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- PDB-4m5s: Human alphaB crystallin core domain in complex with C-terminal peptide -

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Basic information

Entry
Database: PDB / ID: 4m5s
TitleHuman 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
SUCCINIC ACID / Alpha-crystallin B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsLaganowsky, A. / Cascio, D. / Sawaya, M.R. / 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2493
Polymers11,1312
Non-polymers1181
Water1,26170
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


Theoretical massNumber of molelcules
Total (without water)22,4976
Polymers22,2614
Non-polymers2362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-4 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.380, 47.860, 122.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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: 9957.241 Da / Num. of mol.: 1 / Fragment: core domain (UNP residues 68-153)
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: 1173.320 Da / Num. of mol.: 1 / Fragment: C-terminal peptide (UNP residues 156-164)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYA2, CRYAB / Plasmid: pET15-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02511
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M SPG, pH 6.0, 25% PEG1500, 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: Dec 10, 2010
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.37→19.569 Å / Num. obs: 21884 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.64 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 25.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.37-1.410.4863.337360155896
1.41-1.440.4854.7112480152997
1.44-1.490.3686.2712432153197.1
1.49-1.530.2658.4711866145897.4
1.53-1.580.18611.2611480141397.6
1.58-1.640.14913.7411216138097.7
1.64-1.70.12116.4411110136698.3
1.7-1.770.0942010393129098.5
1.77-1.850.0692610183126298.1
1.85-1.940.05232.729438118198.7
1.94-2.040.04337.639016113698.9
2.04-2.170.0440.928544109498.8
2.17-2.320.03744.037859102298.9
2.32-2.50.03645.56732596399.4
2.5-2.740.03647.82675989899.6
2.74-3.060.03150.02597781199.8
3.06-3.540.0352.87543672298.9
3.54-4.330.0351.27413759696
4.33-6.130.02749.38285044389
6.130.03145.23128923176.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→19.569 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.8864 / SU ML: 0.12 / σ(F): 1.99 / Phase error: 17.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 1095 5 %
Rwork0.1563 --
obs0.1579 21882 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.51 Å2 / Biso mean: 24.1899 Å2 / Biso min: 8.13 Å2
Refinement stepCycle: LAST / Resolution: 1.37→19.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 8 70 853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016850
X-RAY DIFFRACTIONf_angle_d1.641148
X-RAY DIFFRACTIONf_chiral_restr0.135126
X-RAY DIFFRACTIONf_plane_restr0.008152
X-RAY DIFFRACTIONf_dihedral_angle_d15.965341
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.37-1.43230.23921330.17432519265296
1.4323-1.50780.2061340.13992538267297
1.5078-1.60230.15191350.11832565270098
1.6023-1.72590.17641360.11882588272498
1.7259-1.89950.16481370.12152607274498
1.8995-2.1740.16441380.12952620275899
2.174-2.73780.19121410.16432681282299
2.7378-19.57060.19921410.18162669281095

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