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- PDB-7byd: Crystal structure of SN45 TCR in complex with lipopeptide-bound M... -

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Basic information

Entry
Database: PDB / ID: 7byd
TitleCrystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104
Components
  • (SN45 T cell receptor ...) x 2
  • B protein
  • Beta-2-microglobulin
  • GLY-GLY-ALA-ILE
KeywordsIMMUNE SYSTEM / Major histocompatibility complex class 1 / T cell receptor / lipopeptide
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane ...antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / early endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / extracellular space / extracellular region
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
IODIDE ION / MYRISTIC ACID / B protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80003270022 Å
AuthorsMorita, D. / Sugita, M. / Iwashita, C.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05791 Japan
Japan Society for the Promotion of Science (JSPS)18K19563 Japan
Japan Society for the Promotion of Science (JSPS)18H02852 Japan
Japan Society for the Promotion of Science (JSPS)19H04805 Japan
Japan Society for the Promotion of Science (JSPS)18K07172 Japan
CitationJournal: Int.Immunol. / Year: 2020
Title: Crystal structure of the ternary complex of TCR, MHC class I and lipopeptides.
Authors: Morita, D. / Iwashita, C. / Mizutani, T. / Mori, N. / Mikami, B. / Sugita, M.
History
DepositionApr 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B protein
B: Beta-2-microglobulin
C: GLY-GLY-ALA-ILE
D: SN45 T cell receptor alpha chain
E: SN45 T cell receptor beta chain
F: B protein
G: Beta-2-microglobulin
H: GLY-GLY-ALA-ILE
I: SN45 T cell receptor alpha chain
J: SN45 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,02738
Polymers187,72510
Non-polymers3,30128
Water90150
1
A: B protein
B: Beta-2-microglobulin
C: GLY-GLY-ALA-ILE
D: SN45 T cell receptor alpha chain
E: SN45 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,45718
Polymers93,8635
Non-polymers1,59513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: B protein
G: Beta-2-microglobulin
H: GLY-GLY-ALA-ILE
I: SN45 T cell receptor alpha chain
J: SN45 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,56920
Polymers93,8635
Non-polymers1,70715
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.937, 95.071, 123.352
Angle α, β, γ (deg.)90.0, 90.894, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPROPROchain 'A'AA1 - 2761 - 276
221GLYGLYPROPROchain 'F'FF1 - 2761 - 276
132ALAALAMETMETchain 'B'BB0 - 991 - 100
242ALAALAMETMETchain 'G'GG0 - 991 - 100
153GLYGLYILEILEchain 'C'CC2 - 51 - 4
263GLYGLYILEILEchain 'H'HH2 - 51 - 4
174ALAALAASPASPchain 'D'DD1 - 1371 - 137
184VALVALPROPROchain 'D'DD142 - 197142 - 197
294ALAALAASPASPchain 'I'II1 - 1371 - 137
2104VALVALPROPROchain 'I'II142 - 197142 - 197
1115ASPASPASNASNchain 'E'EE1 - 571 - 57
1125PROPROSERSERchain 'E'EE61 - 22061 - 220
1135TRPTRPALAALAchain 'E'EE225 - 245225 - 245
2145ASPASPASNASNchain 'J'JJ1 - 571 - 57
2155PROPROSERSERchain 'J'JJ61 - 22061 - 220
2165TRPTRPALAALAchain 'J'JJ225 - 245225 - 245

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 2 types, 4 molecules AFBG

#1: Protein B protein / MHC class I antigen / MHC-class I protein


Mass: 31919.164 Da / Num. of mol.: 2 / Mutation: R149E,K198E,D244E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: Mamu-B, B / Production host: Escherichia coli (E. coli) / References: UniProt: B2ZHY7
#2: Protein Beta-2-microglobulin


Mass: 11731.157 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q6V7J5

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide GLY-GLY-ALA-ILE


Mass: 316.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Simian immunodeficiency virus

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SN45 T cell receptor ... , 2 types, 4 molecules DIEJ

#4: Protein SN45 T cell receptor alpha chain


Mass: 21809.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Escherichia coli (E. coli)
#5: Protein SN45 T cell receptor beta chain


Mass: 28086.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 78 molecules

#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: I
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5 and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 48069 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 51.1104457323 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.02
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.492 / Num. unique obs: 7672

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IWG, 2NW2

6iwg

2nw2


Resolution: 2.80003270022→41.9633912528 Å / SU ML: 0.417444186972 / Cross valid method: FREE R-VALUE / σ(F): 1.36364223881 / Phase error: 26.0969432362
RfactorNum. reflection% reflection
Rfree0.249628129727 2393 5.00229942723 %
Rwork0.185170315463 45445 -
obs0.188415640165 47838 99.7643427666 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.6531146715 Å2
Refinement stepCycle: LAST / Resolution: 2.80003270022→41.9633912528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13174 0 45 50 13269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012150577354213616
X-RAY DIFFRACTIONf_angle_d1.4594377007218454
X-RAY DIFFRACTIONf_chiral_restr0.07387020164941908
X-RAY DIFFRACTIONf_plane_restr0.007748876253822423
X-RAY DIFFRACTIONf_dihedral_angle_d15.53498465535010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.85720.3814136822161370.3057001285242598X-RAY DIFFRACTION99.9634502924
2.8572-2.91930.3520124906681420.2851369073472704X-RAY DIFFRACTION99.9648753073
2.9193-2.98720.3255618526811400.2428543999742658X-RAY DIFFRACTION99.9642729546
2.9872-3.06190.3438181094621410.22984830622675X-RAY DIFFRACTION99.9290276792
3.0619-3.14460.2914579325791400.227105078492653X-RAY DIFFRACTION99.9642090193
3.1446-3.23710.3147662711410.2141083066392694X-RAY DIFFRACTION99.9647390691
3.2371-3.34160.2834250821611400.2085271150392658X-RAY DIFFRACTION99.9285714286
3.3416-3.46090.2692237570111400.1997742122862645X-RAY DIFFRACTION99.8565794191
3.4609-3.59940.2358141000341400.1836108388712661X-RAY DIFFRACTION99.8930099857
3.5994-3.76320.24891370291400.17576828842671X-RAY DIFFRACTION99.8579040853
3.7632-3.96140.2276524211141420.1717771229372703X-RAY DIFFRACTION99.8245614035
3.9614-4.20940.2410810516461410.168791352012663X-RAY DIFFRACTION99.7155049787
4.2094-4.5340.2266983467971400.1509573984612666X-RAY DIFFRACTION99.3978037549
4.534-4.98970.1640481080021400.1408788266992669X-RAY DIFFRACTION99.6806245564
4.9897-5.71010.2148042669551420.1608609393322686X-RAY DIFFRACTION99.8587570621
5.7101-7.18830.2788020938691420.191476862702X-RAY DIFFRACTION99.6845425868
7.1883-41.96310.2288019981491450.1764415930832739X-RAY DIFFRACTION98.5982905983

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