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

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Basic information

Entry
Database: PDB / ID: 9zcs
TitleCrystal structure of HOPS subunits Vps33 and Vps16 in complex with the Nyv1 and Vam3 SNARE motifs
Components
  • Nyv1 SNARE motif
  • SNAP receptor-like protein
  • 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 / : / SNARE complex / Golgi to vacuole transport / SNAP receptor activity / vesicle fusion / endosomal transport / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity ...HOPS complex / vacuole fusion, non-autophagic / : / SNARE complex / Golgi to vacuole transport / SNAP receptor activity / vesicle fusion / endosomal transport / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / vesicle-mediated transport / SNARE binding / endomembrane system / intracellular protein transport / actin binding / endosome / membrane / cytoplasm
Similarity search - Function
Syntaxin-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 ...Syntaxin-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. / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / SNARE domain / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / 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
SNAP receptor-like protein / 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: 3.19 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
D: SNAP receptor-like protein


Theoretical massNumber of molelcules
Total (without water)121,6124
Polymers121,6124
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-62 kcal/mol
Surface area41110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.844, 100.844, 312.412
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: Protein SNAP receptor-like protein / Vam3


Mass: 5669.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SNARE motif truncated at +5 level
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0015850 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S236
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: 3.27 Å3/Da / Density % sol: 62.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.8M K Tartrate, 0.1M Tris-HCl pH8.5, 0.5% w/v PEG 5000 MME

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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: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.19→29.6 Å / Num. obs: 27836 / % possible obs: 99.8 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.069 / Rrim(I) all: 0.312 / Χ2: 0.99 / Net I/σ(I): 11.2 / Num. measured all: 557359
Reflection shellResolution: 3.19→3.38 Å / % possible obs: 99.4 % / Redundancy: 19.9 % / Rmerge(I) obs: 1.943 / Num. measured all: 87050 / Num. unique obs: 4382 / CC1/2: 0.779 / Rpim(I) all: 0.442 / Rrim(I) all: 1.994 / Χ2: 0.87 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→29.6 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 1416 5.11 %
Rwork0.1774 --
obs0.1798 27729 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7455 0 0 0 7455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087569
X-RAY DIFFRACTIONf_angle_d0.97110204
X-RAY DIFFRACTIONf_dihedral_angle_d31.3712863
X-RAY DIFFRACTIONf_chiral_restr0.0491158
X-RAY DIFFRACTIONf_plane_restr0.0051330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.30.36451070.30172576X-RAY DIFFRACTION99
3.31-3.440.30981490.24532545X-RAY DIFFRACTION100
3.44-3.590.2551410.21062607X-RAY DIFFRACTION100
3.59-3.780.27771290.20922592X-RAY DIFFRACTION100
3.78-4.020.22131300.16282605X-RAY DIFFRACTION100
4.02-4.330.19171630.14932589X-RAY DIFFRACTION100
4.33-4.760.17781350.13292637X-RAY DIFFRACTION100
4.76-5.450.20541440.14782631X-RAY DIFFRACTION100
5.45-6.850.26691480.1992699X-RAY DIFFRACTION100
6.85-29.60.19681700.16412832X-RAY DIFFRACTION100
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)
11.7793-0.8260.34454.3799-0.44533.10790.09530.0266-0.23670.0798-0.1286-0.67991.01470.71160.02010.70910.18850.03350.5740.01980.461651.6-9.249842.8922
22.18260.39090.39692.4557-0.61982.1987-0.23650.5950.0409-0.6306-0.1336-0.84830.22820.83210.21070.71480.11610.26970.60760.10720.63354.59514.810916.777
32.19860.68310.9433.04340.85162.9531-0.11810.02190.2834-0.3720.00350.0052-0.1155-0.08680.17060.45660.01420.07740.26810.04010.33135.486710.159526.061
43.50111.75861.19197.9721-0.49793.9770.4117-0.8020.0930.9366-0.2597-0.17380.26120.1767-0.15160.7436-0.0140.11940.45730.02020.464229.6834-9.405553.797
50.97391.0491-1.34962.3213-0.63418.1354-0.15430.2469-0.1915-0.45940.3665-0.09551.4711-0.9881-0.35750.9286-0.1842-0.03220.51940.09460.570419.857-19.199818.4934
68.46473.6941-6.92363.8556-4.63046.9878-0.20030.6445-0.0666-0.23880.24370.11610.8067-0.66640.01750.9671-0.1608-0.0210.78430.04370.362530.8662-2.8573-11.7186
75.33874.4729-6.1134.071-5.24027.03830.1705-0.9374-2.00731.0741-0.23063.11860.37152.50810.13551.91760.22690.2641.89-0.19692.668586.2733-1.58956.4004
82.73042.63153.62883.68145.32889.33281.96480.1271-2.82590.4929-0.0863-0.9389-0.0297-1.8882-1.75032.20330.37670.66731.23760.16263.373174.4386-3.02433.3095
94.83122.46560.44333.756-1.67063.05870.22691.6568-0.4951-0.9298-0.8394-1.09750.19750.61340.54241.97270.69691.0972.11820.56732.187664.24144.8291.2815
105.1545-1.7876-4.53086.39073.06654.37561.58173.00851.3719-2.1878-0.9214-1.0039-0.2179-1.28-0.55392.0277-0.10280.48492.5110.47011.037442.458413.63435.6915
117.7134-0.4052-6.20660.0390.3545.00831.1185-0.5738-1.1544-0.6392-2.3247-2.6218-0.84340.5521.18261.54240.23380.29572.80980.3873.683384.7358-5.541717.8527
125.75030.2343-0.65082.6889-2.62152.65880.43982.3061-0.3627-1.58231.9591-0.465-0.4979-0.5354-2.37631.1853-0.0450.45781.8263-0.03311.657761.6643-16.670924.9536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 216 )
2X-RAY DIFFRACTION2chain 'A' and (resid 217 through 411 )
3X-RAY DIFFRACTION3chain 'A' and (resid 412 through 659 )
4X-RAY DIFFRACTION4chain 'B' and (resid 527 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 178 )
8X-RAY DIFFRACTION8chain 'C' and (resid 179 through 183 )
9X-RAY DIFFRACTION9chain 'C' and (resid 184 through 194 )
10X-RAY DIFFRACTION10chain 'C' and (resid 195 through 206 )
11X-RAY DIFFRACTION11chain 'D' and (resid 196 through 214 )
12X-RAY DIFFRACTION12chain 'D' and (resid 215 through 228 )

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