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- PDB-1ktd: CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO PIGEON CY... -

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Basic information

Entry
Database: PDB / ID: 1ktd
TitleCRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO PIGEON 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 / MHC class II antigen presentation / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / immunoglobulin mediated immune response / : ...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 / MHC class II antigen presentation / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / immunoglobulin mediated immune response / : / mitochondrial intermembrane space / 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 / electron transfer activity / lysosome / external side of plasma membrane / lysosomal membrane / heme binding / metal ion binding / plasma membrane / cytosol
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 / Cytochrome c, class IA/ IB / 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 ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Cytochrome c, class IA/ IB / 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 / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cytochrome c / H-2 class II histocompatibility antigen, E-D alpha chain / MHC class II antigen IEk-beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Columba livia (rock pigeon)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.3Jun 21, 2017Group: Advisory / Database references / Source and taxonomy
Category: entity_src_gen / pdbx_distant_solvent_atoms ...entity_src_gen / pdbx_distant_solvent_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.db_name ..._struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _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_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)92,0919
Polymers91,1104
Non-polymers9815
Water5,711317
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)46,3156
Polymers45,5552
Non-polymers7604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-24 kcal/mol
Surface area19400 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)45,7763
Polymers45,5552
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-38 kcal/mol
Surface area18990 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17240 Å2
ΔGint-70 kcal/mol
Surface area35770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.520, 57.300, 116.570
Angle α, β, γ (deg.)90.00, 94.23, 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 / H2-IE-alpha


Mass: 21167.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ea / 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: 24387.168 Da / Num. of mol.: 2 / Mutation: T12S
Source method: isolated from a genetically manipulated source
Details: Fusion protein consists of pigeon cytochrome C peptide, residues 1-14 (AADLIAYLKQASAK), Glycine rich linker, residues 15-30 (GGGGSLVGGGSGGGGS) and mouse MHC E-beta-k chain
Source: (gene. exp.) Columba livia (rock pigeon), (gene. exp.) Mus musculus (house mouse)
Genus: Columba, Mus / Species: , / Gene: CYC, H2-Eb1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00021, UniProt: Q31163
#3: 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.: 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG4000, 2-propanol, sodium acetate, ethylene glycol and ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
214 %PEG40001reservoir
314 %2-propanol1reservoir
41.4 %ethylene glycol1reservoir
570 mMsodium acetate1reservoirpH5.0
6320 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 12, 1996
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 36433 / Num. obs: 35965 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 34 Å2
Reflection shellResolution: 2.4→2.56 Å / % possible all: 90.2
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 36433 / Redundancy: 3.1 % / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 90.2 % / Num. unique obs: 5970 / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
bioteXdata collection
bioteXdata reduction
AMoREphasing
CNS1refinement
bioteXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 19074514.09 / 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
Rfree0.279 1785 5 %RANDOM
Rwork0.22 ---
all-35965 --
obs-35965 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.5742 Å2 / ksol: 0.332858 e/Å3
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å2-5.17 Å2
2--10.91 Å20 Å2
3----9.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6436 0 61 317 6814
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
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: 2.4→2.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 276 5 %
Rwork0.31 5281 -
obs--90.5 %
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
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0064
X-RAY DIFFRACTIONc_angle_deg1.288
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / Rfactor Rfree: 0.364 / Num. reflection Rfree: 191 / Rfactor Rwork: 0.313 / Num. reflection Rwork: 3773 / Rfactor obs: 0.313

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