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- PDB-6o6i: Endoplasmic reticulum protein 29 (ERp29) C-terminal domain: Struc... -

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Basic information

Entry
Database: PDB / ID: 6o6i
TitleEndoplasmic reticulum protein 29 (ERp29) C-terminal domain: Structure Determination from Backbone Amide Pseudocontact Shifts Generated by Double-histidine Cobalt Tags
ComponentsEndoplasmic reticulum resident protein 29
KeywordsCHAPERONE / GPS-Rosetta structure / dHis-Co2+ / Pseudocontact shifts
Function / homology
Function and homology information


regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein secretion / smooth endoplasmic reticulum / negative regulation of protein secretion / response to endoplasmic reticulum stress / intracellular protein transport / melanosome / protein folding / protein-folding chaperone binding / positive regulation of protein phosphorylation ...regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein secretion / smooth endoplasmic reticulum / negative regulation of protein secretion / response to endoplasmic reticulum stress / intracellular protein transport / melanosome / protein folding / protein-folding chaperone binding / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / negative regulation of gene expression / positive regulation of gene expression / cell surface / endoplasmic reticulum / protein homodimerization activity
Similarity search - Function
Endoplasmic reticulum protein erp29 / Endoplasmic reticulum resident protein 29, C-terminal domain / Endoplasmic reticulum resident protein 29, C-terminal / ERp29, N-terminal / Endoplasmic reticulum resident protein 29 / Endoplasmic reticulum resident protein 29, C-terminal domain superfamily / Endoplasmic reticulum protein ERp29, C-terminal domain / ERp29, N-terminal domain / Endoplasmic reticulum targeting sequence. / Thioredoxin-like superfamily ...Endoplasmic reticulum protein erp29 / Endoplasmic reticulum resident protein 29, C-terminal domain / Endoplasmic reticulum resident protein 29, C-terminal / ERp29, N-terminal / Endoplasmic reticulum resident protein 29 / Endoplasmic reticulum resident protein 29, C-terminal domain superfamily / Endoplasmic reticulum protein ERp29, C-terminal domain / ERp29, N-terminal domain / Endoplasmic reticulum targeting sequence. / Thioredoxin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Endoplasmic reticulum resident protein 29
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / monte carlo
AuthorsBahramzadeh, A. / Huber, T. / Otting, G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Biochemistry / Year: 2019
Title: Three-Dimensional Protein Structure Determination Using Pseudocontact Shifts of Backbone Amide Protons Generated by Double-Histidine Co2+-Binding Motifs at Multiple Sites.
Authors: Bahramzadeh, A. / Huber, T. / Otting, G.
History
DepositionMar 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4May 1, 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

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Assembly

Deposited unit
A: Endoplasmic reticulum resident protein 29


Theoretical massNumber of molelcules
Total (without water)11,7871
Polymers11,7871
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20000target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Endoplasmic reticulum resident protein 29 / ERp29 / Endoplasmic reticulum resident protein 31 / ERp31


Mass: 11787.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Erp29 / Plasmid: pETMCSI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P52555

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
1155isotropic12D 1H-15N HSQC
195isotropic13D HNCO
1105isotropic13D HN(CA)CO
1115isotropic13D HNCA
1125isotropic13D HN(CA)CB
1135isotropic13D HN(COCA)CB
1141isotropic12D 1H-15N HSQC
111anisotropic12D 1H-15N HSQC
152isotropic12D 1H-15N HSQC
122anisotropic12D 1H-15N HSQC
173isotropic12D 1H-15N HSQC
133anisotropic12D 1H-15N HSQC
184isotropic12D 1H-15N HSQC
144anisotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1.258 mM [U-13C; U-15N] ERp29-C, 90% H2O/10% D2O190% H2O/10% D2O
solution2.135 mM [U-13C; U-15N] ERp29-C, 90% H2O/10% D2O290% H2O/10% D2O
solution3.153 mM [U-13C; U-15N] ERp29-C, 90% H2O/10% D2O390% H2O/10% D2O
solution4.320 mM [U-13C; U-15N] ERp29-C, 90% H2O/10% D2O490% H2O/10% D2O
solution5.935 mM [U-13C; U-15N] ERp29-C, 90% H2O/10% D2O590% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
.258 mMERp29-C[U-13C; U-15N]1
.135 mMERp29-C[U-13C; U-15N]2
.153 mMERp29-C[U-13C; U-15N]3
.320 mMERp29-C[U-13C; U-15N]4
.935 mMERp29-C[U-13C; U-15N]5
Sample conditionsIonic strength: 50 mM / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz / Details: TCI Cryoprobe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
GPS-RosettaThomas Huberstructure calculation
CcpNMRCCPNchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: monte carlo / Software ordinal: 1 / Details: GPS-Rosetta
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20000 / Conformers submitted total number: 10

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