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- PDB-1ldp: CRYSTAL STRUCTURE OF MURINE MHC CLASS I H-2LD WITH A MIXTURE OF B... -

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Basic information

Entry
Database: PDB / ID: 1ldp
TitleCRYSTAL STRUCTURE OF MURINE MHC CLASS I H-2LD WITH A MIXTURE OF BOUND PEPTIDES
Components
  • (MHC CLASS I H- ...) x 2
  • (PEPTIDE) x 2
KeywordsCOMPLEX (MHC I/PEPTIDE) / COMPLEX (MHC I-PEPTIDE) / MAJOR HISTOCOMPATIBILITY COMPLEX / IMMUNOLOGY / CELLULAR IMMUNITY / PEPTIDE ANTIGEN / CELL SURFACE RECEPTOR / ANTIGEN RECEPTOR / ANTIGEN PRESENTATION / COMPLEX (MHC I-PEPTIDE) complex
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / defense response / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSpeir, J.A. / Wilson, I.A.
Citation
Journal: Immunity / Year: 1998
Title: Structural basis of 2C TCR allorecognition of H-2Ld peptide complexes.
Authors: Speir, J.A. / Garcia, K.C. / Brunmark, A. / Degano, M. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
#1: Journal: Science / Year: 1998
Title: Structural Basis of Plasticity in T Cell Receptor Recognition of a Self Peptide-Mhc Antigen
Authors: Garcia, K.C. / Degano, M. / Pease, L.R. / Huang, M. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
History
DepositionMar 15, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / 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_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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
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
H: MHC CLASS I H-2LD
L: MHC CLASS I H-2LD
P: PEPTIDE
Q: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5466
Polymers44,9004
Non-polymers6462
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.400, 48.980, 84.060
Angle α, β, γ (deg.)90.00, 97.95, 90.00
Int Tables number3
Space group name H-MP121

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Components

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MHC CLASS I H- ... , 2 types, 2 molecules HL

#1: Protein MHC CLASS I H-2LD


Mass: 31388.924 Da / Num. of mol.: 1
Fragment: CHAIN H IS THE HEAVY CHAIN, PEPTIDE BINDING DOMAIN, CHAIN L IS THE LIGHT CHAIN OR BETA-2-MICROGLOBULIN
Mutation: HEAVY CHAIN TRUNCATED AFTER RESIDUE 274, B2M, LIGHT CHAIN TRUNCATED AFTER RESIDUE 99
Source method: isolated from a genetically manipulated source
Details: ASPARAGINE LINKED N-ACETYL-GLUCOSAMINE CARBOHYDRATES AT CHAIN H, N86 AND N176
Source: (gene. exp.) Mus musculus (house mouse) / Cell: MOST NUCLEATED CELLS / Cellular location: CYTOPLASM, ER, CELL SURFACE / Gene: H-2LD / Cellular location (production host): SECRETED / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01897
#2: Protein MHC CLASS I H-2LD


Mass: 11704.359 Da / Num. of mol.: 1
Fragment: CHAIN H IS THE HEAVY CHAIN, PEPTIDE BINDING DOMAIN, CHAIN L IS THE LIGHT CHAIN OR BETA-2-MICROGLOBULIN
Mutation: HEAVY CHAIN TRUNCATED AFTER RESIDUE 274, B2M, LIGHT CHAIN TRUNCATED AFTER RESIDUE 99
Source method: isolated from a genetically manipulated source
Details: ASPARAGINE LINKED N-ACETYL-GLUCOSAMINE CARBOHYDRATES AT CHAIN H, N86 AND N176
Source: (gene. exp.) Mus musculus (house mouse) / Cell: MOST NUCLEATED CELLS / Cellular location: CYTOPLASM, ER, CELL SURFACE / Gene: H-2LD / Cellular location (production host): SECRETED / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887

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Protein/peptide , 2 types, 2 molecules PQ

#3: Protein/peptide PEPTIDE


Mass: 743.870 Da / Num. of mol.: 1
Fragment: CHAIN P IS A PEPTIDE, CHAIN Q IS A MODEL OF PEPTIDE QL9 DERIVED FROM P
Source method: isolated from a natural source
Details: CHAIN P PEPTIDE IS THE NATURAL PRODUCT OF THE EXPRESSION SYSTEM. IT IS ACTUALLY A MODEL REPRESENTING THE ELECTRON DENSITY OF A MIXTURE OF BOUND PEPTIDES AVAILABLE IN THE PROTEIN EXPRESSION MEDIA.
Source: (natural) Drosophila melanogaster (fruit fly)
#4: Protein/peptide PEPTIDE


Mass: 1063.202 Da / Num. of mol.: 1
Fragment: CHAIN P IS A PEPTIDE, CHAIN Q IS A MODEL OF PEPTIDE QL9 DERIVED FROM P
Source method: isolated from a natural source
Details: CHAIN P PEPTIDE IS THE NATURAL PRODUCT OF THE EXPRESSION SYSTEM. IT IS ACTUALLY A MODEL REPRESENTING THE ELECTRON DENSITY OF A MIXTURE OF BOUND PEPTIDES AVAILABLE IN THE PROTEIN EXPRESSION MEDIA.
Source: (natural) Drosophila melanogaster (fruit fly)

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Sugars , 2 types, 2 molecules

#5: 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.: 1
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
#6: 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.: 1
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: 3

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 100MM SODIUM CACODYLATE, 0.2M AMMONIUM SULFATE, 0.5M SODIUM BROMIDE, 30% PEG 8000, PH 6.5.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlpeptide11
2100 mMsodium cacodylate11
30.2 Mammonium sulfate11
40.5 M11NaBr
530 %PEG800011

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1996 / Details: DOUBLE-MIRROR FOCUSING CAMERAS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 11809 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.358 / % possible all: 63.6
Reflection shell
*PLUS
% possible obs: 63.6 % / Num. unique obs: 926

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.825refinement
XDSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HOC

1hoc


Resolution: 3.1→6 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: ONE B-VALUE PER RESIDUE / Cross valid method: THROUGHOUT / σ(F): 1
Details: SOME LIBRARIES WERE MODIFIED IN-HOUSE TO PROVIDE MISSING CARBOHYDRATE AND PROTEIN SPECIFICATIONS. X-PLOR 3.1 ALSO WAS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.371 556 6 %RANDOM
Rwork0.221 ---
obs0.221 7935 85 %-
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--4.192 Å20 Å2-6.204 Å2
2--2.918 Å20 Å2
3---1.274 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.35 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 3.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3087 0 42 0 3129
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.1→3.22 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.477 59 10.6 %
Rwork0.291 783 -
obs--72 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH3.CHO
X-RAY DIFFRACTION3TOPH19SYED.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.825 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 7379 / Rfactor all: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8
LS refinement shell
*PLUS
Rfactor obs: 0.291

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