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- PDB-9zct: Crystal structure of HOPS subunits Vps33 and Vps16 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9zct
TitleCrystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 SNARE motif
Components
  • Nyv1 SNARE motif
  • Small conjugating protein ligase-like protein
  • Vacuolar protein sorting-associated protein 16
KeywordsTRANSPORT PROTEIN / MEMBRANE TRAFFICKING / SM PROTEIN / HOPS COMPLEX / THERMOPHILE / SNARE DOMAIN
Function / homology
Function and homology information


HOPS complex / vacuole fusion, non-autophagic / endosomal transport / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / vesicle-mediated transport / endomembrane system / intracellular protein transport / actin binding / endosome ...HOPS complex / vacuole fusion, non-autophagic / endosomal transport / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / vesicle-mediated transport / endomembrane system / intracellular protein transport / actin binding / endosome / membrane / cytoplasm
Similarity search - Function
: / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1-like, domain 1 / Sec1-like protein ...: / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Longin-like domain superfamily / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Synaptobrevin homolog YKT6 / Probable vacuolar protein sorting-associated protein 16 homolog / E2 ubiquitin-conjugating enzyme
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsStanton, A.E. / Jeffrey, P.D. / Hughson, F.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007388 United States
Citation
Journal: To Be Published
Title: Structural characterization of intermediates in SM-catalyzed SNARE assembly
Authors: Stanton, A.E. / Midura, I. / Shirai, N. / Su, N. / Jeffrey, P.D. / Hughson, F.M.
#1: Journal: Science / Year: 2015
Title: A direct role for the Sec1/Munc18-family protein Vps33 as a template for SNARE assembly.
Authors: Baker, R.W. / Jeffrey, P.D. / Zick, M. / Phillips, B.P. / Wickner, W.T. / Hughson, F.M.
History
DepositionNov 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small conjugating protein ligase-like protein
B: Vacuolar protein sorting-associated protein 16
C: Nyv1 SNARE motif


Theoretical massNumber of molelcules
Total (without water)115,9433
Polymers115,9433
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-42 kcal/mol
Surface area39820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.492, 99.492, 308.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Small conjugating protein ligase-like protein / SM protein Vps33


Mass: 77119.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0057760 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SCM5
#2: Protein Vacuolar protein sorting-associated protein 16


Mass: 31252.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0026760 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S6M7
#3: Protein Nyv1 SNARE motif


Mass: 7570.556 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SNARE motif 148-212
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0032860 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S5G3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 0.5 M LiCl, 13% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.9→29.5 Å / Num. obs: 35477 / % possible obs: 99.9 % / Redundancy: 10.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.075 / Rrim(I) all: 0.248 / Χ2: 1.22 / Net I/σ(I): 8.9 / Num. measured all: 387603
Reflection shellResolution: 2.9→3.04 Å / % possible obs: 99.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 1.921 / Num. measured all: 51139 / Num. unique obs: 4627 / CC1/2: 0.7 / Rpim(I) all: 0.6 / Rrim(I) all: 2.015 / Χ2: 1.07 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.5 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 1834 5.19 %
Rwork0.1888 --
obs0.192 35326 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7257 0 0 30 7287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077371
X-RAY DIFFRACTIONf_angle_d0.9079933
X-RAY DIFFRACTIONf_dihedral_angle_d31.8322802
X-RAY DIFFRACTIONf_chiral_restr0.0481121
X-RAY DIFFRACTIONf_plane_restr0.0051293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.43061330.32762513X-RAY DIFFRACTION100
2.98-3.070.33041380.27792523X-RAY DIFFRACTION100
3.07-3.170.33021510.26242491X-RAY DIFFRACTION100
3.17-3.280.31551370.25962545X-RAY DIFFRACTION100
3.28-3.410.31341300.22532542X-RAY DIFFRACTION100
3.41-3.560.2641270.19922558X-RAY DIFFRACTION100
3.56-3.750.27911490.19062531X-RAY DIFFRACTION100
3.75-3.990.25631430.17022583X-RAY DIFFRACTION100
3.99-4.290.21831390.15852553X-RAY DIFFRACTION100
4.29-4.720.20921510.14372591X-RAY DIFFRACTION100
4.72-5.40.22351310.16042612X-RAY DIFFRACTION100
5.4-6.790.27761590.20562647X-RAY DIFFRACTION100
6.79-29.50.19181460.17062803X-RAY DIFFRACTION99
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)
11.4249-1.24740.61174.8539-0.72413.19970.0897-0.0705-0.13890.1839-0.1127-0.40890.80180.55840.02190.70020.13740.00630.55870.00960.364450.456-8.379542.4768
23.8411-0.3354-0.68862.1136-0.80222.9643-0.12050.4593-0.0463-0.3381-0.2329-0.69420.24571.13810.28540.75670.06790.20070.78580.09590.592461.01371.642512.9853
32.30420.65890.65091.76010.58082.6288-0.07640.04080.2039-0.3060.03360.0257-0.1184-0.09020.07340.47310.03430.04140.26790.03510.302834.51678.672423.2063
42.59871.13590.95225.80150.25378.74270.3311-0.73130.04861.01630.0531-0.1586-0.46680.1928-0.24770.76340.02630.06660.4591-0.00340.485929.3022-9.623353.7985
50.80480.5339-0.6571.296-1.0888.4421-0.13620.1608-0.1581-0.21890.2781-0.05531.3376-0.6494-0.30530.8833-0.1515-0.00510.40510.03570.523618.753-19.558618.2091
66.56822.134-6.0113.3435-4.34747.5616-0.20790.52720.0723-0.33670.29150.22510.9248-0.6077-0.03810.8574-0.1811-0.020.82390.01690.346429.2916-3.1895-11.8923
77.4891-5.5891-6.14327.65013.97795.762-0.0339-1.4583-2.60921.8525-1.41432.31960.56381.33171.46162.0399-0.01460.41951.20960.40652.388884.0405-4.6664.7116
87.61461.9134-3.9867.60581.94023.64561.40273.42050.4268-1.1686-1.0708-1.4072-0.6491-0.2319-0.61691.22460.24750.49031.308-0.01021.109364.03321.92140.5282
90.15540.4165-0.60893.89711.25747.6458-0.13381.61050.3214-1.6579-0.1147-0.62080.39890.4220.34521.61460.14720.01651.4860.340.803540.764813.29265.4512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 378 )
3X-RAY DIFFRACTION3chain 'A' and (resid 379 through 660 )
4X-RAY DIFFRACTION4chain 'B' and (resid 525 through 597 )
5X-RAY DIFFRACTION5chain 'B' and (resid 598 through 716 )
6X-RAY DIFFRACTION6chain 'B' and (resid 717 through 791 )
7X-RAY DIFFRACTION7chain 'C' and (resid 169 through 180 )
8X-RAY DIFFRACTION8chain 'C' and (resid 181 through 196 )
9X-RAY DIFFRACTION9chain 'C' and (resid 197 through 205 )

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