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- PDB-1hdm: HISTOCOMPATIBILITY ANTIGEN HLA-DM -

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Basic information

Entry
Database: PDB / ID: 1hdm
TitleHISTOCOMPATIBILITY ANTIGEN HLA-DM
Components
  • PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
  • PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)
KeywordsIMMUNE SYSTEM / HISTOCOMPATIBILITY PROTEIN
Function / homology
Function and homology information


MHC class II protein complex assembly / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of T cell proliferation / MHC class II antigen presentation / 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 / positive regulation of T cell activation / peptide antigen binding ...MHC class II protein complex assembly / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of T cell proliferation / MHC class II antigen presentation / 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 / positive regulation of T cell activation / peptide antigen binding / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosomal membrane / intracellular membrane-bounded organelle / cell surface / 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
HLA class II histocompatibility antigen, DM alpha chain / HLA class II histocompatibility antigen, DM beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWiley, D.C. / Mosyak, L.
CitationJournal: Immunity / Year: 1998
Title: The structure of HLA-DM, the peptide exchange catalyst that loads antigen onto class II MHC molecules during antigen presentation.
Authors: Mosyak, L. / Zaller, D.M. / Wiley, D.C.
History
DepositionSep 9, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
B: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)


Theoretical massNumber of molelcules
Total (without water)44,4642
Polymers44,4642
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-34 kcal/mol
Surface area18330 Å2
MethodPISA
2
A: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
B: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)

A: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
B: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)


Theoretical massNumber of molelcules
Total (without water)88,9284
Polymers88,9284
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area14740 Å2
ΔGint-87 kcal/mol
Surface area32510 Å2
MethodPISA
3
A: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
B: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)

A: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN)
B: PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN)


Theoretical massNumber of molelcules
Total (without water)88,9284
Polymers88,9284
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area12710 Å2
ΔGint-84 kcal/mol
Surface area34530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.390, 109.930, 105.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M ALPHA CHAIN) / RING6 / HLA-DMA


Mass: 22855.598 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: DROSOPHILA S2 INSECT CELLS / Cell: B-LYMPHOCYTE / Production host: Drosophila hydei (fry) / References: UniProt: P28067
#2: Protein PROTEIN (CLASS II HISTOCOMPATIBILITY ANTIGEN, M BETA CHAIN) / RING7 / HLA-DMB


Mass: 21608.482 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: DROSOPHILA S2 INSECT CELLS / Cell: B-LYMPHOCYTE / Production host: Drosophila hydei (fry) / References: UniProt: P28068
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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growpH: 5.4 / Details: pH 5.4
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
210 mMTris11
31 M12Li2SO4
40.5 Mammonium sulfate12
50.1 Msodium citrate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→34 Å / Num. obs: 18729 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 40.7 Å2 / Rsym value: 0.55 / Net I/σ(I): 27.7
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 7 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.21 / % possible all: 96.3
Reflection
*PLUS
Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 96.3 % / Redundancy: 7 % / Num. unique obs: 1837 / Rmerge(I) obs: 0.213

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLH

1dlh


Resolution: 2.5→34 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL WAS USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1842 9.8 %RANDOM
Rwork0.197 ---
obs0.197 18727 96.2 %-
Displacement parametersBiso mean: 32.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 0 0 2927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.69
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: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 299 9.7 %
Rwork0.31 2795 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.69
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.354 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.31

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