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- PDB-6l9l: 1D4 TCR recognition of H2-Ld a1a2 A5 Peptide Complexes -

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Basic information

Entry
Database: PDB / ID: 6l9l
Title1D4 TCR recognition of H2-Ld a1a2 A5 Peptide Complexes
Components
  • (T Cell Receptor) x 2
  • H2-Ld a1a2
  • SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex / T Cell Receptor
Function / homology
Function and homology information


MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / TAP complex binding / Golgi medial cisterna / CD8 receptor binding / beta-2-microglobulin binding / endoplasmic reticulum exit site ...MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / TAP complex binding / Golgi medial cisterna / CD8 receptor binding / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / MHC class I protein binding / 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 / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I peptide loading complex / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / phagocytic vesicle membrane / protein-folding chaperone binding / early endosome membrane / early endosome / immune response / receptor ligand activity / signaling receptor binding / Golgi membrane / external side of plasma membrane / lysosomal membrane / cell surface / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / : / identical protein binding / 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. ...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: 2.399 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_bond / 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_close_contact.auth_seq_id_2 / _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_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: 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
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: H2-Ld a1a2
C: T Cell Receptor
D: T Cell Receptor
B: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE
E: H2-Ld a1a2
G: T Cell Receptor
H: T Cell Receptor
F: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)140,9188
Polymers140,9188
Non-polymers00
Water4,594255
1
A: H2-Ld a1a2
C: T Cell Receptor
D: T Cell Receptor
B: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)70,4594
Polymers70,4594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: H2-Ld a1a2
G: T Cell Receptor
H: T Cell Receptor
F: SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Theoretical massNumber of molelcules
Total (without water)70,4594
Polymers70,4594
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.044, 148.044, 169.449
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11chain A or (chain G and (resseq 1:79 or resseq...
21(chain C and (resseq 1:79 or resseq 81:124 or resseq...
12chain B
22chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A or (chain G and (resseq 1:79 or resseq...A1 - 79
121chain A or (chain G and (resseq 1:79 or resseq...A81 - 124
131chain A or (chain G and (resseq 1:79 or resseq...A126 - 145
141chain A or (chain G and (resseq 1:79 or resseq...A147 - 160
151chain A or (chain G and (resseq 1:79 or resseq...A162 - 198
211(chain C and (resseq 1:79 or resseq 81:124 or resseq...C1 - 79
221(chain C and (resseq 1:79 or resseq 81:124 or resseq...C81 - 124
231(chain C and (resseq 1:79 or resseq 81:124 or resseq...C126 - 145
241(chain C and (resseq 1:79 or resseq 81:124 or resseq...C147 - 160
251(chain C and (resseq 1:79 or resseq 81:124 or resseq...C162 - 198
112chain BB1 - 9
212chain FF1 - 9

NCS ensembles :
ID
1
2

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Components

#1: Protein H2-Ld a1a2


Mass: 20555.648 Da / Num. of mol.: 2
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 T Cell Receptor


Mass: 21807.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein T Cell Receptor


Mass: 26995.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE


Mass: 1100.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M lithium sulfate, 0.1 M imidazole malate pH 6.5 and 2% w/v PEG 8000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.399→42.362 Å / Num. obs: 67669 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 18
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4210

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TJH

3tjh


Resolution: 2.399→42.362 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.31
RfactorNum. reflection% reflection
Rfree0.2343 1903 2.81 %
Rwork0.2027 --
obs0.2037 67669 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.38 Å2 / Biso mean: 49.2319 Å2 / Biso min: 28.11 Å2
Refinement stepCycle: final / Resolution: 2.399→42.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9922 0 0 255 10177
Biso mean---48.94 -
Num. residues----1242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610194
X-RAY DIFFRACTIONf_angle_d0.80313866
X-RAY DIFFRACTIONf_chiral_restr0.0541448
X-RAY DIFFRACTIONf_plane_restr0.0061822
X-RAY DIFFRACTIONf_dihedral_angle_d16.3686028
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5816X-RAY DIFFRACTION7.067TORSIONAL
12C5816X-RAY DIFFRACTION7.067TORSIONAL
21B72X-RAY DIFFRACTION7.067TORSIONAL
22F72X-RAY DIFFRACTION7.067TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3993-2.45930.32531190.2838409184
2.4593-2.52580.28211240.276424886
2.5258-2.60010.30191310.2669445890
2.6001-2.6840.28561210.2634452192
2.684-2.77990.31841400.2606463994
2.7799-2.89120.30091420.2544465495
2.8912-3.02270.25091360.2473476497
3.0227-3.1820.26881370.239484098
3.182-3.38130.26661390.2297487998
3.3813-3.64230.25031470.198488399
3.6423-4.00850.20331380.1859491499
4.0085-4.5880.18781440.15974935100
4.588-5.77810.18181410.16424951100
5.7781-42.3620.2251440.1806498999
Refinement TLS params.Method: refined / Origin x: -47.4411 Å / Origin y: -26.5885 Å / Origin z: -24.3218 Å
111213212223313233
T0.3517 Å20.0148 Å2-0.0109 Å2-0.353 Å2-0.0105 Å2--0.3586 Å2
L0.8451 °20.5318 °2-0.1138 °2-0.8404 °2-0.1131 °2--0.0681 °2
S0.0123 Å °-0.0395 Å °0.0409 Å °-0.039 Å °0.0141 Å °0.0444 Å °0.0008 Å °0.0027 Å °-0.0257 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 176
2X-RAY DIFFRACTION1allC1 - 198
3X-RAY DIFFRACTION1allD1 - 239
4X-RAY DIFFRACTION1allB1 - 9
5X-RAY DIFFRACTION1allE2 - 176
6X-RAY DIFFRACTION1allG1 - 198
7X-RAY DIFFRACTION1allH1 - 239
8X-RAY DIFFRACTION1allF1 - 9
9X-RAY DIFFRACTION1allS1 - 255

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