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- PDB-4yg8: CRYSTAL STRUCTURE OF THE CHS5-CHS6 EXOMER CARGO ADAPTOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 4yg8
TitleCRYSTAL STRUCTURE OF THE CHS5-CHS6 EXOMER CARGO ADAPTOR COMPLEX
Components
  • Chitin biosynthesis protein CHS5
  • Chitin biosynthesis protein CHS6
KeywordsTRANSPORT PROTEIN / FN3 / BRCT / TETRATRICOPEPTIDE REPEAT / CARGO ADAPTOR
Function / homology
Function and homology information


exomer complex / conjugation with cellular fusion / chitin biosynthetic process / cellular bud site selection / ascospore wall assembly / Golgi to plasma membrane transport / trans-Golgi network transport vesicle / mating projection tip / chitin catabolic process / trans-Golgi network ...exomer complex / conjugation with cellular fusion / chitin biosynthetic process / cellular bud site selection / ascospore wall assembly / Golgi to plasma membrane transport / trans-Golgi network transport vesicle / mating projection tip / chitin catabolic process / trans-Golgi network / small GTPase binding / protein transport / protein dimerization activity / regulation of DNA-templated transcription / membrane / cytosol / cytoplasm
Similarity search - Function
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) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. ...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) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / TPR repeat region circular profile. / BRCT domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tetratricopeptide-like helical domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chitin biosynthesis protein CHS5 / Chitin biosynthesis protein CHS6 / Chitin biosynthesis protein CHS5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.75 Å
AuthorsPaczkowski, J.E. / Richardson, B.C. / Strassner, A.M. / Fromme, J.C.
CitationJournal: Embo J. / Year: 2012
Title: The exomer cargo adaptor structure reveals a novel GTPase-binding domain.
Authors: Paczkowski, J.E. / Richardson, B.C. / Strassner, A.M. / Fromme, J.C.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionMar 11, 2015ID: 4GNS
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitin biosynthesis protein CHS5
B: Chitin biosynthesis protein CHS6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2034
Polymers118,8732
Non-polymers3302
Water3,657203
1
A: Chitin biosynthesis protein CHS5
B: Chitin biosynthesis protein CHS6
hetero molecules

A: Chitin biosynthesis protein CHS5
B: Chitin biosynthesis protein CHS6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,4068
Polymers237,7464
Non-polymers6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area7520 Å2
ΔGint-35 kcal/mol
Surface area88650 Å2
MethodPISA
2
A: Chitin biosynthesis protein CHS5
B: Chitin biosynthesis protein CHS6
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)715,21924
Polymers713,23712
Non-polymers1,98212
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area37320 Å2
ΔGint-145 kcal/mol
Surface area251180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.750, 165.750, 263.846
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsGel filtration SAXS MALS

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Components

#1: Protein Chitin biosynthesis protein CHS5


Mass: 31781.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: SEY6210 / Gene: CHS5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: B3RHK5, UniProt: Q12114*PLUS
#2: Protein Chitin biosynthesis protein CHS6 / Protein CSD3


Mass: 87091.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: SEY6210 / Gene: CHS6, CSD3, YJL099W, J0838 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: P40955
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsTHE COMPLETE CRYSTALLIZED SEQUENCE OF CHAIN A IS: ...THE COMPLETE CRYSTALLIZED SEQUENCE OF CHAIN A IS: MDPEFSSVDVLLTVGKLDASLALLTTQDHHVIEFPTVLLPENVKAGSIIKMQVS QNLEEEKKQRNHFKSIQAKILEKYGTHKPESPVLKIVNVTQTSCVLAWDP LKLGSAKLKSLILYRKGIRSMVIPNPFKVTTTKISGLSVDTPYEFQLKLI TTSGTLWSEKVILRTHKMTDMSGITVCLGPLDPLKEISDLQISQCLSHIG ARPLQRHVAIDTTHFVCNDLDNEESNEELIRAKHNNIPIVRPEWVRACEV EKRIVGVRGFYLDADQSILKSYTFPPVNEEELSYSKENEPVAEVADENK. THE N-TERMINAL RESIUES 4-48 ARE IN THE REGION WITH POOR ELECTRON DENSITY AND REPRESENTED AS UNKNOWN RESIDUES (UNK) IN THE COORDINATES SINCE THE SEQUENCE REGISTER IS NOT KNOWN.

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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: 4.4 Å3/Da / Density % sol: 72.05 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.35 M POTASSIUM CHLORIDE, 3 MM DITHIOTHREITOL, 10 MM HEPES PH 7.4, 150 MM NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 299K
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2010
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 56095 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.092 / Net I/σ(I): 18.8
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.708 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.75→47.07 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.23 2841 -
Rwork0.193 --
obs0.194 56094 99.8 %
Refinement stepCycle: LAST / Resolution: 2.75→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7528 0 21 203 7752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d
X-RAY DIFFRACTIONf_dihedral_angle_d13.595
X-RAY DIFFRACTIONf_chiral_restr0.089
X-RAY DIFFRACTIONf_plane_restr0.006
LS refinement shellResolution: 2.7474→2.7947 Å
RfactorNum. reflection% reflection
Rfree0.3737 144 -
Rwork0.2988 2555 -
obs--98 %
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)
10.0009-0.0025-0.00010.0091-0.00810.005-0.07890.00840.03880.05920.02230.0214-0.06660.0028-00.45520.01640.08780.3693-0.00720.4844-12.7913-50.0076-43.524
20.04190.0249-0.0222-0.0050.01640.0090.01220.0552-0.0512-0.1947-0.0922-0.16980.02970.0188-0.06410.81670.57940.36060.460.06060.3904-47.0021-28.2635-23.7814
30.0311-0.010.01990.00880.00130.09480.0233-0.0338-0.0746-0.1221-0.03110.03380.20490.04890.00710.53810.16860.02430.24520.09510.3266-64.027-22.8524-7.2933
40.0899-0.03120.02530.03230.02470.05130.0574-0.0083-0.16230.03790.0729-0.0640.0176-0.0170.21840.22930.07860.08830.21310.01660.2742-27.1663-101.4027-23.9066
50.03650.0614-0.01050.0997-0.01760.03960.00770.04210.06040.0868-0.0066-0.10770.0066-0.0046-0.0660.13160.07360.03340.2508-0.03590.2457-21.4385-76.182-27.3197
60.00490.0088-0.00280.01570.00030.0153-0.03210.0797-0.0276-0.12330.018-0.1116-0.1070.0171-0.00040.20480.05790.04690.44860.03190.3808-19.2365-60.5779-45.5992
7-0.00330.0018-0.005-0-0.0020.00360.0480.03480.0462-0.02310.0262-0.0232-0.02030.00100.50810.14380.02190.5754-0.06340.4101-27.8072-77.4075-51.8129
80.04470.0156-0.02560.0941-0.01020.0290.01970.0627-0.1403-0.0318-0.02890.28470.0931-0.2075-0.01730.1944-0.01280.02620.4129-0.03140.3294-47.4658-96.6136-36.0235
90.0236-0.02390.00440.0520.00610.00740.04740.00330.0171-0.0976-0.0210.0441-0.0434-0.07880.08040.14530.29450.03370.54950.0290.1745-45.9195-70.6608-53.4503
100.01440.0140.01360.06860.01660.01130.1064-0.02170.12190.0207-0.02830.029-0.088-0.02850.02980.13490.16960.13020.4221-0.02840.1877-46.476-75.3645-24.8385
110.0002-0.0002-0.0017-0.00040.00020.00320.00420.00570.02280.00420.0056-0.0208-0.0269-0.034-00.49540.05670.21370.79860.0420.48996.9537-62.7583-73.2428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 50:78)
2X-RAY DIFFRACTION2(chain A and resid 79:188)
3X-RAY DIFFRACTION3(chain A and resid 189:285)
4X-RAY DIFFRACTION4(chain B and resid 31:161)
5X-RAY DIFFRACTION5(chain B and resid 162:309)
6X-RAY DIFFRACTION6(chain B and resid 310:388)
7X-RAY DIFFRACTION7(chain B and resid 389:418)
8X-RAY DIFFRACTION8(chain B and resid 419:522)
9X-RAY DIFFRACTION9(chain B and resid 523:642)
10X-RAY DIFFRACTION10(chain B and resid 643:743)
11X-RAY DIFFRACTION11(chain A and resid 4:48)

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