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- PDB-5v90: Crystal structure of ERp29 D-domain in complex with the P-domain ... -

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Basic information

Entry
Database: PDB / ID: 5v90
TitleCrystal structure of ERp29 D-domain in complex with the P-domain of calreticulin
Components
  • Calreticulin
  • Endoplasmic reticulum resident protein 29
KeywordsCHAPERONE / protein binding / protein folding
Function / homology
Function and homology information


Calnexin/calreticulin cycle / regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / cytolytic granule / positive regulation of dendritic cell chemotaxis / Assembly of Viral Components at the Budding Site / cortical granule / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding ...Calnexin/calreticulin cycle / regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / cytolytic granule / positive regulation of dendritic cell chemotaxis / Assembly of Viral Components at the Budding Site / cortical granule / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / endoplasmic reticulum quality control compartment / cellular response to electrical stimulus / intracellular glucocorticoid receptor signaling pathway / regulation of meiotic nuclear division / sequestering of calcium ion / response to glycoside / sarcoplasmic reticulum lumen / protein folding in endoplasmic reticulum / hormone binding / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / molecular sequestering activity / cardiac muscle cell differentiation / protein maturation by protein folding / Scavenging by Class F Receptors / Scavenging by Class A Receptors / cortical actin cytoskeleton organization / nuclear androgen receptor binding / response to testosterone / cellular response to lithium ion / smooth endoplasmic reticulum / protein localization to nucleus / protein secretion / protein unfolding / negative regulation of neuron differentiation / negative regulation of protein secretion / positive regulation of cell cycle / positive regulation of phagocytosis / : / positive regulation of substrate adhesion-dependent cell spreading / protein folding chaperone / transport vesicle / endocytic vesicle lumen / protein export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of endothelial cell migration / acrosomal vesicle / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / intracellular protein transport / positive regulation of MAP kinase activity / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / cellular response to virus / intracellular calcium ion homeostasis / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / cellular senescence / unfolded protein binding / melanosome / integrin binding / protein folding / response to estradiol / nuclear envelope / ER-Phagosome pathway / protein-folding chaperone binding / spermatogenesis / carbohydrate binding / collagen-containing extracellular matrix / regulation of apoptotic process / negative regulation of translation / protein stabilization / ribosome / response to xenobiotic stimulus / positive regulation of protein phosphorylation / iron ion binding / external side of plasma membrane / endoplasmic reticulum lumen / negative regulation of gene expression / focal adhesion / mRNA binding / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / calcium ion binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / protein homodimerization activity / DNA binding / extracellular space / RNA binding / extracellular exosome / zinc ion binding / extracellular region
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 / Calreticulin / Calreticulin family repeated motif signature. ...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 / Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / Concanavalin A-like lectin/glucanase domain superfamily / Thioredoxin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Calreticulin / Endoplasmic reticulum resident protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.255 Å
AuthorsKozlov, G. / Munoz-Escobar, J. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN 238873 Canada
CitationJournal: Structure / Year: 2017
Title: Mapping the ER Interactome: The P Domains of Calnexin and Calreticulin as Plurivalent Adapters for Foldases and Chaperones.
Authors: Kozlov, G. / Munoz-Escobar, J. / Castro, K. / Gehring, K.
History
DepositionMar 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: Endoplasmic reticulum resident protein 29
A: Endoplasmic reticulum resident protein 29
B: Calreticulin
D: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2295
Polymers33,1374
Non-polymers921
Water0
1
C: Endoplasmic reticulum resident protein 29
D: Calreticulin


Theoretical massNumber of molelcules
Total (without water)16,5692
Polymers16,5692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-9 kcal/mol
Surface area6770 Å2
MethodPISA
2
A: Endoplasmic reticulum resident protein 29
B: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6613
Polymers16,5692
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-5 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.573, 68.573, 167.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Endoplasmic reticulum resident protein 29 / ERp29 / Endoplasmic reticulum resident protein 28 / ERp28 / Endoplasmic reticulum resident protein 31 / ERp31


Mass: 11903.626 Da / Num. of mol.: 2 / Fragment: UNP residues 158-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERP29, C12orf8, ERP28 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / References: UniProt: P30040
#2: Protein/peptide Calreticulin / / CRP55 / Calregulin / Endoplasmic reticulum resident protein 60 / ERp60 / HACBP / grp60


Mass: 4665.040 Da / Num. of mol.: 2 / Fragment: UNP residues 238-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALR, CRTC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P27797
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.98 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.0 M ammonium sulfate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6307 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6307 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 6735 / % possible obs: 99.4 % / Redundancy: 9.7 % / Rsym value: 0.106 / Net I/σ(I): 19.1
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 6.9 / Num. unique all: 632 / Num. unique obs: 368 / Rsym value: 0.494 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QC7

2qc7


Resolution: 3.255→43.34 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.68
RfactorNum. reflection% reflection
Rfree0.2621 368 5.46 %
Rwork0.2401 --
obs0.2413 6735 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.255→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 6 0 1856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031886
X-RAY DIFFRACTIONf_angle_d0.5342550
X-RAY DIFFRACTIONf_dihedral_angle_d11.491158
X-RAY DIFFRACTIONf_chiral_restr0.039280
X-RAY DIFFRACTIONf_plane_restr0.004337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2552-3.7260.37651130.27862058X-RAY DIFFRACTION99
3.726-4.69350.25281250.22742084X-RAY DIFFRACTION100
4.6935-43.34360.23421300.23482225X-RAY DIFFRACTION99

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