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- PDB-6xmd: SM Protein Vps45 in Complex with Qa SNARE Tlg2 (1-310) -

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Basic information

Entry
Database: PDB / ID: 6xmd
TitleSM Protein Vps45 in Complex with Qa SNARE Tlg2 (1-310)
Components
  • Tlg2 Qa SNARE
  • Vps45
KeywordsTRANSPORT PROTEIN / MEMBRANE TRAFFICKING / SM PROTEIN / QA SNARE / THERMOPHILE / SNARE DOMAIN
Function / homology
Function and homology information


membrane-bounded organelle / SNARE complex / SNAP receptor activity / endomembrane system / vesicle-mediated transport / intracellular protein transport / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
Syntaxin-16 / Sec1-like, domain 1 / Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site ...Syntaxin-16 / Sec1-like, domain 1 / Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family / 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
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: 3.9 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 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)105,8212
Polymers105,8212
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-31 kcal/mol
Surface area34500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.380, 89.434, 209.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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


Mass: 70799.602 Da / Num. of mol.: 1
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: 35020.992 Da / Num. of mol.: 1 / Fragment: UNP residues 1-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0SGW7

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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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4 mg/ml protein in well buffer consisting of 0.125 M potassium citrate, 15 % (w/v) PEG 3350, 15% (v/v) glycerol, and 1 mM DTT

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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: 0.97935 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 3.88→29.51 Å / Num. obs: 10653 / % possible obs: 99.3 % / Redundancy: 13 % / CC1/2: 0.993 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.071 / Rrim(I) all: 0.256 / Net I/σ(I): 6.9 / Num. measured all: 138267 / Scaling rejects: 108
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
3.88-4.3413.42.1493885628910.6490.6032.2341.398.1
8.67-29.5111.90.0881241710400.990.0270.09227.597.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17_3644refinement
XDSdata reduction
Aimless0.7.1data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XJL

6xjl


Resolution: 3.9→29.51 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 505 4.85 %
Rwork0.1907 9900 -
obs0.1932 10405 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 473.49 Å2 / Biso mean: 212.8478 Å2 / Biso min: 105.88 Å2
Refinement stepCycle: final / Resolution: 3.9→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5707 0 0 0 5707
Num. residues----734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9-4.290.38161350.29062318245396
4.29-4.910.20911050.189624762581100
4.91-6.180.22231360.215924742610100
6.18-29.510.23241290.16526322761100
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)
12.0091-0.21621.07135.656-1.35392.9308-0.2278-0.4280.20870.30080.19-0.2527-0.21370.4309-0.02931.20510.0897-0.01621.5228-0.1091.29187.4329-39.618-39.9143
22.02650.50861.50370.98641.79148.089-0.4843-0.28870.00980.03280.0054-0.5839-0.48780.10960.53762.0238-0.0495-0.32641.6669-0.0862.346621.7682-11.0044-42.3252
34.2991.7083-1.14146.0583-0.58384.284-0.2562-0.10481.0932-0.08450.29930.3409-0.2323-0.15150.01831.57650.0591-0.21371.4483-0.09751.87335.0785-20.2115-55.6055
41.60691.30420.1163.33571.68236.21850.07590.57210.65050.9031.0735-0.49050.61680.504-1.3721.91040.30190.1711.8152-0.12721.84432.3675-52.1996-29.8791
50.79650.61-0.67154.76822.32292.29070.1566-1.33610.47862.73730.8155-0.06181.12251.6684-0.98693.8426-0.1408-0.38473.6867-0.38812.554917.3189-33.8190.4965
63.81290.3119-0.04742.2311-1.55411.10330.2678-0.46841.13613.44881.7116-2.25160.82360.3553-0.92072.88590.6606-0.58153.1364-0.65642.014919.6088-31.1642-9.439
74.1177-0.62014.09227.31682.05774.89270.38660.0077-2.3234-0.02780.1429-0.55072.1567-0.612-0.24772.4455-0.29790.37753.3268-0.46742.454625.8443-13.615410.8127
86.45462.70275.66647.0456-0.22896.1-1.1226-1.01290.95981.7028-1.3414-0.47062.34060.43212.62782.35710.1211-0.16612.1717-0.20762.063124.0526-30.133-25.5497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 246 )A1 - 246
2X-RAY DIFFRACTION2chain 'A' and (resid 247 through 431 )A247 - 431
3X-RAY DIFFRACTION3chain 'A' and (resid 432 through 609 )A432 - 609
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 81 )B-1 - 81
5X-RAY DIFFRACTION5chain 'B' and (resid 82 through 159 )B82 - 159
6X-RAY DIFFRACTION6chain 'B' and (resid 160 through 199 )B160 - 199
7X-RAY DIFFRACTION7chain 'B' and (resid 200 through 282 )B200 - 282
8X-RAY DIFFRACTION8chain 'B' and (resid 283 through 304 )B283 - 304

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