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- PDB-5mu7: Crystal Structure of the beta/delta-COPI Core Complex -

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Basic information

Entry
Database: PDB / ID: 5mu7
TitleCrystal Structure of the beta/delta-COPI Core Complex
Components
  • Coatomer subunit beta
  • Coatomer subunit delta-like protein
KeywordsPROTEIN TRANSPORT / coatomer / COPI / beta COP / delta COP
Function / homology
Function and homology information


COPI vesicle coat / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / vesicle-mediated transport / intracellular protein transport / protein transport / Golgi membrane / structural molecule activity
Similarity search - Function
Coatomer beta subunit, C-terminal / Coatomer beta subunit (COPB1) / Coatomer beta subunit, appendage platform domain / Coatomer beta C-terminal region / Coatomer beta subunit appendage platform / Coatomer delta subunit / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily ...Coatomer beta subunit, C-terminal / Coatomer beta subunit (COPB1) / Coatomer beta subunit, appendage platform domain / Coatomer beta C-terminal region / Coatomer beta subunit appendage platform / Coatomer delta subunit / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Longin-like domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Coatomer subunit beta / Coatomer subunit delta
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.57 Å
AuthorsKopp, J. / Aderhold, P. / Wieland, F. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB638 Germany
CitationJournal: Elife / Year: 2017
Title: 9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments.
Authors: Svetlana O Dodonova / Patrick Aderhold / Juergen Kopp / Iva Ganeva / Simone Röhling / Wim J H Hagen / Irmgard Sinning / Felix Wieland / John A G Briggs /
Abstract: COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that ...COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that recruits the coatomer complex to the membrane, triggering polymerization and budding. The vesicle uncoats before fusion with a target membrane. Coat components are structurally conserved between COPI and clathrin/adaptor proteins. Using cryo-electron tomography and subtomogram averaging, we determined the structure of the COPI coat assembled on membranes in vitro at 9 Å resolution. We also obtained a 2.57 Å resolution crystal structure of βδ-COP. By combining these structures we built a molecular model of the coat. We additionally determined the coat structure in the presence of ArfGAP proteins that regulate coat dissociation. We found that Arf1 occupies contrasting molecular environments within the coat, leading us to hypothesize that some Arf1 molecules may regulate vesicle assembly while others regulate coat disassembly.
History
DepositionJan 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coatomer subunit beta
B: Coatomer subunit delta-like protein


Theoretical massNumber of molelcules
Total (without water)62,6502
Polymers62,6502
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-12 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.591, 177.472, 62.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Coatomer subunit beta / Beta-coat protein


Mass: 42386.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0034860 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0S6G7
#2: Protein Coatomer subunit delta-like protein


Mass: 20264.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0026330 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0S6I4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: protein concentration 13 mg/ml reservoir composition: 0.2 M magnesium formate 0.1 M Tris pH 7.0 24 % PEG3350 drop composition: 400 nl protein + 400 nl reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.57→32.1 Å / Num. obs: 24909 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.1
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 2440 / CC1/2: 0.502 / Rpim(I) all: 0.644 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.57→32.072 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.59
RfactorNum. reflection% reflection
Rfree0.2287 1229 4.93 %
Rwork0.1715 --
obs0.1744 24905 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.57→32.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 0 0 44 4213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084232
X-RAY DIFFRACTIONf_angle_d0.895718
X-RAY DIFFRACTIONf_dihedral_angle_d15.432633
X-RAY DIFFRACTIONf_chiral_restr0.047675
X-RAY DIFFRACTIONf_plane_restr0.004733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.67280.32321290.27232602X-RAY DIFFRACTION100
2.6728-2.79440.32661370.25772575X-RAY DIFFRACTION100
2.7944-2.94170.28321220.24462588X-RAY DIFFRACTION100
2.9417-3.12580.31691390.23772623X-RAY DIFFRACTION100
3.1258-3.36690.2711320.2092610X-RAY DIFFRACTION100
3.3669-3.70530.29451270.18962631X-RAY DIFFRACTION100
3.7053-4.24040.21481320.15482641X-RAY DIFFRACTION100
4.2404-5.33850.19751500.1362641X-RAY DIFFRACTION100
5.3385-32.07480.18681610.14922765X-RAY DIFFRACTION100
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)
17.10821.3095-1.87246.10660.12814.77970.34450.46690.9469-0.92950.0823-1.4404-0.89590.5623-0.22550.9932-0.23540.29410.6910.05081.030234.968765.118-21.0979
23.9584-0.90870.7044.5546-0.32846.707-0.12230.24480.6497-0.04780.1221-0.7145-0.86210.78460.1050.7394-0.11790.0420.60920.04860.913128.88164.6624-8.6359
33.31440.10590.55934.5919-0.99676.7330.03-0.20130.31290.1731-0.10040.4023-0.2491-0.5310.04990.4968-0.01670.07390.5683-0.07580.645916.531256.84370.4485
41.16350.9270.81957.91783.97412.5660.3013-0.3963-0.07981.44-0.3710.4470.7859-0.39120.05350.7464-0.24780.060.76290.04550.564610.104729.08360.8161
54.06261.2890.57088.51986.24264.67670.1466-0.2615-0.18850.76-0.2996-0.03730.5850.26220.13650.6306-0.082-0.03880.50440.03320.538910.14886.773-17.6477
62.3976-0.1309-1.43796.1107-2.17327.04770.1646-0.4248-0.10380.84140.2244-0.5518-0.33061.24770.00120.8089-0.0323-0.13640.8707-0.03330.769415.92451.8242-23.3515
78.9078-1.1937-2.34697.6271-1.66337.0138-0.249-0.3291-0.4897-0.0372-0.193-0.70730.4230.35410.46490.5144-0.13590.0230.62750.08140.538331.223138.4977-15.3228
81.33651.57391.01473.34762.0161.23440.73930.3515-1.3501-1.40730.999-0.30890.66461.0563-1.40181.46150.0614-0.13121.1782-0.20991.365824.396123.1776-19.062
96.05920.0192-2.29688.8471-0.28146.9421-0.01490.3016-0.219-0.3524-0.2135-0.07430.2043-0.20570.27970.4064-0.1679-0.05180.56460.01310.492722.604239.2846-19.5795
109.88360.39437.00531.20690.38165.0876-0.2418-0.04030.66360.2109-0.08030.3003-0.1826-0.31930.34390.6355-0.1964-0.040.93780.0240.708313.881543.9126-9.8295
119.19930.6232-0.89114.19726.09739.1974-0.46850.58711.037-2.2565-0.03741.5806-0.9557-1.52770.08080.72770.055-0.17991.02280.17670.66999.554754.0915-19.5817
126.6312-3.7217-1.09969.09121.54586.7763-1.12260.53942.2894-0.46350.0936-0.9657-0.51740.16490.72590.99930.0256-0.31781.01850.19331.42414.532273.5026-14.2362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 109 )
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 185 )
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 310 )
5X-RAY DIFFRACTION5chain 'A' and (resid 311 through 370 )
6X-RAY DIFFRACTION6chain 'A' and (resid 371 through 390 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 42 )
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 47 )
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 116 )
10X-RAY DIFFRACTION10chain 'B' and (resid 117 through 126 )
11X-RAY DIFFRACTION11chain 'B' and (resid 127 through 138 )
12X-RAY DIFFRACTION12chain 'B' and (resid 139 through 151 )

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