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- PDB-6zxr: Crystal structure of the KDEL receptor bound to RDEL peptide at pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 6zxr
TitleCrystal structure of the KDEL receptor bound to RDEL peptide at pH 6.0
Components
  • ALA-GLU-ARG-ASP-GLU-LEU
  • ER lumen protein-retaining receptor 2
KeywordsMEMBRANE PROTEIN / KDEL receptor / trafficking receptor
Function / homology
Function and homology information


KDEL sequence binding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-coated vesicle membrane / ER retention sequence binding / protein retention in ER lumen / COPI-mediated anterograde transport / maintenance of protein localization in endoplasmic reticulum / cis-Golgi network / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport ...KDEL sequence binding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-coated vesicle membrane / ER retention sequence binding / protein retention in ER lumen / COPI-mediated anterograde transport / maintenance of protein localization in endoplasmic reticulum / cis-Golgi network / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
ER lumen protein retaining receptor / ER lumen protein retaining receptor / ER lumen protein retaining receptor signature 1. / ER lumen protein retaining receptor signature 2.
Similarity search - Domain/homology
ER lumen protein-retaining receptor 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsNewstead, S. / Parker, J.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust219531/Z/19/Z United Kingdom
CitationJournal: Elife / Year: 2021
Title: A signal capture and proofreading mechanism for the KDEL-receptor explains selectivity and dynamic range in ER retrieval.
Authors: Gerondopoulos, A. / Brauer, P. / Sobajima, T. / Wu, Z. / Parker, J.L. / Biggin, P.C. / Barr, F.A. / Newstead, S.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ER lumen protein-retaining receptor 2
B: ALA-GLU-ARG-ASP-GLU-LEU


Theoretical massNumber of molelcules
Total (without water)26,0622
Polymers26,0622
Non-polymers00
Water77543
1
A: ER lumen protein-retaining receptor 2


Theoretical massNumber of molelcules
Total (without water)25,3291
Polymers25,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ALA-GLU-ARG-ASP-GLU-LEU


  • defined by author
  • 733 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7331
Polymers7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.520, 37.450, 62.650
Angle α, β, γ (deg.)90.000, 95.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ER lumen protein-retaining receptor 2 / KDEL endoplasmic reticulum protein retention receptor 2 / KDEL receptor 2


Mass: 25328.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: KDELR2, RCJMB04_8l23 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q5ZKX9
#2: Protein/peptide ALA-GLU-ARG-ASP-GLU-LEU


Mass: 732.760 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 292 K / Method: lipidic cubic phase / pH: 6 / Details: 30% PEG 600, 0.1M MES pH 6.0, 0.1M Sodium Nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980109 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 18, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980109 Å / Relative weight: 1
ReflectionResolution: 2.31→47.33 Å / Num. obs: 9815 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.074 / Rrim(I) all: 0.192 / Net I/σ(I): 8 / Num. measured all: 65692 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.31-2.375.81.50640346910.2570.6711.6540.993.6
10.34-47.335.40.0486741250.9980.0230.05428.498.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6i6h

6i6h


Resolution: 2.31→47.33 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.981 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.456 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 491 5 %RANDOM
Rwork0.1997 ---
obs0.2026 9316 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.65 Å2 / Biso mean: 46.127 Å2 / Biso min: 28.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å20 Å2-0.3 Å2
2--0.58 Å20 Å2
3---1.4 Å2
Refinement stepCycle: final / Resolution: 2.31→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 0 43 1828
Biso mean---47.15 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131847
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171769
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.6272512
X-RAY DIFFRACTIONr_angle_other_deg1.3011.5624064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92521.23581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29715310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.164157
X-RAY DIFFRACTIONr_chiral_restr0.0730.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
LS refinement shellResolution: 2.311→2.371 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.32 35 -
Rwork0.3 651 -
obs--93.46 %

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