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- PDB-4wjw: Crystal Structure of the Chs5-Chs6 Exomer Cargo Adaptor Complex B... -

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Basic information

Entry
Database: PDB / ID: 4wjw
TitleCrystal Structure of the Chs5-Chs6 Exomer Cargo Adaptor Complex Bound to portion of Chs3
Components
  • CHITIN SYNTHASE 3
  • Chitin biosynthesis protein CHS5
  • Chitin biosynthesis protein CHS6
Keywordstransport protein/transferase / Adaptor protein / cargo binding / vesicular trafficking / chitin synthase / Biosynthetic Protein / transport protein-transferase complex
Function / homology
Function and homology information


exomer complex / protein localization to bud neck / chitosome / conjugation with cellular fusion / chitin synthase / chitin synthase activity / prospore membrane / chitin biosynthetic process / cellular bud site selection / ascospore wall assembly ...exomer complex / protein localization to bud neck / chitosome / conjugation with cellular fusion / chitin synthase / chitin synthase activity / prospore membrane / chitin biosynthetic process / cellular bud site selection / ascospore wall assembly / incipient cellular bud site / Golgi to plasma membrane transport / cell septum / cellular bud neck / trans-Golgi network transport vesicle / mating projection tip / chitin catabolic process / cytoplasmic vesicle membrane / cell periphery / trans-Golgi network / small GTPase binding / protein transport / protein dimerization activity / regulation of DNA-templated transcription / endoplasmic reticulum / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Chitin synthase / Chitin synthase 4-like domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #50 / Fibronectin type III domain, fungi / Chitin biosynthesis protein Chs5, N-terminal / : / Chitin biosynthesis protein CHS5 N-terminus / Fibronectin type III domain / Chs5p-Arf1p binding / ChAPs (Chs5p-Arf1p-binding proteins) ...Chitin synthase / Chitin synthase 4-like domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #50 / Fibronectin type III domain, fungi / Chitin biosynthesis protein Chs5, N-terminal / : / Chitin biosynthesis protein CHS5 N-terminus / Fibronectin type III domain / Chs5p-Arf1p binding / ChAPs (Chs5p-Arf1p-binding proteins) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Chitin synthase / Other non-globular / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / TPR repeat region circular profile. / BRCT domain superfamily / Nucleotide-diphospho-sugar transferases / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Special / Tetratricopeptide-like helical domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chitin synthase 3 / Chitin biosynthesis protein CHS6 / Chitin biosynthesis protein CHS5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsWeiskoff, A.M. / Fromme, J.C.
CitationJournal: Front Cell Dev Biol / Year: 2014
Title: Distinct N-terminal regions of the exomer secretory vesicle cargo Chs3 regulate its trafficking itinerary.
Authors: Weiskoff, A.M. / Fromme, J.C.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionOct 15, 2014ID: 4U9T
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / refine_hist
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin biosynthesis protein CHS5
B: Chitin biosynthesis protein CHS6
P: CHITIN SYNTHASE 3


Theoretical massNumber of molelcules
Total (without water)98,9793
Polymers98,9793
Non-polymers00
Water1,65792
1
A: Chitin biosynthesis protein CHS5
B: Chitin biosynthesis protein CHS6
P: CHITIN SYNTHASE 3

A: Chitin biosynthesis protein CHS5
B: Chitin biosynthesis protein CHS6
P: CHITIN SYNTHASE 3


Theoretical massNumber of molelcules
Total (without water)197,9576
Polymers197,9576
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Unit cell
Length a, b, c (Å)218.613, 218.613, 137.848
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-810-

HOH

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Components

#1: Protein Chitin biosynthesis protein CHS5 / Protein CAL3


Mass: 8653.009 Da / Num. of mol.: 1 / Fragment: unp residues 1-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CHS5, CAL3, YLR330W, L8543.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12114
#2: Protein Chitin biosynthesis protein CHS6 / Protein CSD3


Mass: 87977.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CHS6, CSD3, YJL099W, J0838 / Production host: Escherichia coli (E. coli) / References: UniProt: P40955
#3: Protein/peptide CHITIN SYNTHASE 3 / CHITIN-UDP ACETYL-GLUCOSAMINYL TRANSFERASE 3 / CLASS-IV CHITIN SYNTHASE 3


Mass: 2348.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P29465*PLUS, chitin synthase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 4.8 Å3/Da / Density % sol: 74.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.3 M AMMONIUM SULFATE, 0.1 M CITRIC ACID / PH range: 4.0-4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 16, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 2.59→44.65 Å / Num. obs: 59936 / % possible obs: 99 % / Redundancy: 12.2 % / Rsym value: 0.09 / Net I/σ(I): 19.45
Reflection shellResolution: 2.59→2.683 Å / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GNS

4gns
PDB Unreleased entry


Resolution: 2.59→44.65 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2000 3.34 %RANDOM
Rwork0.18 ---
obs0.181 59892 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6006 0 0 92 6098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.65480.26891350.22753908X-RAY DIFFRACTION95
2.6548-2.72660.22091410.19664076X-RAY DIFFRACTION99
2.7266-2.80680.23941410.18824095X-RAY DIFFRACTION99
2.8068-2.89740.22741400.18494078X-RAY DIFFRACTION99
2.8974-3.00090.21871430.19524128X-RAY DIFFRACTION100
3.0009-3.1210.22811420.19344111X-RAY DIFFRACTION100
3.121-3.2630.23961430.19244121X-RAY DIFFRACTION100
3.263-3.4350.2321420.19194126X-RAY DIFFRACTION100
3.435-3.65010.19571440.1784162X-RAY DIFFRACTION100
3.6501-3.93180.21221440.16634164X-RAY DIFFRACTION100
3.9318-4.32720.19341440.15774178X-RAY DIFFRACTION100
4.3272-4.95260.17871440.15284201X-RAY DIFFRACTION100
4.9526-6.23710.24891470.20314232X-RAY DIFFRACTION99
6.2371-44.65960.18631500.18154312X-RAY DIFFRACTION96

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