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- PDB-1bx2: CRYSTAL STRUCTURE OF HLA-DR2 (DRA*0101,DRB1*1501) COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1bx2
TitleCRYSTAL STRUCTURE OF HLA-DR2 (DRA*0101,DRB1*1501) COMPLEXED WITH A PEPTIDE FROM HUMAN MYELIN BASIC PROTEIN
Components(PROTEIN (HLA-DR2)) x 3
KeywordsIMMUNE SYSTEM / HLA-DR2 / MYELIN BASIC PROTEIN / MULTIPLE SCLEROSIS / AUTOIMMUNITY
Function / homology
Function and homology information


structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / compact myelin / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation ...structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / compact myelin / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / EGR2 and SOX10-mediated initiation of Schwann cell myelination / positive regulation of CD4-positive, alpha-beta T cell activation / membrane organization / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / maintenance of blood-brain barrier / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / substantia nigra development / myelination / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / central nervous system development / cell periphery / lumenal side of endoplasmic reticulum membrane / sensory perception of sound / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / response to toxic substance / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / positive regulation of interleukin-6 production / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / MAPK cascade / Downstream TCR signaling / myelin sheath / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / chemical synaptic transmission / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / protease binding / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / neuronal cell body / lipid binding / synapse / positive regulation of DNA-templated transcription / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / membrane / nucleus
Similarity search - Function
Myelin basic protein / Myelin basic protein / Myelin basic protein signature. / 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 ...Myelin basic protein / Myelin basic protein / Myelin basic protein signature. / 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, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Myelin basic protein / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSmith, K.J. / Pyrdol, J. / Gauthier, L. / Wiley, D.C. / Wucherpfennig, K.
Citation
Journal: J.Exp.Med. / Year: 1998
Title: Crystal structure of HLA-DR2 (DRA*0101, DRB1*1501) complexed with a peptide from human myelin basic protein.
Authors: Smith, K.J. / Pyrdol, J. / Gauthier, L. / Wiley, D.C. / Wucherpfennig, K.W.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Molecular Mimicry in T Cell Mediated Autoimmunity:Viral Peptides Activate Human T Cell Clones Specific for Myelin Basic Protein
Authors: Wucherpfennig, K. / Strominger, J.L.
History
DepositionOct 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 1.4Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HLA-DR2)
B: PROTEIN (HLA-DR2)
C: PROTEIN (HLA-DR2)
D: PROTEIN (HLA-DR2)
E: PROTEIN (HLA-DR2)
F: PROTEIN (HLA-DR2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6208
Polymers90,1776
Non-polymers4422
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: PROTEIN (HLA-DR2)
E: PROTEIN (HLA-DR2)
F: PROTEIN (HLA-DR2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3104
Polymers45,0893
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-27 kcal/mol
Surface area18110 Å2
MethodPISA
3
A: PROTEIN (HLA-DR2)
B: PROTEIN (HLA-DR2)
C: PROTEIN (HLA-DR2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3104
Polymers45,0893
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-27 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.403, 95.403, 295.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (HLA-DR2)


Mass: 20971.670 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS ALPHA 1, ALPHA 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location (production host): SECRETED / Production host: unidentified baculovirus / References: UniProt: P01903
#2: Protein PROTEIN (HLA-DR2)


Mass: 22316.930 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS BETA 1, BETA 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide PROTEIN (HLA-DR2)


Mass: 1800.086 Da / Num. of mol.: 2 / Fragment: PEPTIDE FROM HUMAN MYELIN BASIC PROTEIN / Source method: isolated from a natural source
Details: MYELIN BASIC PROTEIN PEPTIDE WAS COVALENTLY LINKED TO THE N-TERMINUS OF THE HLA-DR2 BETA CHAIN
Source: (natural) Homo sapiens (human) / References: UniProt: P02686*PLUS
#4: 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.: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growpH: 3.5 / Details: 15-18% PEG6000 100MM GLYCINE PH3.5
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
250 mMTris-HCl11
3100 mMglycine11
415-18 %PEG600011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorType: ADSC / Detector: CCD / Date: Mar 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 42589 / % possible obs: 88.3 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 23
Reflection shellResolution: 2.49→2.6 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.9 / % possible all: 83.1
Reflection
*PLUS
Num. measured all: 263333
Reflection shell
*PLUS
% possible obs: 83.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLH

1dlh


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1893 5 %RANDOM
Rwork0.238 ---
obs0.238 37678 87.9 %-
Displacement parametersBiso mean: 35.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-20 Å
Luzzati sigma a0.42 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6206 0 28 48 6282
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.691.5
X-RAY DIFFRACTIONx_mcangle_it2.882
X-RAY DIFFRACTIONx_scbond_it2.542
X-RAY DIFFRACTIONx_scangle_it4.012.5
LS refinement shellResolution: 2.6→2.72 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.386 234 5.5 %
Rwork0.377 4013 -
obs--81.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.PEP
X-RAY DIFFRACTION3PARAM3.CHOTOPH3.CHO

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