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- PDB-5t8l: Crystal structure of Snf7 under 350 MPa -

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Basic information

Entry
Database: PDB / ID: 5t8l
TitleCrystal structure of Snf7 under 350 MPa
ComponentsVacuolar-sorting protein SNF7
KeywordsPROTEIN TRANSPORT / Snf7 / high-pressure cryocooling / resolution
Function / homology
Function and homology information


Sealing of the nuclear envelope (NE) by ESCRT-III / intralumenal vesicle formation / Macroautophagy / peroxisome organization / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / late endosome to vacuole transport via multivesicular body sorting pathway / ATP export / vesicle budding from membrane / late endosome to vacuole transport ...Sealing of the nuclear envelope (NE) by ESCRT-III / intralumenal vesicle formation / Macroautophagy / peroxisome organization / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / late endosome to vacuole transport via multivesicular body sorting pathway / ATP export / vesicle budding from membrane / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / reticulophagy / multivesicular body / cytoplasmic side of plasma membrane / nuclear envelope / protein transport / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Vacuolar-sorting protein SNF7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHuang, Q. / Szebenyi, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
Citation
Journal: To Be Published
Title: Crystal structure of Snf7 under 350 MPa
Authors: Huang, Q. / Szebenyi, D.
#1: Journal: Elife / Year: 2015
Title: Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.
Authors: Tang, S. / Henne, W.M. / Borbat, P.P. / Buchkovich, N.J. / Freed, J.H. / Mao, Y. / Fromme, J.C. / Emr, S.D.
History
DepositionSep 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

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Assembly

Deposited unit
A: Vacuolar-sorting protein SNF7


Theoretical massNumber of molelcules
Total (without water)15,8031
Polymers15,8031
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.033, 47.467, 45.664
Angle α, β, γ (deg.)90.00, 99.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vacuolar-sorting protein SNF7 / DOA4-independent degradation protein 1 / Sucrose nonfermenting protein 7 / Vacuolar protein-sorting- ...DOA4-independent degradation protein 1 / Sucrose nonfermenting protein 7 / Vacuolar protein-sorting-associated protein 32


Mass: 15803.133 Da / Num. of mol.: 1 / Fragment: UNP residues 12-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SNF7, DID1, VPS32, YLR025W / Production host: Escherichia coli (E. coli) / References: UniProt: P39929
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.03 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 6% PEG20000, 110 mM NaCl, 70 mM Mes pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 6489 / % possible obs: 99.1 % / Redundancy: 3.2 % / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.365 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fd9

5fd9


Resolution: 2.2→32.69 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.34
RfactorNum. reflection% reflection
Rfree0.2592 647 10 %
Rwork0.1905 --
obs0.1975 6472 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 0 47 1039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007997
X-RAY DIFFRACTIONf_angle_d0.8171329
X-RAY DIFFRACTIONf_dihedral_angle_d16.771643
X-RAY DIFFRACTIONf_chiral_restr0.04156
X-RAY DIFFRACTIONf_plane_restr0.006171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1994-2.36920.35981220.2421107X-RAY DIFFRACTION95
2.3692-2.60750.30641300.24381165X-RAY DIFFRACTION100
2.6075-2.98460.33011310.23261178X-RAY DIFFRACTION100
2.9846-3.75940.25471310.1841174X-RAY DIFFRACTION100
3.7594-32.69340.21171330.15611201X-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)
10.1426-0.2634-0.0510.37950.19570.11930.3331-0.2831-0.2874-0.1745-0.0583-0.04460.3676-0.17750.00050.2816-0.0205-0.010.24880.03140.306821.6292-0.81420.3688
20.1272-0.21210.11120.0388-0.2601-0.0561-0.13830.16240.3776-0.008-0.0082-0.0086-0.0372-0.0191-0.00020.262-0.00290.00890.3041-0.00990.25915.22119.194515.7829
30.1573-0.09480.07130.16220.01850.0655-0.1357-0.1154-0.0069-0.2318-0.29320.0325-0.10540.2165-0.00130.4571-0.01990.02050.46420.05030.4022-41.366428.72295.2157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 142 )

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