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- PDB-6rpv: Extremely stable monomeric variant of human cystatin C with singl... -

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Basic information

Entry
Database: PDB / ID: 6rpv
TitleExtremely stable monomeric variant of human cystatin C with single amino acid substitution
ComponentsCystatin-C
KeywordsHYDROLASE / protein structure / human cystatin C / hCC V57G mutation
Function / homology
Function and homology information


negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / negative regulation of peptidase activity / peptidase inhibitor activity / negative regulation of extracellular matrix disassembly / regulation of tissue remodeling / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / supramolecular fiber organization ...negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / negative regulation of peptidase activity / peptidase inhibitor activity / negative regulation of extracellular matrix disassembly / regulation of tissue remodeling / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / supramolecular fiber organization / negative regulation of proteolysis / Post-translational protein phosphorylation / defense response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / tertiary granule lumen / amyloid-beta binding / protease binding / vesicle / ficolin-1-rich granule lumen / Amyloid fiber formation / endoplasmic reticulum lumen / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SOLUTION SCATTERING / molecular dynamics
AuthorsZhukov, I. / Rodziewicz-Motowidlo, S. / Maszota-Zieleniak, M. / Jurczak, P. / Kozak, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO/2011/03/N/ST4/01293 Poland
CitationJournal: Febs J. / Year: 2020
Title: NMR and crystallographic structural studies of the extremely stable monomeric variant of human cystatin C with single amino acid substitution.
Authors: Maszota-Zieleniak, M. / Jurczak, P. / Orlikowska, M. / Zhukov, I. / Borek, D. / Otwinowski, Z. / Skowron, P. / Pietralik, Z. / Kozak, M. / Szymanska, A. / Rodziewicz-Motowidlo, S.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Structure summary / Category: audit_author / pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystatin-C


Theoretical massNumber of molelcules
Total (without water)13,3231
Polymers13,3231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7590 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1target function

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Components

#1: Protein Cystatin-C / Cystatin-3 / Gamma-trace / Neuroendocrine basic polypeptide / Post-gamma-globulin


Mass: 13323.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CST3 / Production host: Escherichia coli (E. coli) / References: UniProt: P01034

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic13D HNCO
142isotropic13D HNCA
152isotropic13D HN(CO)CA
172isotropic13D CBCA(CO)NH
162isotropic13D HBHA(CO)NH
182isotropic13D (H)CCH-TOCSY
192isotropic13D 1H-13C NOESY aliphatic
1101isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 15N] hCC V57G, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] hCC V57G, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMhCC V57G[U-99% 15N]1
0.5 mMhCC V57G[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7.4 / PH err: 0.1 / Pressure: 1 Pa / Temperature: 298 K

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Data collection

NMR spectrometerType: Agilent DDR2 / Manufacturer: Agilent / Model: DDR2 / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
YASARAKrieger E.refinement
RefinementMethod: molecular dynamics / Software ordinal: 7
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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