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- PDB-8hqx: The complex structure of COPI cargo sorting module with TAT-WDM p... -

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Basic information

Entry
Database: PDB / ID: 8hqx
TitleThe complex structure of COPI cargo sorting module with TAT-WDM peptide
Components
  • Coatomer subunit beta'
  • TAT-WDM KxKxx motif
KeywordsTRANSPORT PROTEIN / TAT-WDM / COPI vesicle / KxKxx motif / retention signal
Function / homology
Function and homology information


COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity
Similarity search - Function
Coatomer beta' subunit (COPB2) / : / Coatomer, WD associated region / Coatomer WD associated region / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...Coatomer beta' subunit (COPB2) / : / Coatomer, WD associated region / Coatomer WD associated region / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Coatomer subunit beta'
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.538 Å
AuthorsMa, W.F. / Nan, Y.N. / Yang, M.R. / Li, Y.Q.
Funding support China, 1items
OrganizationGrant numberCountry
Beijing University of Chinese Medicine (BUCM)90011451310011, 1000061223476, ZYYCXTD-C-202006 China
CitationJournal: To Be Published
Title: The complex structure of COPI cargo sorting module with TAT-WDM peptide
Authors: Ma, W.F. / Nan, Y.N. / Yang, M.R. / Li, Y.Q.
History
DepositionDec 14, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coatomer subunit beta'
B: TAT-WDM KxKxx motif


Theoretical massNumber of molelcules
Total (without water)34,9722
Polymers34,9722
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint3 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.863, 50.831, 72.643
Angle α, β, γ (deg.)90.00, 93.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Coatomer subunit beta'


Mass: 34293.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Gene: SEC27, SCY_1929 / Production host: Escherichia coli (E. coli) / References: UniProt: A6ZU46
#2: Protein/peptide TAT-WDM KxKxx motif


Mass: 678.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 281.15 K / Method: evaporation / Details: 0.1 M MES, pH 6.5 and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.538→50 Å / Num. obs: 28943 / % possible obs: 98.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.2
Reflection shellResolution: 1.55→1.6 Å / Rmerge(I) obs: 0.414 / Num. unique obs: 240

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Processing

Software
NameVersionClassification
PHENIX1.16.3549refinement
HKL-3000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.538→36.495 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 1989 6.87 %
Rwork0.2237 --
obs0.2248 28943 65.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.538→36.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 0 143 2513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042450
X-RAY DIFFRACTIONf_angle_d0.7393341
X-RAY DIFFRACTIONf_dihedral_angle_d12.6841420
X-RAY DIFFRACTIONf_chiral_restr0.057372
X-RAY DIFFRACTIONf_plane_restr0.005421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5384-1.57680.370190.2794151X-RAY DIFFRACTION5
1.5768-1.61950.299200.3162269X-RAY DIFFRACTION9
1.6195-1.66710.3266350.3031423X-RAY DIFFRACTION15
1.6671-1.72090.3189540.3269793X-RAY DIFFRACTION27
1.7209-1.78240.4071140.33291413X-RAY DIFFRACTION49
1.7824-1.85380.35531280.32841997X-RAY DIFFRACTION67
1.8538-1.93820.33591740.2862186X-RAY DIFFRACTION76
1.9382-2.04040.29161880.26042343X-RAY DIFFRACTION80
2.0404-2.16820.27331800.2532664X-RAY DIFFRACTION89
2.1682-2.33560.28512170.24672866X-RAY DIFFRACTION98
2.3356-2.57050.26712170.22452929X-RAY DIFFRACTION99
2.5705-2.94240.21572190.22192937X-RAY DIFFRACTION99
2.9424-3.70650.20192130.19742974X-RAY DIFFRACTION99
3.7065-36.4950.212210.19953009X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.0853 Å / Origin y: 19.8744 Å / Origin z: 18.2034 Å
111213212223313233
T0.1239 Å20.0176 Å2-0.0142 Å2-0.1604 Å2-0.0106 Å2--0.1523 Å2
L1.6931 °2-0.391 °2-0.7622 °2-2.336 °20.72 °2--2.4974 °2
S0.039 Å °-0.0387 Å °0.0774 Å °0.0358 Å °-0.0285 Å °0.0549 Å °-0.0517 Å °-0.2935 Å °-0.0167 Å °
Refinement TLS groupSelection details: all

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