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- PDB-2n3j: Solution Structure of the alpha-crystallin domain from the redox-... -

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Basic information

Entry
Database: PDB / ID: 2n3j
TitleSolution Structure of the alpha-crystallin domain from the redox-sensitive chaperone, HSPB1
ComponentsHeat shock protein beta-1
KeywordsCHAPERONE / crystallin / redox-sensitive chaperone / small heat shock protein
Function / homology
Function and homology information


anterograde axonal protein transport / cornified envelope / regulation of translational initiation / regulation of canonical NF-kappaB signal transduction / positive regulation of endothelial cell chemotaxis / 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 / vascular endothelial growth factor receptor signaling pathway ...anterograde axonal protein transport / cornified envelope / regulation of translational initiation / regulation of canonical NF-kappaB signal transduction / positive regulation of endothelial cell chemotaxis / 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 / vascular endothelial growth factor receptor signaling pathway / chaperone-mediated protein folding / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein folding chaperone / axon cytoplasm / proteasome complex / positive regulation of interleukin-1 beta production / ubiquitin binding / regulation of autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / protein kinase C binding / regulation of protein phosphorylation / negative regulation of protein kinase activity / MAPK6/MAPK4 signaling / response to virus / platelet aggregation / VEGFA-VEGFR2 Pathway / Z disc / spindle / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / unfolded protein binding / 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 / RNA binding / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol
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)
MethodSOLUTION NMR / molecular dynamics
AuthorsRajagopal, P. / Liu, Y. / Shi, L. / Klevit, R.E.
CitationJournal: J.Biomol.Nmr / Year: 2015
Title: Structure of the alpha-crystallin domain from the redox-sensitive chaperone, HSPB1.
Authors: Rajagopal, P. / Liu, Y. / Shi, L. / Clouser, A.F. / Klevit, R.E.
History
DepositionJun 3, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,7882
Polymers21,7882
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-5 kcal/mol
Surface area13700 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Heat shock protein beta-1 / 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: 10894.154 Da / Num. of mol.: 2 / Fragment: Alpha-crystallin domain (UNP residues 80-176)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB1, HSP27, HSP28 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / References: UniProt: P04792

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
2313D 1H-13C NOESY
1423D HN(CA)CB
1523D HBHA(CO)NH
1623D HN(CO)CA
1723D HN(COCA)CB
1823D HNCA
1933D H(CCO)NH
21013D (H)CCH-TOCSY
11112D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium phosphate, 100 mM sodium chloride, 1 mM PMSF, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N; U-80% 2H] protein, 50 mM sodium phosphate, 100 mM sodium chloride, 1 mM PMSF, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N; U-50% 2H] protein, 50 mM sodium phosphate, 100 mM sodium chloride, 1 mM PMSF, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMentity-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
100 mMsodium chloride-31
1 mMPMSF-41
0.1 mMEDTA-51
1.0 mMentity-6[U-100% 13C; U-100% 15N; U-80% 2H]2
50 mMsodium phosphate-72
100 mMsodium chloride-82
1 mMPMSF-92
0.1 mMEDTA-102
1.0 mMentity-11[U-100% 13C; U-100% 15N; U-50% 2H]3
50 mMsodium phosphate-123
100 mMsodium chloride-133
1 mMPMSF-143
0.1 mMEDTA-153
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 7.5 ambient atm295 K
2100 7.5 ambient atm310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003
Varian INOVAVarianINOVA6004
Varian INOVAVarianINOVA8005

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
CS-ROSETTAShen, Vernon, Baker and Baxstructure solution
CcpNMrCCPNdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2021 / NOE intraresidue total count: 223 / NOE long range total count: 879 / NOE medium range total count: 279 / NOE sequential total count: 635 / Protein phi angle constraints total count: 115 / Protein psi angle constraints total count: 115
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10 / Maximum upper distance constraint violation: 1.7 Å

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