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- PDB-3sgr: Tandem repeat of amyloid-related segment of alphaB-crystallin res... -

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Basic information

Entry
Database: PDB / ID: 3sgr
TitleTandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
ComponentsTandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
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 / 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 / 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 / SIRAS / Resolution: 2.17 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 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
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

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Assembly

Deposited unit
A: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
B: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
C: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
D: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
E: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
F: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7298
Polymers15,4936
Non-polymers2362
Water63135
1
A: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
C: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
D: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L

B: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
E: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
F: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7298
Polymers15,4936
Non-polymers2362
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z+1/31
Buried area6860 Å2
ΔGint-58 kcal/mol
Surface area8540 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-58 kcal/mol
Surface area8520 Å2
MethodPISA
3
A: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
C: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
D: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L

B: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
E: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
F: Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7298
Polymers15,4936
Non-polymers2362
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area6920 Å2
ΔGint-56 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.340, 52.340, 87.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsThe biological unit is a three stranded beta cylindrin. The asymmetric unit is formed by two beta cylindrins.

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Components

#1: Protein/peptide
Tandem repeat of amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L


Mass: 2582.128 Da / Num. of mol.: 6 / Mutation: V91L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYAB / Plasmid: pET15-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02511
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M SODIUM CACODYLATE pH 6.5, 30% MPD, 0.2M MAGNESIUM ACETATE, 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: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.01→19.67 Å / Num. obs: 8991 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 55.449 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.53
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.01-2.060.82174863395.8
2.06-2.121.44229264899.1
2.12-2.181.792368638100
2.18-2.252.26222060399.2
2.25-2.322.68215659199.5
2.32-2.43.232191582100
2.4-2.494.572128568100
2.49-2.596.331961526100
2.59-2.718.26186650599.8
2.71-2.8410.661853500100
2.84-2.9913.22174847699.8
2.99-3.1816.381582435100
3.18-3.3920.06152942499.3
3.39-3.6724.77135838699.2
3.67-4.0225.61124135899.4
4.02-4.4927.74110731798.8
4.49-5.1828.671010290100
5.18-6.3527.3819246100
6.35-8.9827.8963418697.4
8.9826.982397974.5

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.17→19.67 Å / Cor.coef. Fo:Fc: 0.9535 / Cor.coef. Fo:Fc free: 0.9319 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 626 9.75 %RANDOM
Rwork0.1843 ---
obs0.1889 6421 --
Displacement parametersBiso max: 153.83 Å2 / Biso mean: 63.9852 Å2 / Biso min: 33.27 Å2
Baniso -1Baniso -2Baniso -3
1--3.5497 Å20 Å20 Å2
2---3.5497 Å20 Å2
3---7.0995 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: LAST / Resolution: 2.17→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 16 35 1129
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d408SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes143HARMONIC5
X-RAY DIFFRACTIONt_it1086HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion134SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1118SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1086HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1450HARMONIC21.4
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion21.31
LS refinement shellResolution: 2.17→2.43 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2549 118 9.06 %
Rwork0.2209 1184 -
all0.2239 1302 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.99654.65931.5719.83381.43645.29820.2363-0.4493-0.1073-0.0539-0.29490.0389-0.1108-0.5060.0586-0.15080.1296-0.05580.0123-0.10140.0459-8.2293-25.7999-7.4886
211.26181.94522.18113.5382.100512.24210.1893-0.59070.37930.3741-0.27440.2237-0.6644-0.08690.0851-0.2103-0.07540.0042-0.0324-0.0404-0.006-28.1533-27.3348-20.1207
38.5834-0.55691.37488.93521.24098.43870.115-0.5645-0.03570.2446-0.2448-0.8802-0.21870.12360.1298-0.13610.08750.0479-0.1384-0.04280.0517-2.9382-26.6459-4.9424
49.78423.8976-0.27629.54590.454511.68490.09030.1567-0.3768-0.7213-0.1703-0.34950.0327-0.11680.08-0.2360.0669-0.0292-0.0582-0.0430.0163-4.7822-28.9612-10.1202
517.65781.55943.08213.4230.04585.96630.9981-0.5042-0.9728-0.0524-0.37470.06830.5605-0.1868-0.6234-0.08810.0072-0.029-0.0525-0.02160.0194-26.5002-32.0927-21.9012
610.3007-2.11152.7111.8119-1.703711.4310.10060.38520.4921-0.1413-0.1871-0.2665-0.70610.11180.0865-0.1610.06210.0125-0.05480.04040.008-24.15-27.3546-23.7617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 24
2X-RAY DIFFRACTION2{ B|* }B0 - 24
3X-RAY DIFFRACTION3{ C|* }C1 - 24
4X-RAY DIFFRACTION4{ D|* }D0 - 24
5X-RAY DIFFRACTION5{ E|* }E0 - 24
6X-RAY DIFFRACTION6{ F|* }F0 - 24

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