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- PDB-7roj: Amyloid-related segment of alphaB-crystallin residues 90-100 with... -

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Basic information

Entry
Database: PDB / ID: 7roj
TitleAmyloid-related segment of alphaB-crystallin residues 90-100 with G95W mutation
ComponentsAlpha-crystallin B chain peptide
KeywordsPROTEIN FIBRIL / amyloid oligomer
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
trifluoroacetic acid / Alpha-crystallin B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
Model detailsAmyloid Oligomer
AuthorsSawaya, M.R. / Do, T.D. / Eisenberg, D.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Protein Sci. / Year: 2022
Title: Atomic view of an amyloid dodecamer exhibiting selective cellular toxic vulnerability in acute brain slices.
Authors: Gray, A.L.H. / Sawaya, M.R. / Acharyya, D. / Lou, J. / Edington, E.M. / Best, M.D. / Prosser, R.A. / Eisenberg, D.S. / Do, T.D.
History
DepositionJul 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-crystallin B chain peptide
B: Alpha-crystallin B chain peptide
C: Alpha-crystallin B chain peptide
D: Alpha-crystallin B chain peptide
E: Alpha-crystallin B chain peptide
F: Alpha-crystallin B chain peptide
G: Alpha-crystallin B chain peptide
H: Alpha-crystallin B chain peptide
I: Alpha-crystallin B chain peptide
J: Alpha-crystallin B chain peptide
K: Alpha-crystallin B chain peptide
L: Alpha-crystallin B chain peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,52718
Polymers15,95612
Non-polymers5716
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.270, 36.330, 64.130
Angle α, β, γ (deg.)90.000, 91.920, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide
Alpha-crystallin B chain peptide / 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: 1329.625 Da / Num. of mol.: 12 / Fragment: residues 90-100 / Mutation: G95W / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02511
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.84 Å3/Da / Density % sol: 33.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1,4-butanediol, HEPES, NaCl, trifluoroacetic acid, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 31, 2020
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→64.09 Å / Num. obs: 14376 / % possible obs: 92.5 % / Redundancy: 2.042 % / Biso Wilson estimate: 32.292 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.111 / Χ2: 0.89 / Net I/σ(I): 6.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.642.0510.9161.2210910.5191.21594.7
1.64-1.692.0510.6521.5110190.730.86192.1
1.69-1.742.0320.5591.89880.7490.74692.9
1.74-1.791.960.4882.269340.8040.65587
1.79-1.852.0770.3892.799090.8420.51791
1.85-1.912.0980.3153.519370.8640.4294.4
1.91-1.982.1070.2254.468530.9430.30191.8
1.98-2.072.0420.2425.028630.9010.32693.3
2.07-2.162.0880.2585.948220.8810.34793.5
2.16-2.262.0580.2486.548130.8790.33495.4
2.26-2.392.0170.2036.877470.9130.27293.3
2.39-2.531.9210.1867.296680.9110.2588
2.53-2.72.0710.1418.236790.9520.18995.6
2.7-2.922.0860.10210.046500.9730.13596.7
2.92-3.22.0270.07211.565910.9850.09694.7
3.2-3.582.0350.05513.735160.9910.07392
3.58-4.132.050.04415.234590.9950.05892.7
4.13-5.061.8820.03717.043720.9940.04987.5
5.06-7.162.0730.03716.953030.9960.04991.3
7.16-64.091.9940.02617.321620.9980.03483.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å64.09 Å
Translation1.6 Å64.09 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ROL

7rol


Resolution: 1.6→64.09 Å / SU ML: 0.2624 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.9721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2769 1436 10 %
Rwork0.2393 12917 -
obs0.2431 14353 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.78 Å2
Refinement stepCycle: LAST / Resolution: 1.6→64.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 35 38 1201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621180
X-RAY DIFFRACTIONf_angle_d0.88991604
X-RAY DIFFRACTIONf_chiral_restr0.0625205
X-RAY DIFFRACTIONf_plane_restr0.0049174
X-RAY DIFFRACTIONf_dihedral_angle_d14.7975420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.37931440.36851290X-RAY DIFFRACTION94.47
1.66-1.720.41781420.34721279X-RAY DIFFRACTION92.39
1.72-1.80.40281340.3371216X-RAY DIFFRACTION86.43
1.8-1.90.34221440.29821292X-RAY DIFFRACTION94.1
1.9-2.020.31611440.27731297X-RAY DIFFRACTION92.25
2.02-2.170.31811440.26761289X-RAY DIFFRACTION93.72
2.17-2.390.28741480.24981331X-RAY DIFFRACTION94.2
2.39-2.740.28631430.25911287X-RAY DIFFRACTION92.02
2.74-3.450.23361480.22441332X-RAY DIFFRACTION94.99
3.45-64.090.24221450.19021304X-RAY DIFFRACTION89.67
Refinement TLS params.Method: refined / Origin x: 4.03843850142 Å / Origin y: -1.60843806554 Å / Origin z: 16.1599792453 Å
111213212223313233
T0.154193467936 Å20.00477726747325 Å2-0.00821085427233 Å2-0.161693072278 Å20.00153422670038 Å2--0.167182611496 Å2
L0.944036612923 °20.539770829361 °2-0.05283676991 °2-0.504923223901 °20.0847058260395 °2--0.528337623549 °2
S0.00446641257411 Å °0.0902737669297 Å °-0.00331862347865 Å °-0.0192501734717 Å °0.00777825031614 Å °0.103211975402 Å °-0.0102297075103 Å °0.0431092003113 Å °0.00128905307402 Å °
Refinement TLS groupSelection details: all

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