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- PDB-1k8i: CRYSTAL STRUCTURE OF MOUSE H2-DM -

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Basic information

Entry
Database: PDB / ID: 1k8i
TitleCRYSTAL STRUCTURE OF MOUSE H2-DM
Components
  • MHC class II H2-M alpha chain
  • MHC class II H2-M beta 2 chain
KeywordsIMMUNE SYSTEM / MHC
Function / homology
Function and homology information


positive regulation of humoral immune response / positive regulation of germinal center formation / MHC class II antigen presentation / positive thymic T cell selection / positive regulation of T cell differentiation / antigen processing and presentation / inner ear development / immunoglobulin mediated immune response / : / multivesicular body ...positive regulation of humoral immune response / positive regulation of germinal center formation / MHC class II antigen presentation / positive thymic T cell selection / positive regulation of T cell differentiation / antigen processing and presentation / inner ear development / immunoglobulin mediated immune response / : / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class II protein complex binding / late endosome membrane / late endosome / protein transport / protein-containing complex assembly / adaptive immune response / lysosome / endosome membrane / lysosomal membrane / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Class II histocompatibility antigen, M alpha chain / H2-M beta 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / molecular replacement,MIR / Resolution: 3.1 Å
AuthorsFremont, D.H. / Crawford, F. / Marrack, P. / Hendrickson, W. / Kappler, J.
CitationJournal: Immunity / Year: 1998
Title: Crystal structure of mouse H2-M.
Authors: Fremont, D.H. / Crawford, F. / Marrack, P. / Hendrickson, W.A. / Kappler, J.
History
DepositionOct 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 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 1.4Nov 13, 2024Group: 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class II H2-M alpha chain
B: MHC class II H2-M beta 2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2394
Polymers42,7972
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-21 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.700, 142.700, 76.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein MHC class II H2-M alpha chain


Mass: 21466.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-DM / Cell line (production host): high-five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P28078
#2: Protein MHC class II H2-M beta 2 chain


Mass: 21329.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-DM / Cell line (production host): high-five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31099
#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.: 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da / Density % sol: 73.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M lithium sulfate, 0.1M MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1400 mMammonium sulfate1reservoir
20.1 MMES1reservoirpH6.5
35-7 mg/mlprotein1drop
450 mM1dropLi2SO4
550 mMMES1droppH5.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 13888 / Num. obs: 13711 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.56 % / Biso Wilson estimate: 74.5 Å2 / Rsym value: 0.091 / Net I/σ(I): 16.2
Reflection shellResolution: 3.1→3.2 Å / Mean I/σ(I) obs: 1.71 / Num. unique all: 1303 / Rsym value: 0.482 / % possible all: 95.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 13888 / Num. measured all: 63314 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.482

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: molecular replacement,MIR / Resolution: 3.1→12 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 690 5 %RANDOM
Rwork0.205 ---
obs0.205 13711 98.5 %-
all-13888 --
Displacement parametersBiso mean: 64.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å20 Å2
2---1.46 Å20 Å2
3---2.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 3.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 28 0 2962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_improper_angle_d1.26
LS refinement shellResolution: 3.1→3.21 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.345 78 6 %
Rwork0.334 1225 -
obs--95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH3.CHO
X-RAY DIFFRACTION3PARAMCSDX.MISC
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 12 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26
LS refinement shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.2 Å / Rfactor Rfree: 0.334 / Rfactor Rwork: 0.345 / Num. reflection obs: 1303 / Rfactor obs: 0.345

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