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- PDB-2bc4: Crystal structure of HLA-DM -

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Basic information

Entry
Database: PDB / ID: 2bc4
TitleCrystal structure of HLA-DM
Components
  • HLA class II histocompatibility antigen, DM alpha chain
  • HLA class II histocompatibility antigen, DM beta chain
KeywordsIMMUNE SYSTEM / MHC class II
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 / 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 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 / 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 / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsNicholson, M.J. / Moradi, B. / Seth, N.P. / Xing, X. / Cuny, G.D. / Stein, R.L. / Wucherpfennig, K.W.
CitationJournal: J.Immunol. / Year: 2006
Title: Small molecules that enhance the catalytic efficiency of HLA-DM.
Authors: Nicholson, M.J. / Moradi, B. / Seth, N.P. / Xing, X. / Cuny, G.D. / Stein, R.L. / Wucherpfennig, K.W.
History
DepositionOct 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_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_comp_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DM alpha chain
B: HLA class II histocompatibility antigen, DM beta chain
C: HLA class II histocompatibility antigen, DM alpha chain
D: HLA class II histocompatibility antigen, DM beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,78610
Polymers95,1474
Non-polymers1,6396
Water7,566420
1
A: HLA class II histocompatibility antigen, DM alpha chain
B: HLA class II histocompatibility antigen, DM beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3935
Polymers47,5742
Non-polymers8203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-44 kcal/mol
Surface area19250 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DM alpha chain
D: HLA class II histocompatibility antigen, DM beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3935
Polymers47,5742
Non-polymers8203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-49 kcal/mol
Surface area20280 Å2
MethodPISA
3
A: HLA class II histocompatibility antigen, DM alpha chain
B: HLA class II histocompatibility antigen, DM beta chain
hetero molecules

C: HLA class II histocompatibility antigen, DM alpha chain
D: HLA class II histocompatibility antigen, DM beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,78610
Polymers95,1474
Non-polymers1,6396
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area18960 Å2
ΔGint-111 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.068, 108.420, 110.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a heterodimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D).

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Components

#1: Protein HLA class II histocompatibility antigen, DM alpha chain / MHC class II antigen DMA


Mass: 23992.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DMA, DMA, RING6 / Plasmid: pRmHA-3 / Production host: Drosophila melanogaster (fruit fly) / References: GenBank: 18765715, UniProt: P28067*PLUS
#2: Protein HLA class II histocompatibility antigen, DM beta chain / MHC class II antigen DMB


Mass: 23580.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DMB, DMB, RING7 / Plasmid: pRmHA-3 / Production host: Drosophila melanogaster (fruit fly) / References: GenBank: 4504399, UniProt: P28068*PLUS
#3: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1- ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2-3-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 3.1 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1.0M Lithium Sulfate, 0.3M Ammonium Sulfate, 0.1M Sodium Citrate Buffer, pH 5.4, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9195 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionNumber: 59764 / Rmerge(I) obs: 0.057 / Χ2: 1.159 / D res high: 2.2 Å / D res low: 30 Å / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.733099.610.0271.113
3.764.7399.910.0351.477
3.293.7699.910.051.635
2.993.2999.910.0581.047
2.772.9999.910.0890.952
2.612.7799.810.1431.163
2.482.6199.810.1750.861
2.372.4899.710.2360.811
2.282.3799.610.3090.817
2.22.2898.910.5881.777
ReflectionResolution: 2.27→30 Å / Num. all: 60139 / Num. obs: 59797 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Χ2: 1.159 / Net I/σ(I): 12.3
Reflection shellResolution: 2.27→2.37 Å / % possible obs: 98.9 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 5.02 / Num. measured obs: 5836 / Rsym value: 0.31 / Χ2: 1.777 / % possible all: 99.6

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Phasing

Phasing MRRfactor: 0.582 / Cor.coef. Fo:Fc: 0.389
Highest resolutionLowest resolution
Rotation3 Å29.4 Å
Translation3 Å29.4 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1HDM (Alanine substitution)

1hdm


Resolution: 2.27→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1477 2.7 %RANDOM
Rwork0.229 ---
all0.261 54965 --
obs0.248 54814 99.7 %-
Solvent computationBsol: 41.118 Å2
Displacement parametersBiso mean: 39.842 Å2
Baniso -1Baniso -2Baniso -3
1--2.137 Å20 Å20 Å2
2--4.404 Å20 Å2
3----2.267 Å2
Refinement stepCycle: LAST / Resolution: 2.27→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6143 0 104 420 6667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.413
X-RAY DIFFRACTIONc_bond_d0.0063
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top

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