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- PDB-7oye: Crystal structure of the KDEL receptor bound to HDEL peptide at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 7oye
TitleCrystal structure of the KDEL receptor bound to HDEL peptide at pH 7.0
Components
  • ER lumen protein-retaining receptor 2
  • THR-ALA-GLU-HIS-ASP-GLU-LEU
KeywordsMEMBRANE PROTEIN / trafficking receptor
Function / homology
Function and homology information


KDEL sequence binding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-coated vesicle membrane / ER retention sequence binding / 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 / COPI-coated vesicle membrane / ER retention sequence binding / 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
CARBON DIOXIDE / (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: 2.62 Å
AuthorsNewstead, S. / Braeuer, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust219531/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the KDEL receptor bound to HDEL peptide at pH 7.0
Authors: Newstead, S. / Braeuer, P.
History
DepositionJun 24, 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

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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-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1188
Polymers25,2922
Non-polymers1,8276
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-2 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.020, 38.030, 62.510
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: 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-LEU


Mass: 814.817 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.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 7
Details: 30% PEG 500DME 100mM HEPES pH 7.0 100mM Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9698 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9698 Å / Relative weight: 1
ReflectionResolution: 2.62→38.03 Å / Num. obs: 6860 / % possible obs: 98.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 64.14 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.098 / Rrim(I) all: 0.179 / Net I/σ(I): 5.6 / Num. measured all: 21309 / Scaling rejects: 12
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
2.62-2.693.10.99715745040.5310.6681.2041.498.9
11.72-38.032.60.073231900.9860.0530.0912.496

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-APR-2021)refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6i6h

6i6h


Resolution: 2.62→36.29 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.381
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 347 5.06 %RANDOM
Rwork0.2336 ---
obs0.2356 6853 98.3 %-
Displacement parametersBiso max: 121.76 Å2 / Biso mean: 66.24 Å2 / Biso min: 30.57 Å2
Baniso -1Baniso -2Baniso -3
1--10.2484 Å20 Å2-7.827 Å2
2---6.0562 Å20 Å2
3---16.3046 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.62→36.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 128 62 1954
Biso mean--96.35 67 -
Num. residues----215
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d696SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes303HARMONIC5
X-RAY DIFFRACTIONt_it1935HARMONIC10
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_contact1415SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1935HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2588HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion18.89
LS refinement shellResolution: 2.62→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.4388 19 4.7 %
Rwork0.3124 385 -
all0.3175 404 -
obs--98.79 %
Refinement TLS params.Method: refined / Origin x: 45.1961 Å / Origin y: 38.2938 Å / Origin z: 79.9976 Å
111213212223313233
T-0.2737 Å2-0.0214 Å20.1014 Å2--0.113 Å2-0.021 Å2--0.2163 Å2
L1.8309 °2-0.0954 °2-0.5857 °2-2.6843 °2-0.5603 °2--2.6073 °2
S0.0115 Å °0.2241 Å °0.1218 Å °-0.0395 Å °-0.0182 Å °-0.0889 Å °-0.0587 Å °-0.0238 Å °0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A1 - 209
2X-RAY DIFFRACTION1{ *|* }A1 - 209
3X-RAY DIFFRACTION1{ *|* }B1 - 209
4X-RAY DIFFRACTION1{ *|* }S1 - 209
5X-RAY DIFFRACTION1{ *|* }W1 - 209

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