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- PDB-7oxe: Crystal structure of the KDEL receptor bound to HDEF peptide at pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 7oxe
TitleCrystal structure of the KDEL receptor bound to HDEF peptide at pH 6.0
Components
  • ER lumen protein-retaining receptor 2
  • THR-ALA-GLU-HIS-ASP-GLU-PHE
KeywordsMEMBRANE PROTEIN / Trafficking receptor
Function / homology
Function and homology information


KDEL sequence binding / ER retention sequence binding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-coated vesicle membrane / 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 / protein transport ...KDEL sequence binding / ER retention sequence binding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-coated vesicle membrane / 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 / 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
(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: 2.283 Å
AuthorsNewstead, S. / Parker, J.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust219531/Z/19/Z United Kingdom
CitationJournal: Structure / Year: 2024
Title: Molecular basis for pH sensing in the KDEL trafficking receptor.
Authors: Wu, Z. / Smith, K. / Gerondopoulos, A. / Sobajima, T. / Parker, J.L. / Barr, F.A. / Newstead, S. / Biggin, P.C.
History
DepositionJun 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _citation.year
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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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: THR-ALA-GLU-HIS-ASP-GLU-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7526
Polymers25,3262
Non-polymers1,4264
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-0 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.383, 37.533, 62.685
Angle α, β, γ (deg.)90.000, 95.220, 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: 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 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: Q5ZKX9
#2: Protein/peptide THR-ALA-GLU-HIS-ASP-GLU-PHE


Mass: 848.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide / 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.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.88 %
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: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.283→62.28 Å / Num. obs: 10122 / % possible obs: 99.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 37.5 Å2 / Rpim(I) all: 0.159 / Rrim(I) all: 0.289 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible allRrim(I) all
2.283-2.353.20.94890.30.774100
6.27-62.32.918.55210.0698.70.104

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Processing

Software
NameVersionClassification
xia2data scaling
BUSTER2.10.4 (20-APR-2021)refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZXR

6zxr


Resolution: 2.283→39.41 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.859 / SU R Cruickshank DPI: 0.584 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.488 / SU Rfree Blow DPI: 0.281 / SU Rfree Cruickshank DPI: 0.287
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2878 503 4.97 %RANDOM
Rwork0.2449 ---
obs0.247 10122 99 %-
Displacement parametersBiso max: 88.58 Å2 / Biso mean: 39.63 Å2 / Biso min: 14.66 Å2
Baniso -1Baniso -2Baniso -3
1-4.1435 Å20 Å21.5238 Å2
2---0.1156 Å20 Å2
3----4.0279 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.283→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 100 51 1926
Biso mean--60.66 33.13 -
Num. residues----216
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d691SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes310HARMONIC5
X-RAY DIFFRACTIONt_it1921HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion242SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1618SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2081HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2958HARMONIC20.85
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion18.94
LS refinement shellResolution: 2.283→2.31 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.33 23 5.68 %
Rwork0.3 382 -
obs--97.79 %

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