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- PDB-1pzd: Structural Identification of a conserved appendage domain in the ... -

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Basic information

Entry
Database: PDB / ID: 1pzd
TitleStructural Identification of a conserved appendage domain in the carboxyl-terminus of the COPI gamma-subunit.
ComponentsCoatomer gamma subunit
KeywordsENDOCYTOSIS/EXOCYTOSIS / platform domain / appendage domain / ear domain / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


COPI vesicle coat / organelle transport along microtubule / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein secretion / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity ...COPI vesicle coat / organelle transport along microtubule / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein secretion / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity / endoplasmic reticulum / cytosol
Similarity search - Function
Coatomer, gamma subunit, appendage domain / Coatomer, gamma subunit, appendage, Ig-like subdomain / Coatomer gamma subunit / Coatomer subunit gamma, C-terminal / Coatomer, gamma subunit, appendage domain superfamily / Coatomer gamma subunit appendage platform subdomain / Coatomer subunit gamma-1 C-terminal appendage platform / TATA-Binding Protein / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin/coatomer adaptor, adaptin-like, N-terminal ...Coatomer, gamma subunit, appendage domain / Coatomer, gamma subunit, appendage, Ig-like subdomain / Coatomer gamma subunit / Coatomer subunit gamma, C-terminal / Coatomer, gamma subunit, appendage domain superfamily / Coatomer gamma subunit appendage platform subdomain / Coatomer subunit gamma-1 C-terminal appendage platform / TATA-Binding Protein / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TATA-Binding Protein / TBP domain superfamily / Armadillo-like helical / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Coatomer subunit gamma-1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.31 Å
AuthorsHoffman, G.R. / Rahl, P.B. / Collins, R.N. / Cerione, R.A.
CitationJournal: Mol.Cell / Year: 2003
Title: Conserved Structural Motifs in Intracellular Trafficking Pathways. Structure of the gammaCOP Appendage Domain.
Authors: Hoffman, G.R. / Rahl, P.B. / Collins, R.N. / Cerione, R.A.
History
DepositionJul 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE RESIDUES 555-603 were included in the crystalized protein but did not show any electron ...SEQUENCE RESIDUES 555-603 were included in the crystalized protein but did not show any electron density so are presumably disordered.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coatomer gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0364
Polymers35,7481
Non-polymers2883
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.570, 89.560, 98.600
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 gamma subunit / Gamma-coat protein / Gamma-COP


Mass: 35748.184 Da / Num. of mol.: 1 / Fragment: residues 555-874
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COPG / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P53620
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100mM sodium citrate and 1.5-1.7M lithium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
220 mMTris1droppH7.5
31.4-1.7 M1reservoirLi2SO4
4100 mMsodium citrate1reservoirpH6.0

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Data collection

Diffraction
IDCrystal-ID
21
11
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.92
SYNCHROTRONCHESS F220.9789, 0.9783, 0.9500
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.97891
30.97831
40.951
ReflectionResolution: 2.3→44 Å / Num. obs: 19621 / % possible obs: 89.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Biso Wilson estimate: 54.5 Å2 / Rsym value: 0.089 / Net I/σ(I): 6.3
Reflection shellResolution: 2.3→2.44 Å / % possible all: 87.5

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.31→43.19 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1967 10 %RANDOM
Rwork0.199 ---
all0.2041 ---
obs0.199 19621 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.4314 Å2 / ksol: 0.322238 e/Å3
Displacement parametersBiso mean: 67 Å2
Baniso -1Baniso -2Baniso -3
1-20.43 Å20 Å20 Å2
2--0.13 Å20 Å2
3----20.55 Å2
Refine analyzeLuzzati coordinate error free: 0.36 Å / Luzzati sigma a free: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.31→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 15 152 2290
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it6.771.5
X-RAY DIFFRACTIONc_mcangle_it10.022
X-RAY DIFFRACTIONc_scbond_it10.282
X-RAY DIFFRACTIONc_scangle_it13.672.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 292 10.2 %
Rwork0.336 2582 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67
LS refinement shell
*PLUS
Rfactor Rfree: 0.383 / Rfactor Rwork: 0.342

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