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- PDB-1d9k: CRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I-AK/CA -

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Basic information

Entry
Database: PDB / ID: 1d9k
TitleCRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I-AK/CA
Components
  • (T-CELL RECEPTOR D10 ...) x 2
  • CONALBUMIN PEPTIDE
  • MHC I-AK A CHAIN (ALPHA CHAIN)
  • MHC I-AK B CHAIN (BETA CHAIN)
KeywordsIMMUNE SYSTEM / T-CELL RECEPTOR / MHC CLASS II / D10 / I-AK
Function / homology
Function and homology information


extracellular sequestering of iron ion / organomineral extracellular matrix / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / antimicrobial humoral response ...extracellular sequestering of iron ion / organomineral extracellular matrix / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / antimicrobial humoral response / positive regulation of T cell differentiation / T cell receptor complex / antigen processing and presentation / intracellular sequestering of iron ion / negative regulation of T cell proliferation / multivesicular body / ferric iron binding / acute-phase response / recycling endosome / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / 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 / iron ion transport / antibacterial humoral response / adaptive immune response / response to lipopolysaccharide / cell surface receptor signaling pathway / lysosome / early endosome / response to xenobiotic stimulus / iron ion binding / immune response / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / Golgi apparatus / cell surface / extracellular space / membrane / plasma membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Immunoglobulin V-Type / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / T-cell receptor alpha chain V region 2B4 / H-2 class II histocompatibility antigen, A-K alpha chain / Ovotransferrin / T-cell receptor beta chain V region C5 / H-2 class II histocompatibility antigen, A-K beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsReinherz, E.L. / Tan, K. / Tang, L. / Kern, P. / Liu, J.-H. / Xiong, Y. / Hussey, R.E. / Smolyar, A. / Hare, B. / Zhang, R. ...Reinherz, E.L. / Tan, K. / Tang, L. / Kern, P. / Liu, J.-H. / Xiong, Y. / Hussey, R.E. / Smolyar, A. / Hare, B. / Zhang, R. / Joachimiak, A. / Chang, H.-C. / Wagner, G. / Wang, J.-H.
CitationJournal: Science / Year: 1999
Title: The crystal structure of a T cell receptor in complex with peptide and MHC class II.
Authors: Reinherz, E.L. / Tan, K. / Tang, L. / Kern, P. / Liu, J. / Xiong, Y. / Hussey, R.E. / Smolyar, A. / Hare, B. / Zhang, R. / Joachimiak, A. / Chang, H.C. / Wagner, G. / Wang, J.
History
DepositionOct 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 2.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-CELL RECEPTOR D10 (ALPHA CHAIN)
B: T-CELL RECEPTOR D10 (BETA CHAIN)
C: MHC I-AK A CHAIN (ALPHA CHAIN)
D: MHC I-AK B CHAIN (BETA CHAIN)
P: CONALBUMIN PEPTIDE
E: T-CELL RECEPTOR D10 (ALPHA CHAIN)
F: T-CELL RECEPTOR D10 (BETA CHAIN)
G: MHC I-AK A CHAIN (ALPHA CHAIN)
H: MHC I-AK B CHAIN (BETA CHAIN)
Q: CONALBUMIN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,22716
Polymers139,08710
Non-polymers2,1406
Water00
1
A: T-CELL RECEPTOR D10 (ALPHA CHAIN)
B: T-CELL RECEPTOR D10 (BETA CHAIN)


Theoretical massNumber of molelcules
Total (without water)24,5312
Polymers24,5312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MHC I-AK A CHAIN (ALPHA CHAIN)
D: MHC I-AK B CHAIN (BETA CHAIN)
P: CONALBUMIN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0826
Polymers45,0123
Non-polymers1,0703
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-12 kcal/mol
Surface area19970 Å2
MethodPISA
3
E: T-CELL RECEPTOR D10 (ALPHA CHAIN)
F: T-CELL RECEPTOR D10 (BETA CHAIN)


Theoretical massNumber of molelcules
Total (without water)24,5312
Polymers24,5312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: MHC I-AK A CHAIN (ALPHA CHAIN)
H: MHC I-AK B CHAIN (BETA CHAIN)
Q: CONALBUMIN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0826
Polymers45,0123
Non-polymers1,0703
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-16 kcal/mol
Surface area19790 Å2
MethodPISA
5
E: T-CELL RECEPTOR D10 (ALPHA CHAIN)
F: T-CELL RECEPTOR D10 (BETA CHAIN)
G: MHC I-AK A CHAIN (ALPHA CHAIN)
H: MHC I-AK B CHAIN (BETA CHAIN)
Q: CONALBUMIN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6148
Polymers69,5445
Non-polymers1,0703
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-25 kcal/mol
Surface area28500 Å2
MethodPISA
6
A: T-CELL RECEPTOR D10 (ALPHA CHAIN)
B: T-CELL RECEPTOR D10 (BETA CHAIN)
C: MHC I-AK A CHAIN (ALPHA CHAIN)
D: MHC I-AK B CHAIN (BETA CHAIN)
P: CONALBUMIN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6148
Polymers69,5445
Non-polymers1,0703
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-21 kcal/mol
Surface area28650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.600, 345.300, 97.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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T-CELL RECEPTOR D10 ... , 2 types, 4 molecules AEBF

#1: Protein T-CELL RECEPTOR D10 (ALPHA CHAIN)


Mass: 12399.891 Da / Num. of mol.: 2 / Mutation: C115S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: GenBank: 5724764, UniProt: P01739*PLUS
#2: Protein T-CELL RECEPTOR D10 (BETA CHAIN)


Mass: 12131.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: GenBank: 1791255, UniProt: P04213*PLUS

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Protein , 2 types, 4 molecules CGDH

#3: Protein MHC I-AK A CHAIN (ALPHA CHAIN) / MHC I-AK


Mass: 20971.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PEE14 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01910
#4: Protein MHC I-AK B CHAIN (BETA CHAIN) / MHC I-AK


Mass: 22340.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PEE14 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06343

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Protein/peptide , 1 types, 2 molecules PQ

#5: Protein/peptide CONALBUMIN PEPTIDE


Mass: 1700.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PEE14 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02789*PLUS

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Sugars , 2 types, 6 molecules

#6: Polysaccharide
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 5.92 Å3/Da / Density % sol: 79.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, sodium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 78 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 mg/mlprotein1drop
20.1 MTris-HCl1drop
38 %PEG80001reservoir
40.1 MTris1reservoir
50.01 M1reservoirKCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.069
DetectorType: APS-1 / Detector: CCD / Date: Apr 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.069 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 501406 / Num. obs: 52056 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 61.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.26 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 501406 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 3.2 Å / % possible obs: 87.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: I-Ak/CA

Resolution: 3.2→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh&Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.293 4727 10 %RANDOM
Rwork0.247 ---
all0.07 46332 --
obs0.07 46332 95.2 %-
Displacement parametersBiso mean: 62.6 Å2
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9822 0 140 0 9962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d30.16
X-RAY DIFFRACTIONx_improper_angle_d0.67
LS refinement shellResolution: 3.2→3.34 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.42 527 10 %
Rwork0.38 4624 -
obs--87.6 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 62.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.16
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.67
LS refinement shell
*PLUS
Highest resolution: 3.2 Å / Rfactor Rfree: 0.42 / % reflection Rfree: 10 % / Rfactor Rwork: 0.38

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