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- PDB-6xm1: SM Protein Vps45 in Complex with Qa SNARE Tlg2 -

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Basic information

Entry
Database: PDB / ID: 6xm1
TitleSM Protein Vps45 in Complex with Qa SNARE Tlg2
Components
  • Tlg2 Qa SNARE
  • Vps45
KeywordsTRANSPORT PROTEIN / MEMBRANE TRAFFICKING / SM PROTEIN / QA SNARE / THERMOPHILE / SNARE DOMAIN
Function / homology
Function and homology information


SNAP receptor activity / vesicle-mediated transport / intracellular protein transport / Golgi membrane / Golgi apparatus / membrane
Similarity search - Function
Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / Syntaxin / epimorphin family signature. ...Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / 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
Putative vacuolar protein sorting-associated protein / Putative late golgi protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsJeffrey, P.D. / Eisemann, T.J. / Hughson, F.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
CitationJournal: Elife / Year: 2020
Title: The Sec1/Munc18 protein Vps45 holds the Qa-SNARE Tlg2 in an open conformation.
Authors: Eisemann, T.J. / Allen, F. / Lau, K. / Shimamura, G.R. / Jeffrey, P.D. / Hughson, F.M.
History
DepositionJun 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vps45
B: Tlg2 Qa SNARE
C: Vps45
D: Tlg2 Qa SNARE


Theoretical massNumber of molelcules
Total (without water)205,9674
Polymers205,9674
Non-polymers00
Water32418
1
A: Vps45
B: Tlg2 Qa SNARE


Theoretical massNumber of molelcules
Total (without water)102,9842
Polymers102,9842
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-32 kcal/mol
Surface area34390 Å2
MethodPISA
2
C: Vps45
D: Tlg2 Qa SNARE


Theoretical massNumber of molelcules
Total (without water)102,9842
Polymers102,9842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-33 kcal/mol
Surface area35280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.727, 180.057, 202.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain C and (resid 1 through 452 or resid 463 through 469 or resid 483 through 609))
12(chain B and (resid -1 through 78 or (resid 79...
22(chain D and (resid -1 through 200 or resid 251...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLYGLYchain AAA1 - 6091 - 609
211METMETGLNGLN(chain C and (resid 1 through 452 or resid 463 through 469 or resid 483 through 609))CC1 - 4521 - 452
221LEULEUGLYGLY(chain C and (resid 1 through 452 or resid 463 through 469 or resid 483 through 609))CC463 - 469463 - 469
231GLYGLYGLYGLY(chain C and (resid 1 through 452 or resid 463 through 469 or resid 483 through 609))CC483 - 609483 - 609
112GLYGLYVALVAL(chain B and (resid -1 through 78 or (resid 79...BB-1 - 781 - 80
122LEULEULEULEU(chain B and (resid -1 through 78 or (resid 79...BB7981
132GLYGLYTHRTHR(chain B and (resid -1 through 78 or (resid 79...BB-1 - 3041 - 278
142GLYGLYTHRTHR(chain B and (resid -1 through 78 or (resid 79...BB-1 - 3041 - 278
152GLYGLYTHRTHR(chain B and (resid -1 through 78 or (resid 79...BB-1 - 3041 - 278
162GLYGLYTHRTHR(chain B and (resid -1 through 78 or (resid 79...BB-1 - 3041 - 278
212GLYGLYILEILE(chain D and (resid -1 through 200 or resid 251...DD-1 - 2001 - 202
222GLNGLNARGARG(chain D and (resid -1 through 200 or resid 251...DD251 - 260225 - 234
232GLUGLUGLUGLU(chain D and (resid -1 through 200 or resid 251...DD261235
242GLYGLYTHRTHR(chain D and (resid -1 through 200 or resid 251...DD-1 - 3041 - 278
252GLYGLYTHRTHR(chain D and (resid -1 through 200 or resid 251...DD-1 - 3041 - 278
262GLYGLYTHRTHR(chain D and (resid -1 through 200 or resid 251...DD-1 - 3041 - 278
272GLYGLYTHRTHR(chain D and (resid -1 through 200 or resid 251...DD-1 - 3041 - 278

NCS ensembles :
ID
1
2

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Components

#1: Protein Vps45 / Putative vacuolar protein sorting-associated protein


Mass: 70799.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0S539
#2: Protein Tlg2 Qa SNARE / Putative late golgi protein


Mass: 32183.934 Da / Num. of mol.: 2 / Fragment: 1-310 with 201-228 loop deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGW7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.5 mg/ml protein in well buffer, consisting of 0.1 M HEPES pH 8.0, 0.1 M NaCl, 11% (v/v) 2-propanol, and 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→29.68 Å / Num. obs: 53946 / % possible obs: 99.8 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.039 / Rrim(I) all: 0.144 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.8912.31.885550745210.7310.5491.9611.498.9
11.54-29.6812.10.031019984110.0090.03247.994.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17_3644refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XJL

6xjl


Resolution: 2.8→29.68 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 2676 4.96 %
Rwork0.1944 51270 -
obs0.1972 53946 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 265.13 Å2 / Biso mean: 93.3649 Å2 / Biso min: 30.11 Å2
Refinement stepCycle: final / Resolution: 2.8→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11532 0 0 18 11550
Biso mean---60.64 -
Num. residues----1487
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5399X-RAY DIFFRACTION7.284TORSIONAL
12C5399X-RAY DIFFRACTION7.284TORSIONAL
21B1552X-RAY DIFFRACTION7.284TORSIONAL
22D1552X-RAY DIFFRACTION7.284TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.850.32581370.290626232760100
2.85-2.90.35351240.283726532777100
2.9-2.960.35031450.289526782823100
2.96-3.030.38371410.287626202761100
3.03-3.10.2951520.259827092861100
3.1-3.170.35531330.242126312764100
3.17-3.260.27011190.219727422861100
3.26-3.350.28381180.214426452763100
3.35-3.460.25871720.215326712843100
3.46-3.590.27591450.219526442789100
3.59-3.730.28181470.226226842831100
3.73-3.90.24911330.190627272860100
3.9-4.10.26481380.173926702808100
4.1-4.360.1811230.155227092832100
4.36-4.690.19451650.14627002865100
4.7-5.170.19911380.156227402878100
5.17-5.910.25331380.175727622900100
5.91-7.420.24511530.217927752928100
7.42-29.680.22721550.17422887304299
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)
14.23872.04921.26016.35320.5374.3039-0.056-0.4476-0.40170.92070.0931-0.42720.34310.3980.01740.51130.17760.01440.56010.06240.4547-18.0858-44.858221.7544
22.3171.1703-0.81814.0423-1.06742.803-0.32280.0350.1558-0.50910.26350.36120.2768-0.1364-0.04440.48360.0325-0.14750.40050.05150.6111-27.0917-37.94674.2193
32.1660.62980.84085.9623-1.30272.2083-0.2505-0.12420.41340.0790.41831.17370.0531-0.2743-0.24570.55930.0531-0.22460.50890.07350.8782-31.3887-26.94522.7674
46.0139-0.7584-1.07865.2170.26133.08-0.009-0.37630.11130.2108-0.1555-0.2908-0.18630.18760.16720.5722-0.0093-0.20940.4829-0.08180.754-10.1056-17.562814.4147
52.2275-0.24690.0711.6733-1.91648.5759-0.2972-0.56340.33810.8512-0.23320.1745-1.16810.7010.51540.9412-0.1044-0.20350.699-0.20940.9289-6.9003-8.050927.3208
62.6756-0.19380.05045.28540.21043.7789-0.18780.34330.8299-0.77710.080.3567-0.65840.03970.10850.8431-0.1399-0.24080.49630.20950.8483-13.5601-12.3277-12.5899
70.30230.05710.0125.1529-0.71022.4848-0.3840.23911.0167-0.49430.31161.4525-0.2124-0.50330.04620.62050.0165-0.2380.5480.13891.1938-32.6401-19.29280.1176
85.8551-1.5744-4.43774.51451.50876.4512-0.10370.08210.3752-0.11870.1861-0.02950.23420.0164-0.1820.4599-0.1039-0.18970.36460.10060.7191-18.9111-26.4055-4.9366
93.46662.27391.59572.78692.58413.8990.8657-1.09490.42331.1342-0.63690.03110.3777-0.0175-0.24721.2231-0.14060.06441.0974-0.00860.8426-15.0339-34.510943.7263
104.0956-2.03383.86967.5411-5.04965.1334-0.16850.4554-0.5305-1.2958-0.36590.53650.7002-0.59550.54691.1532-0.052-0.10791.3759-0.00590.9579-0.7083-12.893961.9324
114.6353.57392.29445.7997-2.39236.81250.3319-1.00810.37392.4747-0.318-0.4710.41661.25090.01641.05880.064-0.17280.9612-0.11590.6758-6.6828-29.749726.015
123.6988-0.4382-0.98735.9542-1.3035.2430.1750.66240.1322-0.9031-0.2162-0.6058-0.19840.51930.12810.45610.01540.07870.57-0.01670.43818.742341.187-24.03
131.8109-0.83440.13134.0222-1.78822.4883-0.09230.08430.01920.18180.17050.28-0.2231-0.1143-0.08420.3565-0.02910.04860.374-0.02720.4522-0.245139.3444-7.1844
141.35730.16030.74941.7917-0.12866.2495-0.06930.2897-0.5677-0.30430.0608-0.16760.66120.51270.04020.62760.10360.08620.5103-0.12390.805417.061311.0252-16.2527
155.24461.2560.93115.69850.65833.01710.3365-0.7647-0.59440.7617-0.33040.18460.40340.1568-0.040.6730.0110.00790.34390.11130.562212.0615.33614.0939
162.19531.0460.51275.01470.19642.6321-0.09520.0215-0.77330.28940.20721.07190.3228-0.3865-0.14630.6172-0.0880.06720.59260.05820.9809-8.693614.43211.4982
173.17280.68131.80783.79980.62874.28070.03040.0322-0.3071-0.041-0.0460.24780.14110.0123-0.13860.38630.02650.08910.28020.01130.57883.333423.90650.268
183.5365-1.0162-1.95182.83163.08943.82760.65671.1175-0.1726-1.4435-0.63540.2112-0.69280.1351-0.01011.19210.3496-0.251.21940.22570.55643.181642.6938-37.9863
194.5138-0.05852.71015.0897-0.21021.84950.58511.1133-1.6427-2.17190.4257-0.0317-0.15871.4578-0.67641.50370.13830.15052.344-0.4640.955316.382530.2961-53.1362
202.8854-1.5418-4.32841.15952.56765.59980.3983-0.0993-0.0742-0.8286-0.69610.42-0.1214-0.85750.57130.96340.1891-0.0981.1776-0.06360.693816.379927.6948-45.4795
219.8445-5.2282-6.56917.63553.82384.405-0.6125-0.21630.72080.63260.4354-0.05590.4321-0.4713-0.00920.91990.09390.0261.0129-0.11340.9325.523313.7288-61.5701
227.67761.7722-7.42810.4177-1.71797.18660.81943.348-1.4993-2.464-1.26110.89450.2565-2.27630.38171.52530.43650.01181.3489-0.4011.586517.603324.5382-33.9529
239.8267-3.3948-1.78974.22323.91723.89230.1762.0046-0.5533-1.90980.0622-0.6259-0.40040.1156-0.12430.76040.05690.03280.653-0.06250.623820.148433.4897-22.8187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 122 )A1 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 212 )A123 - 212
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 246 )A213 - 246
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 294 )A247 - 294
5X-RAY DIFFRACTION5chain 'A' and (resid 295 through 359 )A295 - 359
6X-RAY DIFFRACTION6chain 'A' and (resid 360 through 493 )A360 - 493
7X-RAY DIFFRACTION7chain 'A' and (resid 494 through 572 )A494 - 572
8X-RAY DIFFRACTION8chain 'A' and (resid 573 through 609 )A573 - 609
9X-RAY DIFFRACTION9chain 'B' and (resid -1 through 199 )B-1 - 199
10X-RAY DIFFRACTION10chain 'B' and (resid 200 through 282 )B200 - 282
11X-RAY DIFFRACTION11chain 'B' and (resid 283 through 304 )B283 - 304
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 84 )C1 - 84
13X-RAY DIFFRACTION13chain 'C' and (resid 85 through 246 )C85 - 246
14X-RAY DIFFRACTION14chain 'C' and (resid 247 through 389 )C247 - 389
15X-RAY DIFFRACTION15chain 'C' and (resid 390 through 475 )C390 - 475
16X-RAY DIFFRACTION16chain 'C' and (resid 476 through 547 )C476 - 547
17X-RAY DIFFRACTION17chain 'C' and (resid 548 through 609 )C548 - 609
18X-RAY DIFFRACTION18chain 'D' and (resid -1 through 107 )D-1 - 107
19X-RAY DIFFRACTION19chain 'D' and (resid 108 through 159 )D108 - 159
20X-RAY DIFFRACTION20chain 'D' and (resid 160 through 253 )D160 - 253
21X-RAY DIFFRACTION21chain 'D' and (resid 254 through 282 )D254 - 282
22X-RAY DIFFRACTION22chain 'D' and (resid 283 through 290 )D283 - 290
23X-RAY DIFFRACTION23chain 'D' and (resid 291 through 304 )D291 - 304

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