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- PDB-1lnu: CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IAb BOUND TO EALPHA3K ... -

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Basic information

Entry
Database: PDB / ID: 1lnu
TitleCRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IAb BOUND TO EALPHA3K PEPTIDE
Components
  • H-2 class II histocompatibility antigen, A beta chain
  • H-2 class II histocompatibility antigen, A-B alpha chain
KeywordsSUGAR BINDING PROTEIN / Protein-peptide complex / T cell receptor / antigen presentation
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / protein antigen binding / B cell affinity maturation / antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / response to type II interferon / antigen processing and presentation / toxic substance binding ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / protein antigen binding / B cell affinity maturation / antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / response to type II interferon / antigen processing and presentation / toxic substance binding / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / cellular response to type II interferon / 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 / early endosome / immune response / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / protein-containing complex binding / Golgi apparatus / cell surface / 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 / 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, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, X. / Dai, S. / Crawford, F. / Fruge, R. / Marrack, P. / Kappler, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Alternate interactions define the binding of peptides to the MHC molecule IA(b).
Authors: Liu, X. / Dai, S. / Crawford, F. / Fruge, R. / Marrack, P. / Kappler, J.
History
DepositionMay 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.auth_comp_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_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Author states two separate sequences, an Ealpha3K peptide(1-13) and linker(14-28), which ...SEQUENCE Author states two separate sequences, an Ealpha3K peptide(1-13) and linker(14-28), which start from residue 1 to residue 28 were added to the N-terminus of the beta chain of the class II MHC IAB of chains B,D,F and H.

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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, A-B alpha chain
B: H-2 class II histocompatibility antigen, A beta chain
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: H-2 class II histocompatibility antigen, A beta chain
E: H-2 class II histocompatibility antigen, A-B alpha chain
F: H-2 class II histocompatibility antigen, A beta chain
G: H-2 class II histocompatibility antigen, A-B alpha chain
H: H-2 class II histocompatibility antigen, A beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,80220
Polymers182,1478
Non-polymers2,65412
Water4,270237
1
A: H-2 class II histocompatibility antigen, A-B alpha chain
B: H-2 class II histocompatibility antigen, A beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2005
Polymers45,5372
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-19 kcal/mol
Surface area19750 Å2
MethodPISA
2
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: H-2 class II histocompatibility antigen, A beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2005
Polymers45,5372
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-19 kcal/mol
Surface area19720 Å2
MethodPISA
3
E: H-2 class II histocompatibility antigen, A-B alpha chain
F: H-2 class II histocompatibility antigen, A beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2005
Polymers45,5372
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-20 kcal/mol
Surface area19680 Å2
MethodPISA
4
G: H-2 class II histocompatibility antigen, A-B alpha chain
H: H-2 class II histocompatibility antigen, A beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2005
Polymers45,5372
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-23 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.040, 274.180, 65.120
Angle α, β, γ (deg.)90.00, 111.42, 90.00
Int Tables number4
Space group name H-MP1211
DetailsOne molecule includes one alpha chain and one beta chain with the peptide

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Components

#1: Protein
H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 20597.957 Da / Num. of mol.: 4
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: P14434
#2: Protein
H-2 class II histocompatibility antigen, A beta chain


Mass: 24938.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SF9 / Production host: Escherichia coli (E. coli) / References: UniProt: P14483
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG8000, MES, KH2PO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
116 %PEG80001reservoir
20.1 MMES1reservoirpH6.0
30.1 M1reservoirKH2PO4
44-5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.99187 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Dec 6, 2001
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 54497 / Num. obs: 54497 / % possible obs: 74.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.352 / Num. unique all: 1829 / % possible all: 21.3
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 40 Å
Reflection shell
*PLUS
% possible obs: 21.3 % / Num. unique obs: 1829 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IAD

2iad


Resolution: 2.5→38.39 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 53511.21 / Data cutoff high rms absF: 53511.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2621 4.9 %RANDOM
Rwork0.211 ---
all-54497 --
obs-54479 74.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.563 Å2 / ksol: 0.342183 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12860 0 168 237 13265
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 115 4.2 %
Rwork0.307 2609 -
obs-1829 22.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 40 Å / Num. reflection obs: 54427
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0105
X-RAY DIFFRACTIONc_angle_deg1.511
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Lowest resolution: 2.59 Å / Rfactor Rfree: 0.313 / Num. reflection Rfree: 66 / Rfactor Rwork: 0.277 / Num. reflection obs: 1591

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