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- PDB-1kt2: CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO MOTH CYTO... -

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Basic information

Entry
Database: PDB / ID: 1kt2
TitleCRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO MOTH CYTOCHROME C PEPTIDE
Components
  • Fusion protein consisting of cytochrome C peptide, glycine rich linker, and MHC E-beta-k
  • H-2 class II histocompatibility antigen, E-D alpha chain
KeywordsIMMUNE SYSTEM / Protein-peptide complex / T cell receptor / antigen presentation / cytochrome
Function / homology
Function and homology information


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 / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity ...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 / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II antigen presentation / positive regulation of memory T cell differentiation / CD4 receptor binding / polysaccharide binding / immunoglobulin mediated immune response / immunological synapse / T cell receptor binding / cognition / positive regulation of T cell mediated cytotoxicity / 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 / adaptive immune response / lysosome / lysosomal membrane / external side of plasma membrane / cell surface / 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 / 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 / MHC classes I/II-like antigen recognition protein ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / H-2 class II histocompatibility antigen, E-D alpha chain / H-2 class II histocompatibility antigen, E-B beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lonomia obliqua (butterflies/moths)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFremont, D.H. / Dai, S. / Chiang, H. / Crawford, F. / Marrack, P. / Kappler, J.
CitationJournal: J.Exp.Med. / Year: 2002
Title: Structural basis of cytochrome c presentation by IE(k).
Authors: Fremont, D.H. / Dai, S. / Chiang, H. / Crawford, F. / Marrack, P. / Kappler, J.
History
DepositionJan 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_unobs_or_zero_occ_residues / pdbx_validate_chiral / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999SEQUENCE RESIDUE 202 OF CHAINS A,C IS IN CONFLICT IN SWISSPROT ENTRY P01904. IT CAN BE EITHER THR OR HIS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, E-D alpha chain
B: Fusion protein consisting of cytochrome C peptide, glycine rich linker, and MHC E-beta-k
C: H-2 class II histocompatibility antigen, E-D alpha chain
D: Fusion protein consisting of cytochrome C peptide, glycine rich linker, and MHC E-beta-k
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5179
Polymers91,2084
Non-polymers1,3095
Water3,873215
1
A: H-2 class II histocompatibility antigen, E-D alpha chain
B: Fusion protein consisting of cytochrome C peptide, glycine rich linker, and MHC E-beta-k
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4715
Polymers45,6042
Non-polymers8673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-21 kcal/mol
Surface area19240 Å2
MethodPISA
2
C: H-2 class II histocompatibility antigen, E-D alpha chain
D: Fusion protein consisting of cytochrome C peptide, glycine rich linker, and MHC E-beta-k
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0464
Polymers45,6042
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-29 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.790, 56.930, 115.990
Angle α, β, γ (deg.)90.00, 92.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H-2 class II histocompatibility antigen, E-D alpha chain


Mass: 21204.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01904
#2: Protein Fusion protein consisting of cytochrome C peptide, glycine rich linker, and MHC E-beta-k /


Mass: 24399.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion protein consists of moth cytochrome C peptide, residues 1-14 (ADLIAYLKQATK), Glycine rich linker, residues 15-30 (GGGGSLVPRGSGGGGS) and mouse MHC E-beta-k chain
Source: (gene. exp.) Lonomia obliqua, Mus musculus / Genus: Lonomia, Mus / Species: , / Strain: , / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: GenBank: 199396, UniProt: P04230*PLUS
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG4000, 2-propanol, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
212 %PEG40001reservoir
312 %2-propanol1reservoir
460 mMsodium acetate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
DetectorType: CUSTOM-MADE / Detector: STORAGE PHOSPHORS / Date: Jan 1, 1996
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 26119 / Num. obs: 22827 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.1 Å2
Reflection shellResolution: 2.8→2.95 Å / % possible all: 93.4
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 93.4 % / Num. unique obs: 3185 / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.93 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 254361.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1088 4.9 %RANDOM
Rwork0.22 ---
all-22378 --
obs-22378 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0734 Å2 / ksol: 0.305321 e/Å3
Displacement parametersBiso mean: 47.2 Å2
Baniso -1Baniso -2Baniso -3
1--10.71 Å20 Å25.11 Å2
2---0.8 Å20 Å2
3---11.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 84 215 6743
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 143 4.6 %
Rwork0.321 2984 -
obs--78.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CARBOHYDRATE.PARAM
X-RAY DIFFRACTION3WATER.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.221 / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_angle_deg0.397
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Lowest resolution: 2.89 Å / Rfactor Rfree: 0.422 / Num. reflection Rfree: 85 / Rfactor Rwork: 0.322 / Num. reflection Rwork: 1845 / Rfactor obs: 0.322

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