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- PDB-1fv1: STRUCTURAL BASIS FOR THE BINDING OF AN IMMUNODOMINANT PEPTIDE FRO... -

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Basic information

Entry
Database: PDB / ID: 1fv1
TitleSTRUCTURAL BASIS FOR THE BINDING OF AN IMMUNODOMINANT PEPTIDE FROM MYELIN BASIC PROTEIN IN DIFFERENT REGISTERS BY TWO HLA-DR2 ALLELES
Components
  • (MAJOR HISTOCOMPATIBILITY COMPLEX ...) x 2
  • MYELIN BASIC PROTEIN
KeywordsIMMUNE SYSTEM / MHC class II DR2a
Function / homology
Function and homology information


positive regulation of metalloendopeptidase activity / compact myelin / structural constituent of myelin sheath / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / 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 metalloendopeptidase activity / compact myelin / structural constituent of myelin sheath / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / 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 / positive regulation of CD4-positive, alpha-beta T cell activation / EGR2 and SOX10-mediated initiation of Schwann cell myelination / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / membrane organization / positive regulation of chemokine (C-X-C motif) ligand 2 production / transport vesicle membrane / maintenance of blood-brain barrier / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / myelination / MHC class II antigen presentation / substantia nigra development / central nervous system development / trans-Golgi network membrane / cell periphery / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / sensory perception of sound / 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 / positive regulation of interleukin-6 production / positive regulation of T cell mediated cytotoxicity / response to toxic substance / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / myelin sheath / MAPK cascade / protease binding / early endosome membrane / chemical synaptic transmission / adaptive immune response / calmodulin binding / lysosome / immune response / Golgi membrane / lysosomal membrane / neuronal cell body / synapse / lipid binding / cell surface / protein-containing complex / extracellular exosome / nucleus / plasma membrane / cytosol
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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / Myelin basic protein / HLA class II histocompatibility antigen, DR beta 5 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsLi, H. / Mariuzza, A.R. / Li, Y. / Martin, R.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structural basis for the binding of an immunodominant peptide from myelin basic protein in different registers by two HLA-DR2 proteins.
Authors: Li, Y. / Li, H. / Martin, R. / Mariuzza, R.A.
History
DepositionSep 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR HISTOCOMPATIBILITY COMPLEX ALPHA CHAIN
B: MAJOR HISTOCOMPATIBILITY COMPLEX BETA CHAIN
C: MYELIN BASIC PROTEIN
D: MAJOR HISTOCOMPATIBILITY COMPLEX ALPHA CHAIN
E: MAJOR HISTOCOMPATIBILITY COMPLEX BETA CHAIN
F: MYELIN BASIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,66211
Polymers91,1906
Non-polymers4725
Water8,899494
1
A: MAJOR HISTOCOMPATIBILITY COMPLEX ALPHA CHAIN
B: MAJOR HISTOCOMPATIBILITY COMPLEX BETA CHAIN
C: MYELIN BASIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8796
Polymers45,5953
Non-polymers2843
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-49 kcal/mol
Surface area18500 Å2
MethodPISA
2
D: MAJOR HISTOCOMPATIBILITY COMPLEX ALPHA CHAIN
E: MAJOR HISTOCOMPATIBILITY COMPLEX BETA CHAIN
F: MYELIN BASIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7835
Polymers45,5953
Non-polymers1882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-56 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.189, 114.892, 63.175
Angle α, β, γ (deg.)90, 90.90, 90
Int Tables number4
Space group name H-MP1211

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Components

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MAJOR HISTOCOMPATIBILITY COMPLEX ... , 2 types, 4 molecules ADBE

#1: Protein MAJOR HISTOCOMPATIBILITY COMPLEX ALPHA CHAIN


Mass: 21084.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HOMO SAPIENS / Production host: Escherichia coli (E. coli) / References: UniProt: P01903
#2: Protein MAJOR HISTOCOMPATIBILITY COMPLEX BETA CHAIN


Mass: 22231.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HOMO SAPIENS / Production host: Escherichia coli (E. coli) / References: UniProt: Q30154

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide MYELIN BASIC PROTEIN


Mass: 2278.627 Da / Num. of mol.: 2 / Fragment: RESIDUES 86-105 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: P02686

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Non-polymers , 3 types, 499 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 2/3 dilution of 30% PEG 8000, 0.1M sodium cacodylate, pH6.5, 0.2M ammonium sulfate, EVAPORATION, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
230 %(w/v)PEG80001reservoir
30.1 Msodium cacodylate1reservoir
40.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 63997 / Num. obs: 49803 / % possible obs: 0.78 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 0.081
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.349 / % possible all: 0.76
Reflection
*PLUS
Num. obs: 63997 / % possible obs: 90.8 % / Num. measured all: 181399
Reflection shell
*PLUS
% possible obs: 75.6 % / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.9→100 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 3233 Random
Rwork0.233 --
all0.233 63975 -
obs0.233 63997 -
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6248 0 27 494 6769
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5

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