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- PDB-4m5t: Disulfide trapped human alphaB crystallin core domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 4m5t
TitleDisulfide trapped human alphaB crystallin core domain in complex with C-terminal peptide
Components(Alpha-crystallin B chainCRYAB) x 2
KeywordsCHAPERONE / small heat shock protein / amyloid
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 / 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 / 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 / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like ...Alpha-crystallin B chain, ACD domain / Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-crystallin B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLaganowsky, A. / Cascio, D. / Hochberg, G. / Sawaya, M.R. / Benesch, J.L.P. / Robinson, C.V. / Eisenberg, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: The structured core domain of alpha B-crystallin can prevent amyloid fibrillation and associated toxicity.
Authors: Hochberg, G.K. / Ecroyd, H. / Liu, C. / Cox, D. / Cascio, D. / Sawaya, M.R. / Collier, M.P. / Stroud, J. / Carver, J.A. / Baldwin, A.J. / Robinson, C.V. / Eisenberg, D.S. / Benesch, J.L. / Laganowsky, A.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version

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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
E: Alpha-crystallin B chain
F: Alpha-crystallin B chain
G: Alpha-crystallin B chain
H: Alpha-crystallin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,95916
Polymers44,1908
Non-polymers7698
Water1,38777
1
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)22,3837
Polymers22,0954
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Alpha-crystallin B chain
F: Alpha-crystallin B chain
G: Alpha-crystallin B chain
H: Alpha-crystallin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5759
Polymers22,0954
Non-polymers4805
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-157 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.010, 46.770, 77.710
Angle α, β, γ (deg.)90.00, 117.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
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: 9931.271 Da / Num. of mol.: 4 / Fragment: core domain (UNP residues 68-153) / Mutation: E117C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYA2, CRYAB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta 2 / References: UniProt: P02511
#2: 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: 1116.268 Da / Num. of mol.: 4 / Fragment: C-terminal peptide (UNP residues 156-164) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02511
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.085 M MES, pH 6.5, 0.17 M ammonium sulfate, 25.5% PEG5000 MME, 15% glycerol, 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: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2012
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→68.799 Å / Num. obs: 24867 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.11 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.050.3653.48197.2
2.05-2.110.2864.57197.7
2.11-2.170.2845.2198
2.17-2.240.2685.94198
2.24-2.310.2447.05196.4
2.31-2.390.2347.39194.3
2.39-2.480.2128.77199
2.48-2.580.16910.66199.3
2.58-2.70.13612.34199.2
2.7-2.830.10514.71199.2
2.83-2.980.0817.43198
2.98-3.160.06519.81197.6
3.16-3.380.05122.27195.1
3.38-3.650.0425.42194.4
3.65-40.03628.19198.6
4-4.470.03230.74198.9
4.47-5.160.03132.87198.5
5.16-6.320.03129.53195.5
6.32-8.940.02731.76195.3
8.940.02333.71198.4

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→68.799 Å / Cor.coef. Fo:Fc: 0.9474 / Cor.coef. Fo:Fc free: 0.9384 / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.26 / SU R Cruickshank DPI: 0.201 / σ(F): 1.99 / SU R Blow DPI: 0.197 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.164 / Phase error: 28.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1268 5.11 %
Rwork0.1927 --
obs0.1954 24830 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.3275 Å2
Baniso -1Baniso -2Baniso -3
1-2.7212 Å20 Å21.9449 Å2
2---7.0596 Å20 Å2
3---4.3384 Å2
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: LAST / Resolution: 2→68.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 40 77 3096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083079
X-RAY DIFFRACTIONf_angle_d1.2414146
X-RAY DIFFRACTIONf_dihedral_angle_d15.0461177
X-RAY DIFFRACTIONf_chiral_restr0.095462
X-RAY DIFFRACTIONf_plane_restr0.004533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.31271350.25262576X-RAY DIFFRACTION97
2.0801-2.17480.30821370.23222624X-RAY DIFFRACTION98
2.1748-2.28950.31381270.21432584X-RAY DIFFRACTION97
2.2895-2.43290.27421500.21152547X-RAY DIFFRACTION96
2.4329-2.62080.25521400.19912674X-RAY DIFFRACTION100
2.6208-2.88450.26141190.19372646X-RAY DIFFRACTION99
2.8845-3.30190.25251590.18422629X-RAY DIFFRACTION98
3.3019-4.160.21731330.16982600X-RAY DIFFRACTION96
4.16-68.83960.21721680.18772682X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 111.4844 Å / Origin y: 2.7788 Å / Origin z: 16.8857 Å
111213212223313233
T0.1801 Å2-0.0063 Å20.0256 Å2-0.2676 Å2-0.0115 Å2--0.217 Å2
L0.8851 °20.0927 °20.2446 °2-0.1363 °2-0.0127 °2---0.0092 °2
S-0.0134 Å °0.0412 Å °-0.0255 Å °-0.0148 Å °0.0337 Å °0.0057 Å °-0.0044 Å °0.0038 Å °-0.0174 Å °
Refinement TLS groupSelection details: all

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