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- PDB-6tzt: Crystal structure of human alpha/epsilon-COP of the COPI vesicula... -

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Basic information

Entry
Database: PDB / ID: 6tzt
TitleCrystal structure of human alpha/epsilon-COP of the COPI vesicular coat bound to alpha-COP STM2
Components
  • Coatomer subunit alpha
  • Coatomer subunit epsilon
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


protein localization to axon / protein localization to cell leading edge / pancreatic juice secretion / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / COPI-mediated anterograde transport ...protein localization to axon / protein localization to cell leading edge / pancreatic juice secretion / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / COPI-mediated anterograde transport / intracellular protein transport / hormone activity / protein transport / growth cone / Golgi membrane / mRNA binding / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / extracellular space / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
Coatomer epsilon subunit / Coatomer, epsilon subunit / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / : / : / COPA/B second beta-propeller ...Coatomer epsilon subunit / Coatomer, epsilon subunit / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Coatomer subunit epsilon / Coatomer subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.065 Å
AuthorsTravis, S.M. / Hughson, F.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM12676 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007388 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Roles of singleton tryptophan motifs in COPI coat stability and vesicle tethering.
Authors: Travis, S.M. / Kokona, B. / Fairman, R. / Hughson, F.M.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coatomer subunit epsilon
B: Coatomer subunit alpha
C: Coatomer subunit epsilon
D: Coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)152,2294
Polymers152,2294
Non-polymers00
Water181
1
A: Coatomer subunit epsilon
B: Coatomer subunit alpha

A: Coatomer subunit epsilon
B: Coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)152,2294
Polymers152,2294
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
2
A: Coatomer subunit epsilon
B: Coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)76,1152
Polymers76,1152
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-37 kcal/mol
Surface area30080 Å2
MethodPISA
3
C: Coatomer subunit epsilon
D: Coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)76,1152
Polymers76,1152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-37 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.470, 138.470, 192.868
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 17 through 63 or resid 65...
21(chain C and (resid 17 through 63 or resid 65 through 239 or resid 241 through 306))
12(chain B and ((resid 907 and (name N or name...
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLNGLN(chain A and (resid 17 through 63 or resid 65...AA17 - 6331 - 77
121LYSLYSLEULEU(chain A and (resid 17 through 63 or resid 65...AA65 - 16979 - 183
131LYSLYSLYSLYS(chain A and (resid 17 through 63 or resid 65...AA170184
141VALVALSERSER(chain A and (resid 17 through 63 or resid 65...AA16 - 30730 - 321
151VALVALSERSER(chain A and (resid 17 through 63 or resid 65...AA16 - 30730 - 321
161VALVALSERSER(chain A and (resid 17 through 63 or resid 65...AA16 - 30730 - 321
171VALVALSERSER(chain A and (resid 17 through 63 or resid 65...AA16 - 30730 - 321
211ASPASPGLNGLN(chain C and (resid 17 through 63 or resid 65 through 239 or resid 241 through 306))CC17 - 6331 - 77
221LYSLYSLEULEU(chain C and (resid 17 through 63 or resid 65 through 239 or resid 241 through 306))CC65 - 23979 - 253
231GLUGLUPROPRO(chain C and (resid 17 through 63 or resid 65 through 239 or resid 241 through 306))CC241 - 306255 - 320
112PHEPHEPHEPHE(chain B and ((resid 907 and (name N or name...BB90739
122GLYGLYARGARG(chain B and ((resid 907 and (name N or name...BB878 - 122410 - 356
132GLYGLYARGARG(chain B and ((resid 907 and (name N or name...BB878 - 122410 - 356
142GLYGLYARGARG(chain B and ((resid 907 and (name N or name...BB878 - 122410 - 356
152GLYGLYARGARG(chain B and ((resid 907 and (name N or name...BB878 - 122410 - 356
212PHEPHEARGARGchain DDD907 - 122439 - 356

NCS ensembles :
ID
1
2

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Components

#1: Protein Coatomer subunit epsilon / Epsilon-coat protein / Epsilon-COP


Mass: 36139.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: Epithelial / Cell line: T47D / Gene: COPE / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): C43 (DE3) / References: UniProt: O14579
#2: Protein Coatomer subunit alpha / Alpha-coat protein / Alpha-COP / HEP-COP / HEPCOP


Mass: 39975.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: Epithelial / Cell line: T47D / Gene: COPA / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): C43 (DE3) / References: UniProt: P53621
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.86 Å3/Da / Density % sol: 56.94 % / Description: Cubic, 0.1 mm
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium citrate, pH 6.0, 1% (v/v) Tacsimate, pH 5.0, 9% (w/v) PEG 3350, 5 mM dithiothreitol Cryoprotected with 30% (v/v) ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2018
RadiationMonochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3.065→29.624 Å / Num. obs: 40664 / % possible obs: 99.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 81.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 20.6
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
3.065-3.149.70.7952829029240.8190.2650.8392.897.9
13.71-29.629.30.03543874710.9990.0120.03757.690.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.06 Å29.62 Å
Translation6.06 Å29.62 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.8.2phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MKR

3mkr


Resolution: 3.065→29.624 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 1998 4.92 %Random selection
Rwork0.1777 ---
obs0.18 40615 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.41 Å2 / Biso mean: 74.5309 Å2 / Biso min: 31.17 Å2
Refinement stepCycle: final / Resolution: 3.065→29.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9786 0 0 1 9787
Biso mean---69.04 -
Num. residues----1230
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2785X-RAY DIFFRACTION9.007TORSIONAL
12C2785X-RAY DIFFRACTION9.007TORSIONAL
21B3110X-RAY DIFFRACTION9.007TORSIONAL
22D3110X-RAY DIFFRACTION9.007TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0652-3.14180.31131390.2939267098
3.1418-3.22660.3131400.2552728100
3.2266-3.32150.31561380.24482705100
3.3215-3.42850.29681410.24072747100
3.4285-3.55090.29941410.2342748100
3.5509-3.69280.25781410.21672716100
3.6928-3.86050.2641430.19952747100
3.8605-4.06360.21911410.18862763100
4.0636-4.31740.19811440.16282756100
4.3174-4.64960.17061390.14862741100
4.6496-5.11540.18761450.14542786100
5.1154-5.85060.23971430.16632769100
5.8506-7.35250.22021460.16442822100
7.3525-29.6240.16821570.13732919100

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