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- PDB-6i6j: Crystal structure of the KDEL receptor bound to synthetic nanobody. -

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Basic information

Entry
Database: PDB / ID: 6i6j
TitleCrystal structure of the KDEL receptor bound to synthetic nanobody.
Components
  • ER lumen protein-retaining receptor 2
  • Sybody
KeywordsMEMBRANE PROTEIN / Intracellular protein receptor / KDEL / ERD2
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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 26, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Jan 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Sybody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0044
Polymers37,2912
Non-polymers7132
Water1,42379
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-7 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.400, 52.976, 133.062
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 23679.887 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: Antibody Sybody


Mass: 13611.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 9 / Details: 30% (v/v) PEG 400, 100 mM Tris pH 9.0

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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: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.23→52.97 Å / Num. obs: 18081 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.869 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.055 / Rrim(I) all: 0.134 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.23-2.296.31.24713170.5360.5361.36100
9.97-52.974.80.0712560.6650.050.08899.5

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M13

5m13


Resolution: 2.23→47.132 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.57
RfactorNum. reflection% reflection
Rfree0.2472 825 4.58 %
Rwork0.2114 --
obs0.213 18018 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.08 Å2 / Biso mean: 49.3756 Å2 / Biso min: 22.62 Å2
Refinement stepCycle: final / Resolution: 2.23→47.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 38 79 2755
Biso mean--67.94 48.4 -
Num. residues----325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2273-2.36690.29661260.26342758288498
2.3669-2.54960.2741580.24427922950100
2.5496-2.80610.28031340.215228622996100
2.8061-3.21210.22431250.214928472972100
3.2121-4.04660.23761270.196629113038100
4.0466-47.14250.24011550.205330233178100
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)
11.70680.1039-0.34242.10030.95994.7626-0.19280.169-0.15280.02290.12360.00690.5541-0.18340.03380.2438-0.02820.02810.24760.00810.2449-13.65782.1157-3.8627
22.2076-0.2131-0.21742.4151.05636.18350.0965-0.27530.06220.5858-0.0011-0.10940.3492-0.0361-0.00980.43710.0667-0.02270.31080.02290.2759-15.559912.538127.8531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 204)A1 - 204
2X-RAY DIFFRACTION2(chain 'C' and resid 2 through 122)C2 - 122

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