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- PDB-4j87: Crystal structure of alpha-COP -

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Basic information

Entry
Database: PDB / ID: 4j87
TitleCrystal structure of alpha-COP
Componentscoatomer subunit alpha
KeywordsPROTEIN TRANSPORT / Beta propeller domain / Vesicle trafficking
Function / homology
Function and homology information


COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity ...COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity / Golgi apparatus / cytoplasm
Similarity search - Function
Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / : / Coatomer WD associated region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / : / Coatomer WD associated region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Putative coatomer subunit alpha
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMa, W. / Goldberg, J.
CitationJournal: Embo J. / Year: 2013
Title: Rules for the recognition of dilysine retrieval motifs by coatomer.
Authors: Ma, W. / Goldberg, J.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)37,5261
Polymers37,5261
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.432, 53.614, 157.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein coatomer subunit alpha


Mass: 37525.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q96WV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.76 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.67→50.769 Å / Num. all: 37929 / Num. obs: 35377 / % possible obs: 98.2 % / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
ADSCdata collection
PHENIX(phenix.refine: 1.8_1069)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→50.769 Å / SU ML: 0.15 / σ(F): 0.03 / Phase error: 17.07 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1915 2000 5.65 %
Rwork0.1672 --
all0.196 37929 -
obs0.1686 35375 93.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→50.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 0 189 2737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092608
X-RAY DIFFRACTIONf_angle_d1.2573540
X-RAY DIFFRACTIONf_dihedral_angle_d12.884923
X-RAY DIFFRACTIONf_chiral_restr0.094379
X-RAY DIFFRACTIONf_plane_restr0.006449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.71140.28561260.24312112X-RAY DIFFRACTION84
1.7114-1.75770.26731320.20852184X-RAY DIFFRACTION87
1.7577-1.80940.23121330.19582240X-RAY DIFFRACTION89
1.8094-1.86780.21041370.1752288X-RAY DIFFRACTION90
1.8678-1.93460.19391400.16282320X-RAY DIFFRACTION93
1.9346-2.0120.17221420.15212375X-RAY DIFFRACTION94
2.012-2.10360.19531450.1662422X-RAY DIFFRACTION95
2.1036-2.21450.19441450.16222419X-RAY DIFFRACTION96
2.2145-2.35320.19291470.17142463X-RAY DIFFRACTION96
2.3532-2.53490.19041460.17792433X-RAY DIFFRACTION96
2.5349-2.790.1961480.17362477X-RAY DIFFRACTION97
2.79-3.19370.18831500.16252491X-RAY DIFFRACTION96
3.1937-4.02340.16641520.14662532X-RAY DIFFRACTION97
4.0234-50.79280.17911570.1632619X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.36760.3605-0.47232.76220.15241.97030.03220.0774-0.00710.00930.01540.13030.2021-0.0188-0.06470.1884-0.0031-0.01920.16630.00440.2026-16.0253-2.2661-28.1353
20.07220.4170.01442.44070.23751.5746-0.02290.0385-0.0188-0.12130.0553-0.00840.04090.0863-0.02430.16260.0098-0.01350.1838-0.00180.1844-11.29933.948-34.7865
31.5927-0.00741.12391.7216-0.30432.3764-0.030.02660.00610.0199-0.0067-0.0382-0.11950.16520.04720.1620.0016-0.00480.17390.01010.1771-6.241315.7052-30.1109
41.1425-0.53281.12481.5185-0.85273.5749-0.1096-0.07480.05220.14480.07350.0395-0.3234-0.02620.03050.21110.0137-0.01350.1824-0.00840.1924-6.572819.0275-18.4091
50.5378-1.75061.28788.1853-5.82214.1483-0.0104-0.0294-0.1123-0.23660.08850.12280.67660.233-0.02220.36240.0587-0.01940.2315-0.02710.3015-13.973634.7316-26.3622
60.2503-0.33760.08220.5497-0.10530.02730.1939-0.0368-0.11190.01470.05070.0641-0.0421-0.2373-0.03620.31660.08360.03590.2261-0.03880.1716-5.849733.0388-21.9746
70.70720.274-0.08131.52930.35881.68640.0742-0.0598-0.07630.1292-0.05810.07050.0589-0.0748-0.01810.21040.0094-0.0090.237-0.00030.1899-10.19527.7092-7.3141
84.2993-1.0835-0.38253.52120.40743.09660.1136-0.2673-0.13350.2831-0.04280.25730.2433-0.1822-0.05560.236-0.0377-0.00250.24110.02260.2081-16.7769-2.2112-9.3175
93.7012-0.16690.60632.09760.04253.3354-0.069-0.2429-0.14220.04310.04090.01810.1795-0.09980.01730.19310.0035-0.00590.1867-0.00040.2203-14.2586-3.5769-21.9424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 166 )
5X-RAY DIFFRACTION5chain 'A' and (resid 167 through 180 )
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 209 )
7X-RAY DIFFRACTION7chain 'A' and (resid 210 through 264 )
8X-RAY DIFFRACTION8chain 'A' and (resid 265 through 295 )
9X-RAY DIFFRACTION9chain 'A' and (resid 296 through 327 )

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