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- PDB-6bp9: HSPB5 alpha-crystallin domain mutant R120G-ACD -

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Basic information

Entry
Database: PDB / ID: 6bp9
TitleHSPB5 alpha-crystallin domain mutant R120G-ACD
ComponentsAlpha-crystallin B chainCRYAB
KeywordsCHAPERONE / cataract-causing heat shock protein alpha-crystallin B Chain beta sandwich
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)
MethodSOLUTION NMR / simulated annealing
AuthorsRajagopal, P. / Klevit, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)RO! EY017370 United States
CitationJournal: To Be Published
Title: HSPB5 alpha-crystallin domain mutant R120G-ACD
Authors: Rajagopal, P. / Klevit, R.E.
History
DepositionNov 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-crystallin B chain
B: Alpha-crystallin B chain


Theoretical massNumber of molelcules
Total (without water)20,1992
Polymers20,1992
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2870 Å2
ΔGint-12 kcal/mol
Surface area9690 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 100structures with the lowest energy
RepresentativeModel #1medoid

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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: 10099.370 Da / Num. of mol.: 2 / Mutation: R120G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYAB, CRYA2, HSPB5 / Production host: Escherichia coli (E. coli) / References: UniProt: P02511

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic43D NOESY
122isotropic23D HNCA
133isotropic23D HNCA
141isotropic23D HNCO
153isotropic23D HN(CA)CB
163isotropic23D HN(COCA)CB
173isotropic23D HN(CO)CA
181isotropic53D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-13C; U-15N] HSPB5 mutant R120G-ACD, 50 mM no label sodium phosphate, 100 mM no label sodium chloride, 100 uM no label EDTA, 1 mM no label PMSF, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution21 mM [U-13C; U-15N; 50%-2H] HSPB5 mutant R120G-ACD, 50 mM no label sodium phosphate, 100 mM no label sodium chloride, 100 uM no label EDTA, 1 mM no label PMSF, 90% H2O/10% D2O13C15N2H_50sample90% H2O/10% D2O
solution31 mM [U-13C; U-15N; U-2H] HSPB5 mutant R120G-ACD, 50 mM no label sodium phosphate, 100 mM no label sodium chloride, 100 uM no label EDTA, 1 mM no label PMSF, 90% H2O/10% D2O13C15N2H_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHSPB5 mutant R120G-ACD[U-13C; U-15N]1
50 mMsodium phosphateno label1
100 mMsodium chlorideno label1
100 uMEDTAno label1
1 mMPMSFno label1
1 mMHSPB5 mutant R120G-ACD[U-13C; U-15N; 50%-2H]2
50 mMsodium phosphateno label2
100 mMsodium chlorideno label2
100 uMEDTAno label2
1 mMPMSFno label2
1 mMHSPB5 mutant R120G-ACD[U-13C; U-15N; U-2H]3
50 mMsodium phosphateno label3
100 mMsodium chlorideno label3
100 uMEDTAno label3
1 mMPMSFno label3
Sample conditionsIonic strength: 100mM NaCl mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIIBrukerAVANCE III5003
Varian UNITYPLUSVarianUNITYPLUS8002
Varian UNITYPLUSVarianUNITYPLUS9004
Varian UNITYPLUSVarianUNITYPLUS6005

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Processing

NMR software
NameDeveloperClassification
CSRosettaDavid Bakerstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 8

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