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- PDB-7q83: Crystal structure of S. cerevisiae Sso2 in complex with the pleck... -

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Basic information

Entry
Database: PDB / ID: 7q83
TitleCrystal structure of S. cerevisiae Sso2 in complex with the pleckstrin homology domain of Sec3
Components
  • Exocyst complex component SEC3
  • Protein SSO2
KeywordsEXOCYTOSIS / exocyst / membrane trafficking / protein complex / yeast
Function / homology
Function and homology information


vesicle fusion to plasma membrane / Disinhibition of SNARE formation / ascospore-type prospore assembly / exocyst assembly / exocyst localization / endoplasmic reticulum inheritance / exocyst / trans-Golgi Network Vesicle Budding / Golgi vesicle fusion to target membrane / prospore membrane ...vesicle fusion to plasma membrane / Disinhibition of SNARE formation / ascospore-type prospore assembly / exocyst assembly / exocyst localization / endoplasmic reticulum inheritance / exocyst / trans-Golgi Network Vesicle Budding / Golgi vesicle fusion to target membrane / prospore membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / incipient cellular bud site / cellular bud tip / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / Golgi to plasma membrane transport / cellular bud neck / phosphatidic acid binding / mating projection tip / vesicle docking involved in exocytosis / exocytosis / endomembrane system / phosphatidylinositol-4,5-bisphosphate binding / SNARE binding / cell periphery / intracellular protein transport / small GTPase binding / protein transport / Golgi membrane / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Exocyst complex component Sec3, C-terminal / Exocyst complex component Sec3, PIP2-binding N-terminal domain / : / Exocyst complex component Sec3, coiled-coil / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Sec3, C-terminal / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain ...Exocyst complex component Sec3, C-terminal / Exocyst complex component Sec3, PIP2-binding N-terminal domain / : / Exocyst complex component Sec3, coiled-coil / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Sec3, C-terminal / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain
Similarity search - Domain/homology
Exocyst complex component SEC3 / Protein SSO2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsZhang, Y. / Dong, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP28231-B28 Austria
CitationJournal: Elife / Year: 2022
Title: Double NPY motifs at the N-terminus of the yeast t-SNARE Sso2 synergistically bind Sec3 to promote membrane fusion.
Authors: Peer, M. / Yuan, H. / Zhang, Y. / Korbula, K. / Novick, P. / Dong, G.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exocyst complex component SEC3
B: Protein SSO2
C: Exocyst complex component SEC3
D: Protein SSO2


Theoretical massNumber of molelcules
Total (without water)120,0984
Polymers120,0984
Non-polymers00
Water7,530418
1
A: Exocyst complex component SEC3
B: Protein SSO2


Theoretical massNumber of molelcules
Total (without water)60,0492
Polymers60,0492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-5 kcal/mol
Surface area17730 Å2
MethodPISA
2
C: Exocyst complex component SEC3
D: Protein SSO2


Theoretical massNumber of molelcules
Total (without water)60,0492
Polymers60,0492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-4 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.961, 58.402, 83.286
Angle α, β, γ (deg.)104.284, 98.494, 113.198
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Exocyst complex component SEC3 / Protein PSL1


Mass: 28513.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SEC3, PSL1, YER008C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33332
#2: Protein Protein SSO2


Mass: 31535.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: In chain B, the sequence "ANPYE" in the structure should be aligned to position 8-12 of the sample sequence. Similarly, in chain D, the sequence "AAAANNPYA" in the structure should be ...Details: In chain B, the sequence "ANPYE" in the structure should be aligned to position 8-12 of the sample sequence. Similarly, in chain D, the sequence "AAAANNPYA" in the structure should be aligned to position 10-18 of the sample sequence.
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SSO2, YMR183C, YM8010.13C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39926
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 1.77 Å3/Da / Density % sol: 30.52 %
Description: Needle-shaped crystals by approximately 10, 10, and 100 micrometer
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate (pH 5.0), 0.2 M ammonium acetate, and 30% (w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.19→19.95 Å / Num. obs: 40853 / % possible obs: 96.08 % / Redundancy: 4 % / Biso Wilson estimate: 31.13 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.1641 / Rpim(I) all: 0.09332 / Rrim(I) all: 0.1894 / Net I/σ(I): 6.73
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.094 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 3771 / CC1/2: 0.438 / CC star: 0.781 / Rpim(I) all: 0.636 / % possible all: 89.79

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122+SVNrefinement
PHENIX1.19.1_4122+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M4Y

5m4y


Resolution: 2.19→19.95 Å / SU ML: 0.3097 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.8861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 2008 4.95 %
Rwork0.1967 38581 -
obs0.1988 40589 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.87 Å2
Refinement stepCycle: LAST / Resolution: 2.19→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5419 0 0 418 5837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245507
X-RAY DIFFRACTIONf_angle_d0.4897414
X-RAY DIFFRACTIONf_chiral_restr0.037810
X-RAY DIFFRACTIONf_plane_restr0.0027971
X-RAY DIFFRACTIONf_dihedral_angle_d4.6688714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.250.34931320.28882522X-RAY DIFFRACTION87.25
2.25-2.310.31381400.27072748X-RAY DIFFRACTION96.72
2.31-2.370.3031470.26182771X-RAY DIFFRACTION96.59
2.37-2.450.3091440.25332785X-RAY DIFFRACTION96.86
2.45-2.540.291490.24972772X-RAY DIFFRACTION96.18
2.54-2.640.32651430.23492740X-RAY DIFFRACTION96.78
2.64-2.760.27441390.22512744X-RAY DIFFRACTION95.5
2.76-2.910.25251470.212776X-RAY DIFFRACTION97.17
2.91-3.090.24011460.20452786X-RAY DIFFRACTION97.64
3.09-3.320.21521440.19282775X-RAY DIFFRACTION96.82
3.32-3.660.21411390.17462777X-RAY DIFFRACTION96.59
3.66-4.180.20711480.16122803X-RAY DIFFRACTION97.65
4.18-5.250.20961400.15462772X-RAY DIFFRACTION97.07
5.25-19.950.2071500.18072810X-RAY DIFFRACTION98.08
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)
15.633796158722.751692341251.782879655393.713879800961.389375259943.30992900078-0.09353425473830.4090850646970.060918147395-0.3969206554880.0622350635006-0.100052045460.1731927008480.3061917090040.03512752121570.2589700304410.03642927518650.03823402217580.368197021018-0.03997572299040.30732892199816.9201918359-32.1361873799-60.6143324307
22.922136398012.86168910151.026592726635.911415327161.533921990631.0205840563-0.0485124466802-0.6176407161431.12391707834-0.0665740055682-0.129941930798-0.031588080962-0.8741339918750.3910525211080.2491999694140.466664843374-0.141814770382-0.08170237281330.595513638495-0.1132028665220.50430399774126.9628216415-18.6847631456-49.0177812826
32.075550271050.102583485897-0.09731291633351.83261346016-0.8225067761933.29067386756-0.07631686233810.2802971466750.1535315050060.008960788071790.1799874349860.154608013021-0.437770742965-0.582020252971-0.08879008171590.3070071474050.03388358533820.004189558323110.308055299020.02371809808360.2087376244713.10171566195-22.317458253-56.556979628
41.719464742080.0886155139851-0.5535636473921.30747375176-0.2367650732473.502076685720.148801240448-0.1461358327170.1662679385220.144777045985-0.228256838214-0.0606248242704-0.6328628642040.5696727074540.05993994975790.338816083076-0.05805699298270.01252908662440.28195390245-0.009351797956180.28994997478714.5303857489-21.4982010048-49.3997407021
51.8744220794-0.03190851695970.1474055795112.45900528805-0.5704647800113.22553472618-0.03820129839180.134207957217-0.147134301292-0.03437730940810.1093209363960.204774415944-0.0905535100666-0.487901260528-0.05970117214270.185274853154-0.01284116105810.01538717447340.2546629992760.04497372178490.2289393066081.10914394641-29.6569249406-48.5305020981
62.555623056420.881939670432-0.2357324867164.0038681616-0.9959039191313.271995770660.0533987823805-0.344159616313-0.5707546117830.165379396855-0.10110057619-0.05772167457180.3878280159-0.06466829762270.09671963488080.2745809881910.003621131802220.03470793540040.2787364755620.06010523811360.3313202464931.31776428615-36.5571591401-39.4542700861
75.328935581630.04380844772920.2652117460826.8701476252-2.049247162344.91552782307-0.08571797516640.0866119929933-0.2360159359511.03504692332-0.195043665630.6083226999590.194684980539-0.5459287595140.3534595592920.4366129574330.0589796280270.1292850179460.3712389031160.001293062390990.423550453456-1.65817784334-36.3457647325-31.3933982259
80.1185618963920.573046197927-0.4525513700752.59368605076-1.898725104661.38191879264-0.3919763170840.157691143224-0.07518925791110.2038092077990.541087890695-1.50357169092-0.139992526694-0.326941286704-0.1431036378050.398936889674-0.016256191638-0.03436990485250.433831411299-0.06912943351230.53272594783411.9595660873-51.250423208-54.09607218
91.15686880924-0.373681994653-0.7337150969813.232665085343.861361595124.678290504170.1584405889270.0281120078885-0.003024057461920.0155491990008-0.177243038295-0.071090480338-0.057491204519-0.306182302239-0.01269759094410.282348527069-0.003630028604060.008263523140810.216307811680.05669810673610.2886805590927.49914348573-54.7637186206-29.1480703897
101.84238605098-0.443259363409-0.6574624190142.241805722230.6764513450123.279891069550.1516512597980.00857961295405-0.02412474905560.0148406128393-0.0693754923904-0.254370610451-0.009413567400910.0559151871358-0.08855031714030.2474082875-0.00970928862628-0.01923431217980.2125532540070.06732214188080.31492683808111.5536449051-49.2012990737-31.3153876105
111.94238804757-0.475215272672-0.8160164030643.109258047220.5542445307071.5202139893-0.129586373347-0.1676432908710.36283912491-0.2014917079710.0372382781809-0.155919979411-0.6469525211020.273920557068-0.1181248616870.418553019568-0.0282525953882-0.001609134947030.3049205571680.06843146991910.47331965878917.9786915822-40.6244046773-30.0218870599
121.350258815010.471162257965-0.1576977061495.84869250517-3.092464294055.41019817799-0.0618548771672-0.456361328745-0.4514566323630.418002507842-0.02066801131410.191185953831-0.486955489082-0.5294748966050.04744427095540.3321993850440.1279129290570.06925117296560.3723275163440.0604082168230.371908541530.153287168772-23.3261344809-72.9044494165
132.570279956181.20170469943-1.379658375942.65583089831-1.542718865721.704340031960.311731525770.1613401721990.698321272564-0.1193436618810.0318633393463-0.994345791444-0.1735172207830.356040457342-0.343991754930.7501828031270.08677128375140.1104985588460.3524022436960.05310138011430.5819156548185.61263050877-7.49149534391-84.3861122045
140.882183922817-0.288151657492-0.1996230938381.19206388671-0.1965155896951.53542491682-0.0666395530286-0.177469557974-0.01504767267350.1461548572050.103388724808-0.1221875258040.01507376337370.184246240077-0.02905770174750.213496235553-0.0126829001227-0.01718306276630.218811971188-0.01138998651830.21065061502316.0258942157-29.2642217844-76.8620464023
151.95982949987-0.787378719534-0.1004786176772.106513497690.9631184531883.49386933096-0.0741382280580.0786504882544-0.03220596503630.07362428671630.120663437028-0.0673591233024-0.2030066886530.141710533557-0.05950844150240.208669977804-0.01285202373610.01489603454470.197465935209-0.02999944492130.19830041172411.9036360367-26.4402258676-84.3417123185
162.781255651210.162257728251-0.6027674061751.794660025980.4940473325911.7095726341-0.1993796259980.1534112274970.135151615303-0.246542484560.2038709149360.120027973966-0.02345413261560.118803870444-0.03282133522980.223362183284-0.030238637587-0.01720315140440.322019490106-0.0107920317660.25592382301916.7488916728-32.5276847967-82.2470144615
171.976812743420.1606077737950.09264992528961.96736655397-0.04392733835732.53791462925-0.0157566226140.142801919191-0.213564560818-0.241983054846-0.0650700806284-0.02849377346870.01556026171320.1131146894540.004647764886160.255621082618-0.0245759945848-0.05286620983320.235647846676-0.07307785445890.2846729044265.60107534154-34.9578343906-90.0599901896
184.181320490750.2960588146320.4967413301574.096780858670.3925489904245.51372606311-0.1771409545820.474908010208-0.814468229239-0.250212603808-0.1227750704870.1747126902680.362051950566-0.2522831651260.2201727593780.253824209279-0.00199114538518-0.02192885410540.298995974947-0.05647469056250.365836133464.73670641826-41.5559440395-98.2552662875
192.80273012642-1.21099734912.451193322910.584275107681-1.324791494633.33892228409-0.639623449150.3870001870121.093531291290.217845959175-0.738915041560.425828011062-0.6787179357210.09618817935610.6606366149090.3723841463510.181482532974-0.1562679111590.629238024959-0.1608693718490.898037777338-8.20604437462-30.6297794813-79.2884803619
202.310853028570.677758012681-3.025794998282.15812486103-1.975145207354.77698169194-0.1661426874460.05313217963180.035428177207-0.06644747035550.2555081144750.3841218892620.5800002546010.0132859914548-0.09632479819610.294549891271-0.0149498702428-0.006718522143420.216804336104-0.02573498198190.320694323703-15.1628597771-45.2398957982-101.123818807
212.67469125925-0.63000264253-1.613336800721.647034427721.125822509243.73371290793-0.00597767533645-0.04415725487180.179409517696-0.123884355470.04954089576380.0129488417046-0.1215147899730.0721012386028-0.04033564638820.21815671272-0.00655737261413-0.0610531106380.138880564102-0.0260973673930.286356107588-10.9733189376-37.753944096-102.857724584
223.702520045970.741397577469-2.011252672162.703846291440.3417522942093.601110844390.507864847972-0.0394500210150.57263661449-0.4498264577280.113063457298-0.187480225601-0.6624264476180.819302305291-0.6251356057970.441440029311-0.04653514464420.05319501237710.388690184127-0.04801933590950.539786799426-6.4624838708-27.5372464145-104.912773255
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 76 through 93 )AA76 - 931 - 18
22chain 'A' and (resid 94 through 106 )AA94 - 10619 - 31
33chain 'A' and (resid 107 through 144 )AA107 - 14432 - 69
44chain 'A' and (resid 145 through 174 )AA145 - 17470 - 99
55chain 'A' and (resid 175 through 220 )AA175 - 220100 - 145
66chain 'A' and (resid 221 through 239 )AA221 - 239146 - 164
77chain 'A' and (resid 240 through 250 )AA240 - 250165 - 175
88chain 'B' and (resid 4 through 35 )BB4 - 351 - 8
99chain 'B' and (resid 36 through 73 )BB36 - 739 - 46
1010chain 'B' and (resid 74 through 148 )BB74 - 14847 - 121
1111chain 'B' and (resid 149 through 226 )BB149 - 226122 - 152
1212chain 'C' and (resid 76 through 93 )CC76 - 931 - 18
1313chain 'C' and (resid 94 through 106 )CC94 - 10619 - 31
1414chain 'C' and (resid 107 through 144 )CC107 - 14432 - 69
1515chain 'C' and (resid 145 through 191 )CC145 - 19170 - 116
1616chain 'C' and (resid 192 through 202 )CC192 - 202117 - 127
1717chain 'C' and (resid 203 through 232 )CC203 - 232128 - 157
1818chain 'C' and (resid 233 through 250 )CC233 - 250158 - 175
1919chain 'D' and (resid 6 through 33 )DD6 - 331 - 10
2020chain 'D' and (resid 34 through 69 )DD34 - 6911 - 46
2121chain 'D' and (resid 70 through 145 )DD70 - 14547 - 122
2222chain 'D' and (resid 146 through 226 )DD146 - 226123 - 156

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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