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- PDB-3sgp: Amyloid-related segment of alphaB-crystallin residues 90-100 muta... -

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Basic information

Entry
Database: PDB / ID: 3sgp
TitleAmyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
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 / lens development in camera-type eye ...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 / lens development in camera-type eye / muscle organ development / 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 / synaptic membrane / muscle contraction / cellular response to gamma radiation / response to hydrogen peroxide / 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 / negative regulation of apoptotic process / structural molecule activity / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4016 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
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Alpha-crystallin B chain
B: Alpha-crystallin B chain
C: Alpha-crystallin B chain
D: Alpha-crystallin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2127
Polymers4,8584
Non-polymers3553
Water54030
1
A: Alpha-crystallin B chain
B: Alpha-crystallin B chain
hetero molecules

A: Alpha-crystallin B chain
B: Alpha-crystallin B chain
hetero molecules

A: Alpha-crystallin B chain
B: Alpha-crystallin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,99612
Polymers7,2876
Non-polymers7096
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7480 Å2
ΔGint-64 kcal/mol
Surface area4180 Å2
MethodPISA
2
C: Alpha-crystallin B chain
D: Alpha-crystallin B chain
hetero molecules

C: Alpha-crystallin B chain
D: Alpha-crystallin B chain
hetero molecules

C: Alpha-crystallin B chain
D: Alpha-crystallin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6419
Polymers7,2876
Non-polymers3553
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6470 Å2
ΔGint-59 kcal/mol
Surface area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.681, 65.681, 65.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 1214.494 Da / Num. of mol.: 4 / Mutation: V91L / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P02511
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M TRIS pH 7.0, 35% MPD, 0.2M SODIUM CHLORIDE, 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 9431 / % possible obs: 99.8 % / Redundancy: 9 % / Rmerge(I) obs: 0.072 / Χ2: 1.02 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.4550.4999411.0681100
1.45-1.517.40.3869251.0681100
1.51-1.589.80.2929311.0381100
1.58-1.669.70.2149441.021100
1.66-1.769.80.1619341.0231100
1.76-1.99.80.129241.0361100
1.9-2.099.80.0979611.051100
2.09-2.399.80.0859370.9591100
2.39-3.029.70.0889601.0271100
3.02-1008.80.0489740.939197.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SGM

3sgm


Resolution: 1.4016→46.443 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8488 / SU ML: 0.22 / σ(F): 0 / Phase error: 21.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 441 4.8 %
Rwork0.175 --
obs0.1779 9195 97.45 %
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.42 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 74.96 Å2 / Biso mean: 21.7893 Å2 / Biso min: 10.72 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4016→46.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms339 0 24 30 393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006425
X-RAY DIFFRACTIONf_angle_d1.084576
X-RAY DIFFRACTIONf_chiral_restr0.06180
X-RAY DIFFRACTIONf_plane_restr0.00464
X-RAY DIFFRACTIONf_dihedral_angle_d19.248175
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4016-1.60440.23681430.18162782292594
1.6044-2.02140.20951650.12292926309199
2.0214-46.4690.25211330.19033046317999

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