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- PDB-6y7v: Crystal structure of the KDEL receptor bound to HDEL peptide at pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 6y7v
TitleCrystal structure of the KDEL receptor bound to HDEL peptide at pH 6.0
Components
  • ER lumen protein-retaining receptor 2
  • GLU-HIS-ASP-GLU-LEU
KeywordsMEMBRANE PROTEIN / Trafficking receptor / Lipid cubic phase / KDEL 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
CARBON DIOXIDE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / ER lumen protein-retaining receptor 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.241 Å
AuthorsBraeuer, P. / Newstead, S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust219531/Z/19/Z United Kingdom
Wellcome Trust109133/Z/15/A 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
DepositionMar 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 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 24, 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: GLU-HIS-ASP-GLU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3039
Polymers25,1202
Non-polymers2,1837
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint0 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.62, 37.82, 62.42
Angle α, β, γ (deg.)90, 95.18, 90
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: 24476.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: KDELR2, RCJMB04_8l23 / Plasmid: pLeu2d / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: Q5ZKX9
#2: Protein/peptide GLU-HIS-ASP-GLU-LEU


Mass: 642.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 292 K / Method: lipidic cubic phase / pH: 6
Details: 30% (v/v) PEG 600, 100 mM MES pH 6.0, 100 mM Sodium Nitrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.24→37.82 Å / Num. obs: 10570 / % possible obs: 97.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 43.76 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.097 / Rrim(I) all: 0.16 / Net I/σ(I): 6.9
Reflection shellResolution: 2.24→2.27 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 407 / CC1/2: 0.98 / Rpim(I) all: 0.57 / Χ2: 1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I6H

6i6h


Resolution: 2.241→36.16 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.862 / SU R Cruickshank DPI: 0.48 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.487 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.272
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 520 -RANDOM
Rwork0.2375 ---
obs0.2393 10570 97.1 %-
Displacement parametersBiso mean: 48.85 Å2
Baniso -1Baniso -2Baniso -3
1--9.4567 Å20 Å2-2.6643 Å2
2---0.0716 Å20 Å2
3---9.5283 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.241→36.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 153 86 2006
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091971HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.862630HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d725SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes309HARMONIC5
X-RAY DIFFRACTIONt_it1971HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion244SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1474SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion18.88
LS refinement shellResolution: 2.241→2.27 Å
RfactorNum. reflection% reflection
Rfree0.2392 21 -
Rwork0.221 --
obs--98.12 %
Refinement TLS params.Origin x: 44.7213 Å / Origin y: 38.1381 Å / Origin z: 79.1207 Å
111213212223313233
T-0.0248 Å2-0.0042 Å2-0.0953 Å2-0.2184 Å2-0.0165 Å2--0.5056 Å2
L1.9116 °20.0238 °2-0.4667 °2-1.1569 °2-0.6421 °2--1.679 °2
S0.0752 Å °-0.078 Å °0.0262 Å °-0.078 Å °-0.0508 Å °-0.0268 Å °0.0262 Å °-0.0268 Å °-0.0244 Å °
Refinement TLS groupSelection details: { *|* }

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