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- PDB-6u3v: Crystal structure of human alpha/epsilon-COP of the COPI vesicula... -

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Basic information

Entry
Database: PDB / ID: 6u3v
TitleCrystal structure of human alpha/epsilon-COP of the COPI vesicular coat bound to alpha-COP STM1
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 / Resolution: 2.96 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 22, 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)152,2304
Polymers152,2304
Non-polymers00
Water00
1
A: Coatomer subunit epsilon
B: Coatomer subunit alpha

A: Coatomer subunit epsilon
B: Coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)152,2304
Polymers152,2304
Non-polymers00
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 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 area5310 Å2
ΔGint-36 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.103, 138.103, 192.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
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 - 13779 - 151
131ARGARGALAALA(chain A and (resid 17 through 63 or resid 65...AA138 - 139152 - 153
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
122GLUGLUARGARG(chain B and ((resid 907 and (name N or name...BB843 - 122410 - 356
132GLUGLUARGARG(chain B and ((resid 907 and (name N or name...BB843 - 122410 - 356
142GLUGLUARGARG(chain B and ((resid 907 and (name N or name...BB843 - 122410 - 356
152GLUGLUARGARG(chain B and ((resid 907 and (name N or name...BB843 - 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: 39975.102 Da / Num. of mol.: 2 / Mutation: deletion 854-887
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

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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: 3.8 Å3/Da / Density % sol: 67.62 % / 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, 0.05% (v/v) Tacsimate, pH 5.0, 11% (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-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2018
RadiationMonochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.956→29.55 Å / Num. obs: 45037 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 73.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.038 / Rrim(I) all: 0.12 / Net I/σ(I): 16.6
Reflection shellResolution: 2.96→3.03 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.954 / Num. measured all: 31338 / Num. unique obs: 3157 / CC1/2: 0.784 / Rpim(I) all: 0.313 / Rrim(I) all: 1.005 / Net I/σ(I) obs: 2.3 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998: ???refinement
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TZT

6tzt


Resolution: 2.96→29.547 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.25
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 2004 4.45 %Random selection
Rwork0.1721 ---
obs0.1748 44990 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 196.09 Å2 / Biso mean: 71.2289 Å2 / Biso min: 29.54 Å2
Refinement stepCycle: final / Resolution: 2.96→29.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9787 0 0 0 9787
Num. residues----1232
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2789X-RAY DIFFRACTION8.144TORSIONAL
12C2789X-RAY DIFFRACTION8.144TORSIONAL
21B3147X-RAY DIFFRACTION8.144TORSIONAL
22D3147X-RAY DIFFRACTION8.144TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.96-3.02980.37541370.2809294197
3.0298-3.11160.29581420.2513044100
3.1116-3.20310.30191410.23453067100
3.2031-3.30630.29031350.24183029100
3.3063-3.42430.31911440.21893027100
3.4243-3.56120.27671440.20613051100
3.5612-3.7230.22851450.19323063100
3.723-3.91890.25421430.17693033100
3.9189-4.16380.21981420.15183093100
4.1638-4.48420.17121410.13393072100
4.4842-4.93360.17081430.12893085100
4.9336-5.64320.24371420.15333092100
5.6432-7.09360.20271490.17983129100
7.0936-29.5470.20911560.14833260100
Refinement TLS params.Method: refined / Origin x: 59.4106 Å / Origin y: 5.4372 Å / Origin z: 15.4643 Å
111213212223313233
T0.4839 Å2-0.0173 Å20.044 Å2-0.4147 Å20.0001 Å2--0.3938 Å2
L0.7565 °20.564 °20.3197 °2-1.0756 °20.4838 °2--0.6029 °2
S0.0491 Å °-0.121 Å °-0.007 Å °0.2789 Å °-0.0938 Å °0.1576 Å °0.1183 Å °-0.2565 Å °0.0451 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 307
2X-RAY DIFFRACTION1allB843 - 1224
3X-RAY DIFFRACTION1allC17 - 306
4X-RAY DIFFRACTION1allD907 - 1224

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