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- PDB-3b5n: Structure of the yeast plasma membrane SNARE complex -

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Basic information

Entry
Database: PDB / ID: 3b5n
TitleStructure of the yeast plasma membrane SNARE complex
Components
  • (Protein transport protein SEC9) x 2
  • Protein SSO1
  • Synaptobrevin homolog 1
KeywordsMEMBRANE PROTEIN / SNARE complex / syntaxin / synaptobrevin / snap-25 / Sso1p / Snc1p / Sec9p / Sec9 / Sso1 / Snc1 / Coiled coil / Lipoprotein / Membrane / Palmitate / Transmembrane / Ubl conjugation / Phosphorylation / Protein transport / Transport
Function / homology
Function and homology information


Disinhibition of SNARE formation / vesicle fusion to plasma membrane / ascospore-type prospore assembly / RHOQ GTPase cycle / RHOB GTPase cycle / RHOA GTPase cycle / vesicle fusion with Golgi apparatus / Golgi vesicle fusion to target membrane / cellular bud / sporulation ...Disinhibition of SNARE formation / vesicle fusion to plasma membrane / ascospore-type prospore assembly / RHOQ GTPase cycle / RHOB GTPase cycle / RHOA GTPase cycle / vesicle fusion with Golgi apparatus / Golgi vesicle fusion to target membrane / cellular bud / sporulation / trans-Golgi Network Vesicle Budding / prospore membrane / ascospore formation / Golgi to endosome transport / vesicle docking / SNARE complex / SNAP receptor activity / vesicle fusion / cellular bud neck / Golgi to plasma membrane transport / phosphatidic acid binding / phosphatidylinositol-3,4-bisphosphate binding / fungal-type vacuole membrane / retrograde transport, endosome to Golgi / phosphatidylinositol-3,5-bisphosphate binding / syntaxin binding / SNARE complex assembly / transport vesicle membrane / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / endomembrane system / SNARE binding / cell periphery / intracellular protein transport / trans-Golgi network / endocytosis / molecular adaptor activity / endosome membrane / endosome / Golgi membrane / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin/Vesicle-associated membrane protein / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Synaptobrevin homolog 1 / Protein SSO1 / Protein transport protein SEC9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsStrop, P. / Brunger, A.T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Structure of the Yeast Plasma Membrane SNARE Complex Reveals Destabilizing Water-filled Cavities.
Authors: Strop, P. / Kaiser, S.E. / Vrljic, M. / Brunger, A.T.
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptobrevin homolog 1
B: Protein SSO1
C: Protein transport protein SEC9
D: Protein transport protein SEC9
E: Synaptobrevin homolog 1
F: Protein SSO1
G: Protein transport protein SEC9
H: Protein transport protein SEC9
I: Synaptobrevin homolog 1
J: Protein SSO1
K: Protein transport protein SEC9
L: Protein transport protein SEC9


Theoretical massNumber of molelcules
Total (without water)88,81312
Polymers88,81312
Non-polymers00
Water10,665592
1
A: Synaptobrevin homolog 1
B: Protein SSO1
C: Protein transport protein SEC9
D: Protein transport protein SEC9


Theoretical massNumber of molelcules
Total (without water)29,6044
Polymers29,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
MethodPISA
2
E: Synaptobrevin homolog 1
F: Protein SSO1
G: Protein transport protein SEC9
H: Protein transport protein SEC9


Theoretical massNumber of molelcules
Total (without water)29,6044
Polymers29,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11980 Å2
MethodPISA
3
I: Synaptobrevin homolog 1
J: Protein SSO1
K: Protein transport protein SEC9
L: Protein transport protein SEC9


Theoretical massNumber of molelcules
Total (without water)29,6044
Polymers29,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.956, 48.113, 110.265
Angle α, β, γ (deg.)90.00, 97.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Synaptobrevin homolog 1


Mass: 6771.594 Da / Num. of mol.: 3 / Fragment: Residues 27-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNC1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31109
#2: Protein Protein SSO1


Mass: 7797.670 Da / Num. of mol.: 3 / Fragment: Residues 189-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SSO1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32867
#3: Protein Protein transport protein SEC9


Mass: 7685.770 Da / Num. of mol.: 3 / Fragment: Residues 433-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC9, HSS7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40357
#4: Protein Protein transport protein SEC9


Mass: 7349.194 Da / Num. of mol.: 3 / Fragment: Residues 589-650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC9, HSS7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40357
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 100 mM MES pH 6.25, 30 % MPD, 200 mM Sodium bromide, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 90852 / % possible obs: 83.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Χ2: 1.131 / Net I/σ(I): 16
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4177 / Χ2: 0.983 / % possible all: 38.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N7S

1n7s


Resolution: 1.6→34.571 Å / FOM work R set: 0.759 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.248 4521 5.02 %
Rwork0.206 --
obs-90025 84.97 %
Solvent computationBsol: 72.531 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 146.93 Å2 / Biso mean: 44.18 Å2 / Biso min: 19.08 Å2
Baniso -1Baniso -2Baniso -3
1-9.437 Å20 Å20.803 Å2
2--1.729 Å20 Å2
3----14.876 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 0 592 6656
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_deg0.4631
X-RAY DIFFRACTIONf_bond_d0.0031
X-RAY DIFFRACTIONf_chiral_restr0.0331
X-RAY DIFFRACTIONf_dihedral_angle_d9.3981
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.0431
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)
10.7901-0.0992-0.33421.7478-1.4752.27150.3520.0272-0.29590.85720.0989-0.4378-1.60741.32250.02720.5182-0.1474-0.00450.3456-0.00870.359714.13351.786569.7046
20.3445-0.2195-0.1507-0.206-0.28573.7066-0.03040.11440.1551-0.13110.01950.2037-1.12440.0198-0.16440.37450.01960.00070.29490.01860.3397.64483.691645.1131
31.080.34710.23492.3055-0.47950.6991-0.01310.367-0.1072-0.4726-0.25280.04910.2557-0.90730.0380.27850.0648-0.08710.3504-0.01790.28875.9277-5.609911.5318
41.1840.8654-0.57441.4651-1.05484.08240.2402-0.04090.2610.55990.01270.1621-1.4864-0.3641-0.24810.49560.08520.10360.21590.00780.36614.79860.972277.6895
5-0.5246-0.7012-0.48150.69730.25475.03240.09020.0595-0.0764-0.0061-0.10530.1657-0.2905-1.2665-0.25240.2175-0.00160.01630.34850.01680.353.5267-4.104453.2193
61.06360.49581.42621.8991-0.43963.5624-0.08110.3787-0.1793-0.1778-0.0304-0.05660.9823-0.2043-0.22570.21210.0719-0.07990.26440.0240.277210.4339-8.779418.8376
70.914-0.3473-0.6431.320.60643.4197-0.1096-0.0585-0.06050.41440.06140.26440.1851-0.8307-0.1040.25730.03790.07220.26520.03310.35091.8152-7.598579.2375
8-0.5021-0.2231.49270.29280.71051.26550.0057-0.056-0.0071-0.0529-0.03630.04330.79760.5202-0.15380.23420.0461-0.03580.29180.00430.280712.3081-9.07742.3436
91.0738-0.28051.07151.76610.01661.17570.0383-0.01880.0256-0.43110.13410.1821-0.5689-0.3293-0.01730.45960.0657-0.00880.48950.03920.302918.1023-0.47656.5714
102.7689-0.34570.84610.51470.10552.73370.1432-0.3721-0.15890.143-0.02440.0937-0.19640.9304-0.03770.2075-0.0009-0.00010.26260.00280.313712.3918-9.867375.0999
110.3-0.32770.03530.5665-0.42952.12280.16450.06350.0136-0.2023-0.01280.0999-0.38051.1139-0.15620.2457-0.07030.02080.4281-0.01630.297616.8421-1.313450.2544
120.5526-0.14850.18410.48830.36144.70940.02220.23450.064-0.258-0.07780.0212-1.1641-0.0048-0.10440.27690.0239-0.02670.36630.03910.295411.60823.081620.3631
130.6413-0.07460.80782.24440.16592.6407-0.1770.03630.1971-0.40230.2001-0.20640.64010.58780.09420.31350.0074-0.00180.2081-0.02360.265940.98083.2268.9386
140.20161.32791.20661.83340.51063.9647-0.02310.0535-0.1753-0.0425-0.27120.12711.09-0.60610.11610.29560.0112-0.00320.3501-0.04570.284227.15876.597636.2398
150.7841-0.41730.38782.79150.90263.3533-0.1073-0.1789-0.32150.8271-0.34190.60680.5022-1.19620.38150.4062-0.08480.15240.4592-0.09850.386524.630316.00862.329
161.19950.2656-0.19981.2599-0.49763.3019-0.37750.3435-0.1637-0.3102-0.02830.02440.763-0.58440.12450.3532-0.05850.00220.2030.00410.276637.44887.505-2.4742
17-0.2501-0.1722-0.89610.6406-0.79472.14670.0053-0.17460.1263-0.0596-0.0920.0331-0.5312-0.41010.14640.15230.0149-0.00710.3487-0.06010.302129.814215.479937.1893
180.94150.2277-0.38471.5408-0.07390.90680.0012-0.8648-0.531.73060.3866-0.0250.2707-0.43940.13120.49540.00940.00330.5404-0.02710.263933.086416.793665.0112
190.79580.2957-1.46680.82610.33684.14460.29090.7420.6391-1.32310.44690.65890.4098-0.7112-0.08690.7397-0.0871-0.01690.46580.03780.40838.650512.833-19.5764
200.31120.2268-1.32880.15821.08353.3996-0.0276-0.16240.0967-0.03220.0016-0.0363-0.00030.5117-0.06820.14180.0336-0.01250.3105-0.01710.279438.030214.106225.2567
210.5548-0.0748-0.94751.23930.22353.5718-0.2048-0.6476-0.16450.7856-0.065-0.54350.95391.32320.06720.82080.11970.04350.64160.00190.422834.23877.323767.4532
221.05420.41-1.5011.2481-0.16332.9050.11510.04760.1452-0.0388-0.1826-0.2685-0.12860.89710.04150.3029-0.01740.02220.36610.01670.381747.218816.2301-4.8457
230.3101-0.0928-0.89740.7755-0.45613.97010.1912-0.29580.0655-0.0606-0.3467-0.2788-0.63060.94560.09590.15990.0243-0.04130.2411-0.00710.228443.46017.340720.5258
240.31090.5515-2.47410.55790.29823.4081-0.2863-0.3524-0.30440.3493-0.33310.17880.82580.27860.07890.38420.00750.01290.4418-0.03590.349131.99323.944447.833
250.00180.1733-0.42243.933-1.49431.98350.6486-0.11420.2482.2142-0.0744-0.1637-1.75011.351-0.35430.7384-0.08540.04370.313-0.03050.3873-14.07023.242.3087
260.20220.1186-0.60312.5818-1.24710.0207-0.02950.4187-0.0456-0.81490.18720.71130.0486-1.085-0.39720.3921-0.0659-0.14470.49160.03290.424-17.41491.163511.7107
270.09150.2761-1.51913.9126-1.318-0.89680.33150.09060.3371-2.18020.6902-0.46830.8708-1.1549-0.11972.3429-0.4586-0.32840.5638-0.02090.3499-12.4179-8.3256-21.3601
280.77220.3618-0.48232.4794-1.4881.26090.2835-0.12050.56191.31790.06460.6202-0.8997-0.3638-0.30560.7785-0.00540.29070.26490.00740.5875-23.15680.526749.0395
290.37190.1658-0.00452.9008-0.5873.6497-0.23990.4626-0.1555-0.7170.17710.41281.2482-1.2982-0.15310.51-0.2556-0.18690.33860.03290.3378-15.9315-8.12337.9922
302.76960.2073-1.91253.0894-1.52360.47590.16550.5031-0.0514-2.12730.1919-0.37081.4613-1.19830.2872.6255-0.1312-0.07230.36860.0050.2923-1.5869-8.9642-22.8719
310.5620.2461-0.50792.79690.70780.6225-0.3146-0.4538-0.08341.25580.14770.76110.8373-0.92080.40230.87520.00080.33840.49530.06480.522-26.5207-7.257456.2842
32-1.0273-0.01060.33831.0687-0.96311.3718-0.44340.1353-0.2541-0.36260.06690.18991.4565-0.09260.1650.5205-0.0723-0.00660.2619-0.00630.3684-13.6644-9.752424.1695
33-0.3699-0.12130.69642.09570.1630.9761-0.10120.03520.3171-0.65310.011-0.2415-0.34851.34280.14081.4479-0.17510.03730.4082-0.01150.3056-1.8574-1.3151-13.7754
341.25571.1687-2.07012.7648-0.34814.08840.702-0.5307-0.32392.2861-0.6472-0.070.07981.16170.2451.0168-0.20790.08250.39970.01450.4003-17.0176-10.213156.8461
351.74850.548-1.08272.04241.40141.9525-0.0769-0.0496-0.0798-0.0327-0.06010.0136-0.25110.4703-0.00680.13840.0293-0.01910.2042-0.00150.3325-9.2086-1.137723.3236
361.40890.7702-0.67442.28141.16130.67040.3850.52090.4482-1.37930.4142-0.3021-1.4424-0.5251-0.02861.3468-0.0914-0.19870.62260.06390.5258-10.81192.7648-14.1809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 26:40
2X-RAY DIFFRACTION2chain A and resid 41:60
3X-RAY DIFFRACTION3chain A and resid 61:86
4X-RAY DIFFRACTION4chain B and resid 189:209
5X-RAY DIFFRACTION5chain B and resid 210:222
6X-RAY DIFFRACTION6chain B and resid 223:257
7X-RAY DIFFRACTION7chain C and resid 431:450
8X-RAY DIFFRACTION8chain C and resid 451:482
9X-RAY DIFFRACTION9chain C and resid 483:500
10X-RAY DIFFRACTION10chain D and resid 587:608
11X-RAY DIFFRACTION11chain D and resid 609:622
12X-RAY DIFFRACTION12chain D and resid 623:650
13X-RAY DIFFRACTION13chain E and resid 29:51
14X-RAY DIFFRACTION14chain E and resid 52:71
15X-RAY DIFFRACTION15chain E and resid 72:86
16X-RAY DIFFRACTION16chain F and resid 189:219
17X-RAY DIFFRACTION17chain F and resid 220:244
18X-RAY DIFFRACTION18chain F and resid 245:256
19X-RAY DIFFRACTION19chain G and resid 431:440
20X-RAY DIFFRACTION20chain G and resid 441:490
21X-RAY DIFFRACTION21chain G and resid 491:499
22X-RAY DIFFRACTION22chain H and resid 588:608
23X-RAY DIFFRACTION23chain H and resid 609:623
24X-RAY DIFFRACTION24chain H and resid 624:650
25X-RAY DIFFRACTION25chain I and resid 29:41
26X-RAY DIFFRACTION26chain I and resid 42:71
27X-RAY DIFFRACTION27chain I and resid 72:86
28X-RAY DIFFRACTION28chain J and resid 191:211
29X-RAY DIFFRACTION29chain J and resid 212:248
30X-RAY DIFFRACTION30chain J and resid 249:254
31X-RAY DIFFRACTION31chain K and resid 434:444
32X-RAY DIFFRACTION32chain K and resid 445:479
33X-RAY DIFFRACTION33chain K and resid 480:498
34X-RAY DIFFRACTION34chain L and resid 588:598
35X-RAY DIFFRACTION35chain L and resid 599:635
36X-RAY DIFFRACTION36chain L and resid 636:649

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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