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- PDB-5v8z: Crystal structure of ERp29 D-domain in complex with the P-domain ... -

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Basic information

Entry
Database: PDB / ID: 5v8z
TitleCrystal structure of ERp29 D-domain in complex with the P-domain of calmegin
Components
  • Calmegin
  • Endoplasmic reticulum resident protein 29
KeywordsCHAPERONE / protein binding / protein folding
Function / homology
Function and homology information


regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / smooth endoplasmic reticulum / protein secretion / protein unfolding / negative regulation of protein secretion / ERAD pathway / intracellular protein transport / unfolded protein binding / melanosome / protein folding ...regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / smooth endoplasmic reticulum / protein secretion / protein unfolding / negative regulation of protein secretion / ERAD pathway / intracellular protein transport / unfolded protein binding / melanosome / protein folding / protein-folding chaperone binding / positive regulation of MAPK cascade / endoplasmic reticulum lumen / negative regulation of gene expression / calcium ion binding / positive regulation of gene expression / endoplasmic reticulum membrane / cell surface / endoplasmic reticulum / protein homodimerization activity / membrane
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 family repeated motif signature. / Calreticulin/calnexin ...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 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
Calmegin / Endoplasmic reticulum resident protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 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 / Data collection / Category: diffrn_detector / pdbx_audit_support
Item: _diffrn_detector.detector / _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
A: Endoplasmic reticulum resident protein 29
B: Calmegin
C: Endoplasmic reticulum resident protein 29
D: Calmegin


Theoretical massNumber of molelcules
Total (without water)32,4924
Polymers32,4924
Non-polymers00
Water66737
1
A: Endoplasmic reticulum resident protein 29
B: Calmegin


Theoretical massNumber of molelcules
Total (without water)16,2462
Polymers16,2462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-6 kcal/mol
Surface area7360 Å2
MethodPISA
2
C: Endoplasmic reticulum resident protein 29
D: Calmegin


Theoretical massNumber of molelcules
Total (without water)16,2462
Polymers16,2462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-2 kcal/mol
Surface area7530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.782, 67.620, 73.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P30040
#2: Protein/peptide Calmegin


Mass: 4342.601 Da / Num. of mol.: 2 / Fragment: UNP residues 327-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: CLGN / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: E2RA18
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4 M sodium citrate pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9782 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20065 / % possible obs: 99.7 % / Redundancy: 8.6 % / Rsym value: 0.087 / Net I/σ(I): 34.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1948 / Num. unique obs: 1021 / Rsym value: 0.512 / % possible all: 99

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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: 2.105→33.81 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.49
RfactorNum. reflection% reflection
Rfree0.2191 1021 5.09 %
Rwork0.2112 --
obs0.2117 20065 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.105→33.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 0 37 2014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092007
X-RAY DIFFRACTIONf_angle_d1.1232693
X-RAY DIFFRACTIONf_dihedral_angle_d6.5981259
X-RAY DIFFRACTIONf_chiral_restr0.065285
X-RAY DIFFRACTIONf_plane_restr0.007355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1053-2.21630.28341280.22892641X-RAY DIFFRACTION98
2.2163-2.35510.27121500.22772658X-RAY DIFFRACTION100
2.3551-2.53690.28081470.23792684X-RAY DIFFRACTION100
2.5369-2.79210.24291410.24562712X-RAY DIFFRACTION100
2.7921-3.19580.27591460.25842731X-RAY DIFFRACTION100
3.1958-4.02530.24691380.19862757X-RAY DIFFRACTION100
4.0253-33.81430.1651710.18572861X-RAY DIFFRACTION100

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