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- PDB-4j82: Crystal structure of beta'-COP/Insig-2 complex -

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Basic information

Entry
Database: PDB / ID: 4j82
TitleCrystal structure of beta'-COP/Insig-2 complex
Components
  • Coatomer subunit beta'
  • INSIG2
KeywordsPROTEIN TRANSPORT / beta propeller domain / dilysine motif / ER retrieval / vesicle trafficking
Function / homology
Function and homology information


SREBP-SCAP complex retention in endoplasmic reticulum / SREBP-SCAP-Insig complex / cranial suture morphogenesis / negative regulation of steroid biosynthetic process / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / SREBP signaling pathway / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization ...SREBP-SCAP complex retention in endoplasmic reticulum / SREBP-SCAP-Insig complex / cranial suture morphogenesis / negative regulation of steroid biosynthetic process / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / SREBP signaling pathway / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / negative regulation of fatty acid biosynthetic process / intra-Golgi vesicle-mediated transport / Regulation of cholesterol biosynthesis by SREBP (SREBF) / oxysterol binding / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / middle ear morphogenesis / inner ear morphogenesis / triglyceride metabolic process / cholesterol biosynthetic process / roof of mouth development / endoplasmic reticulum to Golgi vesicle-mediated transport / protein sequestering activity / ubiquitin binding / intracellular protein transport / cellular response to insulin stimulus / Golgi membrane / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum
Similarity search - Function
Insulin-induced protein family / Insulin-induced protein (INSIG) / Coatomer beta' subunit (COPB2) / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller ...Insulin-induced protein family / Insulin-induced protein (INSIG) / Coatomer beta' subunit (COPB2) / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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 Beta
Similarity search - Domain/homology
Coatomer subunit beta' / Insulin-induced gene 2 protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.461 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 beta'
B: Coatomer subunit beta'
C: INSIG2
D: INSIG2


Theoretical massNumber of molelcules
Total (without water)69,8474
Polymers69,8474
Non-polymers00
Water9,638535
1
A: Coatomer subunit beta'
C: INSIG2


Theoretical massNumber of molelcules
Total (without water)34,9232
Polymers34,9232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint3 kcal/mol
Surface area11760 Å2
MethodPISA
2
B: Coatomer subunit beta'
D: INSIG2


Theoretical massNumber of molelcules
Total (without water)34,9232
Polymers34,9232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint3 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.056, 48.894, 76.027
Angle α, β, γ (deg.)88.83, 89.15, 62.91
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 34293.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41811
#2: Protein/peptide INSIG2 / Insulin-induced gene 2 protein


Mass: 629.662 Da / Num. of mol.: 2 / Fragment: UNP residues 22-225 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y5U4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.32 Å3/Da / Density % sol: 47.07 %

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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: 1.461→76.01 Å / Num. all: 157300 / Num. obs: 102387 / % possible obs: 95.9 % / Observed criterion σ(I): 2.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.461→43.674 Å / SU ML: 0.22 / σ(F): 1.96 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 2020 1.97 %RANDOM
Rwork0.1686 ---
obs0.1695 102352 93.89 %-
all-135896 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.592 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4867 Å22.1337 Å21.4349 Å2
2---2.708 Å22.2599 Å2
3---2.2213 Å2
Refinement stepCycle: LAST / Resolution: 1.461→43.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4874 0 0 535 5409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065012
X-RAY DIFFRACTIONf_angle_d1.126834
X-RAY DIFFRACTIONf_dihedral_angle_d13.3731771
X-RAY DIFFRACTIONf_chiral_restr0.083754
X-RAY DIFFRACTIONf_plane_restr0.005867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.461-1.49760.3754920.28535319X-RAY DIFFRACTION70
1.4976-1.53810.32961540.27597199X-RAY DIFFRACTION94
1.5381-1.58330.30231340.22937277X-RAY DIFFRACTION95
1.5833-1.63440.32491620.22387263X-RAY DIFFRACTION95
1.6344-1.69280.32361420.22737265X-RAY DIFFRACTION95
1.6928-1.76060.25251330.17177361X-RAY DIFFRACTION96
1.7606-1.84070.22811490.15727275X-RAY DIFFRACTION96
1.8407-1.93780.19871540.15497350X-RAY DIFFRACTION96
1.9378-2.05920.22581500.15397360X-RAY DIFFRACTION97
2.0592-2.21820.1961570.15867362X-RAY DIFFRACTION97
2.2182-2.44140.22051460.15817422X-RAY DIFFRACTION97
2.4414-2.79460.21221600.15987426X-RAY DIFFRACTION98
2.7946-3.52070.17751500.14937428X-RAY DIFFRACTION97
3.5207-43.69320.18011370.16657025X-RAY DIFFRACTION92

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