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- PDB-8apy: Crystal structure of the H12A variant of the KDEL receptor bound ... -

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Basic information

Entry
Database: PDB / ID: 8apy
TitleCrystal structure of the H12A variant of the KDEL receptor bound to sybody
Components
  • ER lumen protein-retaining receptor 2
  • Synthetic nanobody
KeywordsMEMBRANE PROTEIN / Trafficking receptor / synthetic binder / KDELR
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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.34 Å
AuthorsParker, J.L. / Smith, K. / Newstead, S.
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
DepositionAug 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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
C: Synthetic nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3773
Polymers38,0212
Non-polymers3571
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-5 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.190, 71.090, 133.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 24409.818 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 Synthetic nanobody


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 BL21(DE3) (bacteria)
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 30% v/v PEG 400 0.1 M Tris pH 8.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.34→42.79 Å / Num. obs: 18726 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 56 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.094 / Net I/σ(I): 9.4
Reflection shellResolution: 2.34→2.4 Å / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1 / Num. unique obs: 1371 / CC1/2: 0.406 / Rpim(I) all: 1.218 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6i6j

6i6j


Resolution: 2.34→42.79 Å / SU ML: 0.4856 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.9822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3287 943 5.05 %
Rwork0.2681 17733 -
obs0.2711 18676 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.88 Å2
Refinement stepCycle: LAST / Resolution: 2.34→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 25 17 2675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742739
X-RAY DIFFRACTIONf_angle_d1.13013718
X-RAY DIFFRACTIONf_chiral_restr0.066410
X-RAY DIFFRACTIONf_plane_restr0.0082452
X-RAY DIFFRACTIONf_dihedral_angle_d7.4556382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.460.46471340.39882481X-RAY DIFFRACTION99.77
2.46-2.620.46851380.34182489X-RAY DIFFRACTION99.51
2.62-2.820.38171200.31082522X-RAY DIFFRACTION99.81
2.82-3.10.38921370.31352490X-RAY DIFFRACTION99.55
3.1-3.550.35611380.2992524X-RAY DIFFRACTION99.55
3.55-4.470.341250.25742564X-RAY DIFFRACTION99.3
4.47-42.790.25731510.22352663X-RAY DIFFRACTION98.88

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