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- PDB-3sgn: Bromoderivative-8 of amyloid-related segment of alphaB-crystallin... -

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Basic information

Entry
Database: PDB / ID: 3sgn
TitleBromoderivative-8 of amyloid-related segment of alphaB-crystallin residues 90-100
ComponentsAlpha-crystallin B chainCRYAB
KeywordsPROTEIN FIBRIL / amyloid / amyloid oligomer / beta cylindrin
Function / homology
Function and homology information


microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / muscle organ development ...microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / muscle organ development / lens development in camera-type eye / actin filament bundle / HSF1-dependent transactivation / negative regulation of reactive oxygen species metabolic process / negative regulation of protein-containing complex assembly / stress-activated MAPK cascade / muscle contraction / synaptic membrane / response to hydrogen peroxide / cellular response to gamma radiation / negative regulation of cell growth / Z disc / unfolded protein binding / protein folding / response to estradiol / amyloid-beta binding / response to heat / perikaryon / protein refolding / microtubule binding / dendritic spine / lysosome / response to hypoxia / protein stabilization / axon / negative regulation of gene expression / negative regulation of DNA-templated transcription / protein-containing complex binding / structural molecule activity / negative regulation of apoptotic process / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-crystallin B chain, ACD domain / Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
Alpha-crystallin B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.807 Å
AuthorsLaganowsky, A. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
CitationJournal: Science / Year: 2012
Title: Atomic view of a toxic amyloid small oligomer.
Authors: Laganowsky, A. / Liu, C. / Sawaya, M.R. / Whitelegge, J.P. / Park, J. / Zhao, M. / Pensalfini, A. / Soriaga, A.B. / Landau, M. / Teng, P.K. / Cascio, D. / Glabe, C. / Eisenberg, D.
History
DepositionJun 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-crystallin B chain
B: Alpha-crystallin B chain


Theoretical massNumber of molelcules
Total (without water)2,5552
Polymers2,5552
Non-polymers00
Water362
1
A: Alpha-crystallin B chain
B: Alpha-crystallin B chain

A: Alpha-crystallin B chain
B: Alpha-crystallin B chain

A: Alpha-crystallin B chain
B: Alpha-crystallin B chain


Theoretical massNumber of molelcules
Total (without water)7,6646
Polymers7,6646
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Buried area6170 Å2
ΔGint-24 kcal/mol
Surface area4080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.342, 70.342, 70.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein/peptide Alpha-crystallin B chain / CRYAB / Alpha(B)-crystallin / Heat shock protein beta-5 / HspB5 / Renal carcinoma antigen NY-REN-27 / ...Alpha(B)-crystallin / Heat shock protein beta-5 / HspB5 / Renal carcinoma antigen NY-REN-27 / Rosenthal fiber component


Mass: 1277.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P02511
#2: Water ChemComp-HOH / water / 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: 5.68 Å3/Da / Density % sol: 78.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 30% MPD, 0.2M SODIUM CITRATE, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.91963 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91963 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 2765 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.96.90.6631100
2.9-3.026.90.4251100
3.02-3.156.90.3381100
3.15-3.326.90.21100
3.32-3.536.90.141100
3.53-3.86.90.0961100
3.8-4.186.60.0811100
4.18-4.796.70.0721100
4.79-6.036.40.0651100
6.03-505.90.0791100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.807→35.171 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.74 / σ(F): 0.27 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 150 10.18 %
Rwork0.2103 --
obs0.212 1473 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.583 Å2 / ksol: 0.294 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.807→35.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms170 0 0 2 172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011168
X-RAY DIFFRACTIONf_angle_d1.579224
X-RAY DIFFRACTIONf_dihedral_angle_d20.29862
X-RAY DIFFRACTIONf_chiral_restr0.0732
X-RAY DIFFRACTIONf_plane_restr0.00426
LS refinement shellResolution: 2.807→35.1737 Å
RfactorNum. reflection% reflection
Rfree0.2272 150 -
Rwork0.2103 1323 -
obs--98 %

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