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- PDB-6i6h: Crystal structure of the KDEL receptor in the peptide bound state -

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Basic information

Entry
Database: PDB / ID: 6i6h
TitleCrystal structure of the KDEL receptor in the peptide bound state
Components
  • AEKDEL peptide
  • ER lumen protein-retaining receptor 2
KeywordsMEMBRANE PROTEIN / Intracellular protein receptor / KDEL / ERD2
Function / homology
Function and homology information


KDEL sequence binding / COPI-dependent Golgi-to-ER retrograde traffic / ER retention sequence binding / 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 / endoplasmic reticulum to Golgi vesicle-mediated transport ...KDEL sequence binding / COPI-dependent Golgi-to-ER retrograde traffic / ER retention sequence binding / 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 / 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
(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 Å
AuthorsBraeuer, P. / Newstead, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust109133/Z/15/A United Kingdom
CitationJournal: Science / Year: 2019
Title: Structural basis for pH-dependent retrieval of ER proteins from the Golgi by the KDEL receptor.
Authors: Brauer, P. / Parker, J.L. / Gerondopoulos, A. / Zimmermann, I. / Seeger, M.A. / Barr, F.A. / Newstead, S.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: ER lumen protein-retaining receptor 2
B: AEKDEL peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,62213
Polymers24,7002
Non-polymers3,92211
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint0 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.871, 37.503, 62.750
Angle α, β, γ (deg.)90.000, 95.420, 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: 23995.299 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) / Variant (production host): BJ5460 / References: UniProt: Q5ZKX9
#2: Protein/peptide AEKDEL peptide


Mass: 704.746 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.: 11 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 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: 0.968 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2→47.66 Å / Num. obs: 15192 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 23.56 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.282 / Rpim(I) all: 0.096 / Rrim(I) all: 0.298 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.059.12.58810960.7210.8952.742100
8.94-47.68.20.0831930.990.0310.08999.4

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I6B

6i6b


Resolution: 2→47.66 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.216 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.229 812 5.36 %RANDOM
Rwork0.187 ---
obs0.189 15154 99.2 %-
Displacement parametersBiso max: 190.33 Å2 / Biso mean: 31.25 Å2 / Biso min: 8.39 Å2
Baniso -1Baniso -2Baniso -3
1-4.0257 Å20 Å2-0.4863 Å2
2---2.1969 Å20 Å2
3----1.8288 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 2→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 229 137 2115
Biso mean--65.51 44.33 -
Num. residues----213
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d774SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes25HARMONIC2
X-RAY DIFFRACTIONt_gen_planes287HARMONIC5
X-RAY DIFFRACTIONt_it2022HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion244SEMIHARMONIC5
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_contact2388SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2022HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2671HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion18.29
LS refinement shellResolution: 2→2.14 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.263 140 5.34 %
Rwork0.216 2481 -
all0.218 2621 -
obs--96.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.3907-2.90572.66642.0993-1.60013.6930.3180.3805-0.255-0.3918-0.17880.07640.26280.3133-0.13920.07510.00670.00720.0446-0.01160.093448.734432.726472.6191
21.5714-0.30480.11441.03690.02090.8906-0.032-0.0594-0.01420.00040.0344-0.0472-0.0120.0816-0.00240.0449-0.01490.00140.01210.00510.052643.484634.97285.8057
30.95662.73233.09910.12862.88723.3667-0.0709-0.22750.55290.14620.621-1.1001-0.28251.138-0.55010.0629-0.0113-0.04240.51150.00620.535165.02240.606478.755
42.41330.2081-0.44550.7685-0.27312.2924-0.00240.13490.228-0.05790.0301-0.0561-0.11950.1194-0.02770.0908-0.01210.0046-0.00680.03590.084244.60746.337172.8822
5-0.4388-3.27442.01412.11894.66246.3141-0.0231-0.0555-0.15560.0865-0.10180.8439-0.0296-1.08590.1249-0.13860.0283-0.0226-0.0001-0.00380.062928.307837.589476.9529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|33 }A1 - 33
2X-RAY DIFFRACTION2{ A|34 - A|140 }A34 - 140
3X-RAY DIFFRACTION3{ A|141 - A|145 }A141 - 145
4X-RAY DIFFRACTION4{ A|146 - A|206 }A146 - 206
5X-RAY DIFFRACTION5{ B|3 - B|7 }B3 - 8

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