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- PDB-6i6b: Crystal structure of the KDEL receptor in the peptide free state. -

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Basic information

Entry
Database: PDB / ID: 6i6b
TitleCrystal structure of the KDEL receptor in the peptide free state.
ComponentsER 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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 1.3May 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,6204
Polymers23,5511
Non-polymers1,0703
Water95553
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.899, 103.750, 101.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 23550.707 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: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 9
Details: 30% (v/v) PEG 500 DME, 100 mM Tris pH 9.0 and 100 mM Magnesium sulphate.

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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 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.59→51.875 Å / Num. obs: 8193 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.9 / Rmerge(I) obs: 0.359 / Rpim(I) all: 0.158 / Rrim(I) all: 0.393 / Net I/σ(I): 4.1
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
2.59-2.666.31.06936155760.5190.4691.1691.9100
11.58-51.84.80.165481140.6940.0950.18810.899.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
xia2data scaling
PDB_EXTRACT3.24data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse

Resolution: 2.59→51.875 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.16
RfactorNum. reflection% reflection
Rfree0.2711 396 4.85 %
Rwork0.2423 --
obs0.2436 8172 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.41 Å2 / Biso mean: 32.0323 Å2 / Biso min: 11.06 Å2
Refinement stepCycle: final / Resolution: 2.59→51.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 66 53 1788
Biso mean--52.04 34.13 -
Num. residues----203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5901-2.96480.29871290.25525192648
2.9648-3.73520.29431470.235425642711
3.7352-51.88540.24071200.240826932813
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)
12.49580.57250.67240.3866-0.51033.1040.01970.172-0.42730.1708-0.00920.08290.0037-0.0110.04330.171-0.02090.00580.2095-0.01730.119611.651330.06357.5711
21.2467-0.0056-0.81394.80911.72312.9872-0.0240.33250.04620.0403-0.40050.91550.3136-0.49930.35540.11260.00130.04960.19450.02650.273815.906728.904154.4764
30.58230.30360.53324.4013-2.04132.2778-0.002-0.1491-0.00660.27-0.1805-0.4192-0.24520.1020.17680.0948-0.01320.02980.2782-0.04150.206414.510832.832970.9057
41.61910.92070.30752.479-0.82932.99990.0507-0.16270.0103-0.116-0.0297-0.02510.2098-0.3537-0.03510.118-0.0894-0.0230.3453-0.00440.1399-0.214228.638965.0467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 57 )A2 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 79 )A58 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 141 )A80 - 141
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 203 )A142 - 203

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