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- PDB-4x0s: Hexamer formed by a macrocycle containing a sequence from beta-2-... -

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Basic information

Entry
Database: PDB / ID: 4x0s
TitleHexamer formed by a macrocycle containing a sequence from beta-2-microglobulin (63-69).
ComponentsORN-TYR-LEU-LEU-PHI-TYR-VAL-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
KeywordsIMMUNE SYSTEM / Hexamer / microglobulin / iodophenylalnine
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.032 Å
AuthorsSpencer, R.K. / Salveson, P.J. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM097562 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: X-ray Crystallographic Structures of Oligomers of Peptides Derived from beta 2-Microglobulin.
Authors: Spencer, R.K. / Kreutzer, A.G. / Salveson, P.J. / Li, H. / Nowick, J.S.
History
DepositionNov 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy
Category: pdbx_audit_support / pdbx_entity_src_syn ...pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_polymer_linkage
Item: _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Dec 25, 2019Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORN-TYR-LEU-LEU-PHI-TYR-VAL-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1394
Polymers1,9841
Non-polymers1553
Water00
1
A: ORN-TYR-LEU-LEU-PHI-TYR-VAL-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)12,83224
Polymers11,9056
Non-polymers92718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_456y-1/3,x+1/3,-z+4/31
crystal symmetry operation11_566x-y+2/3,-y+4/3,-z+4/31
crystal symmetry operation12_556-x+2/3,-x+y+1/3,-z+4/31
Buried area5040 Å2
ΔGint-213 kcal/mol
Surface area7960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.065, 51.065, 31.423
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-101-

CL

21A-102-

SO4

31A-102-

SO4

41A-103-

NA

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Components

#1: Protein/peptide ORN-TYR-LEU-LEU-PHI-TYR-VAL-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS


Mass: 1984.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Derived from beta-2-microglobulin 63-69 / Source: (synth.) synthetic construct (others) / References: UniProt: P61769*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris at pH 8.5, 0.2 M Li2SO4, and PEG 400 30%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 11, 2014
RadiationMonochromator: VARIMAX VHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.032→25.6172 Å / Num. all: 7604 / Num. obs: 1072 / % possible obs: 98.89 % / Redundancy: 7.1 % / Biso Wilson estimate: 23.01 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 49.07
Reflection shellResolution: 2.032→2.103 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.1041 / Mean I/σ(I) obs: 16.4 / % possible all: 93.33

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.032→25.6172 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 184 9.52 %Phenix random selection
Rwork0.1649 ---
obs0.1681 1933 96.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.032→25.6172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms132 0 7 0 139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008148
X-RAY DIFFRACTIONf_angle_d1.187200
X-RAY DIFFRACTIONf_dihedral_angle_d34.86969
X-RAY DIFFRACTIONf_chiral_restr0.03823
X-RAY DIFFRACTIONf_plane_restr0.00422
LS refinement shellResolution: 2.0318→25.6172 Å
RfactorNum. reflection% reflection
Rfree0.2021 184 -
Rwork0.1649 1749 -
obs--97 %
Refinement TLS params.Method: refined / Origin x: 7.9674 Å / Origin y: 32.0545 Å / Origin z: 8.9696 Å
111213212223313233
T0.1943 Å2-0.0083 Å2-0.1007 Å2-0.4035 Å2-0.0087 Å2--0.4596 Å2
L4.6437 °2-0.4091 °2-0.6783 °2-3.2006 °23.1002 °2--3.0393 °2
S0.2434 Å °-0.3938 Å °0.2424 Å °0.5754 Å °0.0138 Å °-1.4385 Å °-0.1648 Å °1.1829 Å °0.0699 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 1 through 16 )

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