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- PDB-4qxx: Structure of the amyloid forming peptide GNLVS (residues 26-30) f... -

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Basic information

Entry
Database: PDB / ID: 4qxx
TitleStructure of the amyloid forming peptide GNLVS (residues 26-30) from the eosinophil major basic protein (EMBP)
ComponentsBone marrow proteoglycan
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Function / homology
Function and homology information


extracellular matrix structural constituent conferring compression resistance / defense response to nematode / negative regulation of macrophage cytokine production / negative regulation of interleukin-10 production / positive regulation of interleukin-4 production / transport vesicle / heparin binding / carbohydrate binding / collagen-containing extracellular matrix / ficolin-1-rich granule lumen ...extracellular matrix structural constituent conferring compression resistance / defense response to nematode / negative regulation of macrophage cytokine production / negative regulation of interleukin-10 production / positive regulation of interleukin-4 production / transport vesicle / heparin binding / carbohydrate binding / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / defense response to bacterium / immune response / Neutrophil degranulation / extracellular exosome / extracellular region
Similarity search - Function
Eosinophil major basic protein / Eosinophil major basic protein, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / Lectin C-type domain / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Bone marrow proteoglycan
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.445 Å
AuthorsSoriaga, A.B. / Soragni, A. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Mol.Cell / Year: 2015
Title: Toxicity of Eosinophil MBP Is Repressed by Intracellular Crystallization and Promoted by Extracellular Aggregation.
Authors: Soragni, A. / Yousefi, S. / Stoeckle, C. / Soriaga, A.B. / Sawaya, M.R. / Kozlowski, E. / Schmid, I. / Radonjic-Hoesli, S. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / Seibert, M.M. / ...Authors: Soragni, A. / Yousefi, S. / Stoeckle, C. / Soriaga, A.B. / Sawaya, M.R. / Kozlowski, E. / Schmid, I. / Radonjic-Hoesli, S. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / Seibert, M.M. / Cascio, D. / Zatsepin, N.A. / Burghammer, M. / Riekel, C. / Colletier, J.P. / Riek, R. / Eisenberg, D.S. / Simon, H.U.
History
DepositionJul 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
Z: Bone marrow proteoglycan


Theoretical massNumber of molelcules
Total (without water)4891
Polymers4891
Non-polymers00
Water362
1
Z: Bone marrow proteoglycan
x 6


Theoretical massNumber of molelcules
Total (without water)2,9316
Polymers2,9316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
crystal symmetry operation3_755-x+2,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)4.755, 16.816, 35.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11Z-102-

HOH

DetailsThe biological assembly listed in REMARK 350 represents only a segment of a fibril.

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Components

#1: Protein/peptide Bone marrow proteoglycan / BMPG / Proteoglycan 2 / Eosinophil granule major basic protein / EMBP / MBP / Pregnancy-associated ...BMPG / Proteoglycan 2 / Eosinophil granule major basic protein / EMBP / MBP / Pregnancy-associated major basic protein


Mass: 488.536 Da / Num. of mol.: 1 / Fragment: GNLVS peptide (UNP residues 131-135) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13727
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.46 Å3/Da / Density % sol: 15.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 2 M ammonium sulfate, 0.1 M phosphate/citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2012
RadiationMonochromator: cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.445→100 Å / Num. obs: 658 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.46 / Net I/σ(I): 10.36
Reflection shellResolution: 1.445→1.5 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.94 / Num. unique all: 66 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.445→17.879 Å / SU ML: 0.08 / σ(F): 1.41 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 64 10.03 %RANDOM
Rwork0.1641 ---
obs0.1674 638 98 %-
all-638 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.587 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0695 Å2-0 Å20 Å2
2---0.2246 Å20 Å2
3---0.294 Å2
Refinement stepCycle: LAST / Resolution: 1.445→17.879 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms34 0 0 2 36
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533
X-RAY DIFFRACTIONf_angle_d1.26944
X-RAY DIFFRACTIONf_dihedral_angle_d9.42611
X-RAY DIFFRACTIONf_chiral_restr0.0696
X-RAY DIFFRACTIONf_plane_restr0.0026
LS refinement shellResolution: 1.445→17.8809 Å
RfactorNum. reflection% reflection
Rfree0.1918 64 -
Rwork0.1641 574 -
obs-638 98 %

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