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- PDB-4mjh: Human Hsp27 core domain in complex with C-terminal peptide -

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Basic information

Entry
Database: PDB / ID: 4mjh
TitleHuman Hsp27 core domain in complex with C-terminal peptide
Components(Heat shock protein beta-1Heat shock response) x 2
KeywordsCHAPERONE / small heat shock protein / cancer / amyloid
Function / homology
Function and homology information


anterograde axonal protein transport / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cornified envelope / positive regulation of endothelial cell chemotaxis / regulation of translational initiation / regulation of canonical NF-kappaB signal transduction / protein kinase C inhibitor activity / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus ...anterograde axonal protein transport / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cornified envelope / positive regulation of endothelial cell chemotaxis / regulation of translational initiation / regulation of canonical NF-kappaB signal transduction / protein kinase C inhibitor activity / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / chaperone-mediated protein folding / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein folding chaperone / axon cytoplasm / proteasome complex / protein kinase C binding / ubiquitin binding / positive regulation of interleukin-1 beta production / regulation of autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / regulation of protein phosphorylation / negative regulation of protein kinase activity / MAPK6/MAPK4 signaling / response to virus / spindle / platelet aggregation / Z disc / VEGFA-VEGFR2 Pathway / positive regulation of angiogenesis / unfolded protein binding / positive regulation of tumor necrosis factor production / response to heat / protein refolding / RNA polymerase II-specific DNA-binding transcription factor binding / Extra-nuclear estrogen signaling / cytoskeleton / intracellular signal transduction / focal adhesion / negative regulation of apoptotic process / protein kinase binding / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Heat shock protein beta-1, ACD domain / 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
Heat shock protein beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.599 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
DepositionSep 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein beta-1
B: Heat shock protein beta-1
C: Heat shock protein beta-1
D: Heat shock protein beta-1


Theoretical massNumber of molelcules
Total (without water)22,5334
Polymers22,5334
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heat shock protein beta-1
B: Heat shock protein beta-1


Theoretical massNumber of molelcules
Total (without water)11,2672
Polymers11,2672
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-7 kcal/mol
Surface area5750 Å2
MethodPISA
3
C: Heat shock protein beta-1
D: Heat shock protein beta-1


Theoretical massNumber of molelcules
Total (without water)11,2672
Polymers11,2672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-6 kcal/mol
Surface area5650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.280, 48.960, 57.540
Angle α, β, γ (deg.)90.000, 99.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heat shock protein beta-1 / Heat shock response / HspB1 / 28 kDa heat shock protein / Estrogen-regulated 24 kDa protein / Heat shock 27 kDa protein / ...HspB1 / 28 kDa heat shock protein / Estrogen-regulated 24 kDa protein / Heat shock 27 kDa protein / HSP 27 / Stress-responsive protein 27 / SRP27


Mass: 10347.516 Da / Num. of mol.: 2 / Fragment: core domain (UNP residues 84-176)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP27, HSP28, HSPB1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta 2 / References: UniProt: P04792
#2: Protein/peptide Heat shock protein beta-1 / Heat shock response / HspB1 / 28 kDa heat shock protein / Estrogen-regulated 24 kDa protein / Heat shock 27 kDa protein / ...HspB1 / 28 kDa heat shock protein / Estrogen-regulated 24 kDa protein / Heat shock 27 kDa protein / HSP 27 / Stress-responsive protein 27 / SRP27


Mass: 919.072 Da / Num. of mol.: 2 / Fragment: C-terminal peptide (UNP residues 179-186) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04792
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.2 M magnesium chloride, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 27, 2011
RadiationMonochromator: CONFOCAL VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.599→37.05 Å / Num. all: 5331 / Num. obs: 5331 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.45 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.599-2.670.4943.18220034189.5
2.67-2.740.4114.442875387100
2.74-2.820.2825.742719366100
2.82-2.910.2467.06282937899.2
2.91-30.1928.182502334100
3-3.110.15510.62648356100
3.11-3.220.11814240532499.4
3.22-3.360.116.882379322100
3.36-3.50.09418.62254306100
3.5-3.680.07522.142138289100
3.68-3.870.07423.362083287100
3.87-4.110.06125.76185825698.1
4.11-4.390.05828.791791249100
4.39-4.750.0531.58161022398.7
4.75-5.20.04730.081583223100
5.2-5.810.05429.62136018899.5
5.81-6.710.05829.35119617499.4
6.71-8.220.05332.381048151100
8.22-11.620.04234.0479111699.1
11.620.04730.773576189.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.599→37.05 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7105 / SU ML: 0.37 / σ(F): 1.39 / Phase error: 34.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 265 4.99 %
Rwork0.234 --
obs0.2359 5308 98.81 %
all-5331 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.57 Å2 / Biso mean: 50.4712 Å2 / Biso min: 25.79 Å2
Refinement stepCycle: LAST / Resolution: 2.599→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 0 1 1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121426
X-RAY DIFFRACTIONf_angle_d0.9951942
X-RAY DIFFRACTIONf_chiral_restr0.074230
X-RAY DIFFRACTIONf_plane_restr0.005249
X-RAY DIFFRACTIONf_dihedral_angle_d16.408528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.599-3.27410.34861300.27672479260998
3.2741-37.05330.24071350.22032564269999
Refinement TLS params.Method: refined / Origin x: 14.9978 Å / Origin y: 26.0768 Å / Origin z: 52.2274 Å
111213212223313233
T0.2497 Å20.0496 Å20.0102 Å2-0.2187 Å20.0162 Å2--0.3122 Å2
L1.4067 °20.4901 °2-0.4452 °2-0.9515 °2-0.567 °2--2.7307 °2
S-0.0432 Å °-0.0808 Å °-0.2013 Å °0.0428 Å °-0.0142 Å °0.0298 Å °0.0243 Å °0.0645 Å °0.0975 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA85 - 170
2X-RAY DIFFRACTION1allC86 - 169
3X-RAY DIFFRACTION1allB179 - 201
4X-RAY DIFFRACTION1allD179 - 185

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