )
42chain K and (resseq 1:99 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:278 )A1 - 278
211chain D and (resseq 1:278 )D1 - 278
311chain G and (resseq 1:278 )G1 - 278
411chain J and (resseq 1:278 )J1 - 278
112chain B and (resseq 1:99 )B1 - 99
212chain E and (resseq 1:99 )E1 - 99
312chain H and (resseq 1:99 )H1 - 99
412chain K and (resseq 1:99 )K1 - 99

NCS ensembles :
ID
1
2

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Components

#1: Protein
MHC


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-ALA-TYR-HIS-GLN-PHE


Mass: 1100.160 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.: 207 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging 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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 53822 / % possible obs: 97.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.431 / Num. unique obs: 4798 / R split: 2

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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→19.964 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.6
RfactorNum. reflection% reflection
Rfree0.2535 2005 3.73 %
Rwork0.2088 --
obs0.2105 53822 97.33 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Bsol: 26.692 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso max: 186.59 Å2 / Biso mean: 50.18 Å2 / Biso min: 17.91 Å2
Baniso -1Baniso -2Baniso -3
1-6.3053 Å2-8.0096 Å29.8119 Å2
2---5.7743 Å2-1.5284 Å2
3----0.531 Å2
Refinement stepCycle: final / Resolution: 2.6→19.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12672 0 0 207 12879
Biso mean---39.2 -
Num. residues----1544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02113080
X-RAY DIFFRACTIONf_angle_d1.74217780
X-RAY DIFFRACTIONf_chiral_restr0.1041784
X-RAY DIFFRACTIONf_plane_restr0.0082328
X-RAY DIFFRACTIONf_dihedral_angle_d16.5234808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2268X-RAY DIFFRACTIONPOSITIONAL0.172
12D2268X-RAY DIFFRACTIONPOSITIONAL0.172
13G2268X-RAY DIFFRACTIONPOSITIONAL0.131
14J2268X-RAY DIFFRACTIONPOSITIONAL0.15
21B821X-RAY DIFFRACTIONPOSITIONAL0.117
22E821X-RAY DIFFRACTIONPOSITIONAL0.117
23H821X-RAY DIFFRACTIONPOSITIONAL0.08
24K821X-RAY DIFFRACTIONPOSITIONAL0.093
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6001-2.69290.35061740.3095462487
2.6929-2.80040.3911930.3242498794
2.8004-2.92750.42381980.3335511196
2.9275-3.08130.32151990.2738524999
3.0813-3.27360.31182090.2315332100
3.2736-3.5250.27752080.22535300100
3.525-3.87740.25232020.21365297100
3.8774-4.43320.21272070.16315316100
4.4332-5.56520.18382030.15765320100
5.5652-19.9640.19062120.1641528199
Refinement TLS params.Method: refined / Origin x: -17.3773 Å / Origin y: 21.4106 Å / Origin z: 41.8482 Å
111213212223313233
T0.3091 Å2-0.0093 Å20.0381 Å2-0.3129 Å2-0.024 Å2--0.2973 Å2
L0.0878 °20.0759 °2-0.0386 °2-0.3189 °2-0.1853 °2--0.1469 °2
S0.0651 Å °-0.0793 Å °0.0439 Å °0.1457 Å °-0.0564 Å °0.0255 Å °-0.0851 Å °0.0253 Å °-0.0059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 278
2X-RAY DIFFRACTION1allB1 - 99
3X-RAY DIFFRACTION1allC1 - 9
4X-RAY DIFFRACTION1allD1 - 278
5X-RAY DIFFRACTION1allE1 - 99
6X-RAY DIFFRACTION1allF1 - 9
7X-RAY DIFFRACTION1allG1 - 278
8X-RAY DIFFRACTION1allH1 - 99
9X-RAY DIFFRACTION1allI1 - 9
10X-RAY DIFFRACTION1allJ1 - 278
11X-RAY DIFFRACTION1allK1 - 99
12X-RAY DIFFRACTION1allL1 - 9
13X-RAY DIFFRACTION1allS1 - 207

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