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- PDB-8ay2: Crystal structure of the C-terminal part of rat Sec8 -

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Basic information

Entry
Database: PDB / ID: 8ay2
TitleCrystal structure of the C-terminal part of rat Sec8
ComponentsExocyst complex component 4
KeywordsEXOCYTOSIS / exocyst / helical bundle / membrane trafficking / vesicle fusion
Function / homology
Function and homology information


Golgi to transport vesicle transport / Insulin processing / VxPx cargo-targeting to cilium / vesicle tethering involved in exocytosis / paraxial mesoderm formation / membrane biogenesis / exocyst / vesicle targeting / myelin sheath abaxonal region / regulation of protein transport ...Golgi to transport vesicle transport / Insulin processing / VxPx cargo-targeting to cilium / vesicle tethering involved in exocytosis / paraxial mesoderm formation / membrane biogenesis / exocyst / vesicle targeting / myelin sheath abaxonal region / regulation of protein transport / growth cone membrane / protein transmembrane transport / Golgi to plasma membrane transport / Flemming body / vesicle docking involved in exocytosis / protein targeting to membrane / establishment of cell polarity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / microvillus / cell leading edge / exocytosis / oligodendrocyte differentiation / postsynaptic density, intracellular component / ionotropic glutamate receptor binding / positive regulation of calcium-mediated signaling / dendritic shaft / PDZ domain binding / Schaffer collateral - CA1 synapse / synaptic vesicle / growth cone / chemical synaptic transmission / neuron projection / endosome / postsynaptic density / neuronal cell body / synapse / dendrite / centrosome / protein-containing complex binding / protein-containing complex
Similarity search - Function
Exocyst complex component Sec8, N-terminal / Exocyst complex component Sec8/EXOC4 / : / Exocyst complex component Sec8 N-terminal / Exocyst complex component Sec8 C-terminal
Similarity search - Domain/homology
Exocyst complex component 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsDong, G. / Lesigang, J.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundI5960-B2 Austria
CitationJournal: Front Cell Dev Biol / Year: 2023
Title: Sec8 specifically interacts with the PDZ2 domain of synapse associated protein 102 (SAP102).
Authors: Korbula, K. / Hammerschmid, I. / Lesigang, J. / Dong, G.
History
DepositionSep 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exocyst complex component 4
B: Exocyst complex component 4


Theoretical massNumber of molelcules
Total (without water)96,4432
Polymers96,4432
Non-polymers00
Water1,62190
1
A: Exocyst complex component 4


Theoretical massNumber of molelcules
Total (without water)48,2211
Polymers48,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exocyst complex component 4


Theoretical massNumber of molelcules
Total (without water)48,2211
Polymers48,2211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.004, 190.004, 175.275
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Exocyst complex component 4 / Exocyst complex component Sec8 / rSec8


Mass: 48221.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Exoc4, Sec8, Sec8l1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q62824
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 297 K / Method: evaporation / pH: 6.5
Details: 0.1M 2-(N-morpholino)ethanesulfonic acid, 1.5-2M NaCl, 10-15% (v/v) PEG6000, 2mM MgCl2, 10mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97944 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.5→19.99 Å / Num. obs: 94874 / % possible obs: 89.2 % / Redundancy: 14.9 % / Biso Wilson estimate: 50.54 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1335 / Rpim(I) all: 0.0355 / Rrim(I) all: 0.1382 / Net I/σ(I): 20.47
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 2815 / CC1/2: 0.601

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.99 Å / SU ML: 0.2842 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 23.9882
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 3839 4.05 %
Rwork0.1894 91035 -
obs0.1904 94874 89.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 0 90 6184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00376185
X-RAY DIFFRACTIONf_angle_d0.74628350
X-RAY DIFFRACTIONf_chiral_restr0.0452973
X-RAY DIFFRACTIONf_plane_restr0.00391063
X-RAY DIFFRACTIONf_dihedral_angle_d4.2776818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.2863880.31131819X-RAY DIFFRACTION48.61
2.53-2.560.3557730.31411948X-RAY DIFFRACTION51.83
2.56-2.60.3248790.30392132X-RAY DIFFRACTION56.69
2.6-2.640.30861060.29822323X-RAY DIFFRACTION61.35
2.64-2.680.29251340.28782507X-RAY DIFFRACTION66.84
2.68-2.720.3266920.27722823X-RAY DIFFRACTION74.55
2.72-2.760.34221210.27473092X-RAY DIFFRACTION83.22
2.76-2.810.25971850.26143671X-RAY DIFFRACTION97.2
2.81-2.860.29811460.25273669X-RAY DIFFRACTION98.3
2.86-2.920.27091580.23843718X-RAY DIFFRACTION98.4
2.92-2.980.30541610.24323681X-RAY DIFFRACTION98.56
2.98-3.040.23611410.23933733X-RAY DIFFRACTION98.68
3.04-3.110.26631680.22533688X-RAY DIFFRACTION98.42
3.11-3.190.24961400.21433712X-RAY DIFFRACTION98.59
3.19-3.270.28421610.20893780X-RAY DIFFRACTION99.04
3.27-3.370.27121580.19773664X-RAY DIFFRACTION98.51
3.37-3.480.21421630.18593716X-RAY DIFFRACTION99.03
3.48-3.60.20281540.17823727X-RAY DIFFRACTION98.98
3.6-3.740.16771430.16073728X-RAY DIFFRACTION98.9
3.74-3.910.21991540.15883768X-RAY DIFFRACTION99.12
3.91-4.120.19811520.15363717X-RAY DIFFRACTION99.18
4.12-4.370.18571560.14193714X-RAY DIFFRACTION99.1
4.37-4.710.13821650.13813744X-RAY DIFFRACTION99.39
4.71-5.170.19581660.15923743X-RAY DIFFRACTION99.24
5.17-5.90.21241580.20393738X-RAY DIFFRACTION99.46
5.91-7.380.21061610.21743733X-RAY DIFFRACTION99.54
7.38-19.990.16141560.16333747X-RAY DIFFRACTION99.14
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)
11.855198032840.902598028542-0.7526494007390.903030553145-0.5696300388270.8696907887450.102031901365-0.189958169176-0.07254970475240.284383019956-0.1353471444720.186618897809-0.03003988608610.00089982621430.06659115801250.453582371346-0.04907261890030.1065533659390.3828719243120.04191886780940.47685206349335.949166927668.652594711455.431023373
21.449399210110.129012011343-0.6820884110631.6792830692-0.2479223378952.195820615270.01339164921860.1276438693770.06709054697-0.213943702170.000985888731828-0.121138577121-0.01504674252520.189031632619-0.01682237430030.239787876483-0.0320874423806-0.01411672973970.267471963880.06021021423290.32226491153858.921534362975.777445384431.9526312384
32.76366724234-1.549276146881.784705495741.88271295589-1.169154859054.202365963350.08278481656260.134067989150.33456083771-0.1718967407260.124131939804-0.00125135064137-0.390646887629-0.575919133848-0.1868408490290.7235310422320.04288958835510.03417310833980.6308280720870.1702975399550.48594289148440.56861918115.2206906560.841113308342
43.62759279677-1.8621318751.092810544183.21434122657-1.553000216923.929550659740.0807907883849-0.2161053180380.102223936113-0.06401225562470.03432358386760.0926508240391-0.392119579962-0.429700510762-0.1450705676990.356532398996-0.09007527018370.03940866140990.340482787970.07699995762620.36097851826446.541638199104.36354376228.1637560169
50.547124368058-0.458890495780.7540505519521.53253774099-0.5546143108922.95795373957-0.0695841322588-0.0949500066840.121810015282-0.2846053062620.1446600843040.134493216738-0.257083657379-0.820985920825-0.0885438593070.518436280694-0.018892148844-0.01263842810650.5324874552290.1398582889940.39502530414542.7383348025110.67066813915.3309818557
65.11960833941-0.5385608124641.932861267991.850584155670.6606683043493.59471594444-0.1892110184270.191176499261-0.05243406282390.098590235226-0.214609158078-0.803107343870.4306946804310.37398225230.2586648066160.48827052746-0.06263740018180.04660226854930.2594377624460.03497480807760.56603247309666.8666547242104.34761682431.3387652684
72.407209253720.4311273695850.5030295506532.689347890470.1099077711112.681246187810.0960962795691-0.4398655170280.1544118949620.731375553361-0.237278369402-0.153983971921-0.213206211576-0.03337138478690.05031056550350.595426876498-0.09701926040380.02006937289670.404435574639-0.02842939399190.41563680052157.8251022991106.80266184947.1644173177
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 557 through 754 )AA557 - 7541 - 187
22chain 'A' and (resid 755 through 967 )AA755 - 967188 - 400
33chain 'B' and (resid 556 through 628 )BB556 - 6281 - 73
44chain 'B' and (resid 629 through 704 )BB629 - 70474 - 137
55chain 'B' and (resid 705 through 794 )BB705 - 794138 - 206
66chain 'B' and (resid 795 through 830 )BB795 - 830207 - 237
77chain 'B' and (resid 831 through 967 )BB831 - 967238 - 367

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