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- PDB-5fd7: X-ray Crystal Structure of ESCRT-III Snf7 core domain (conformation A) -

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Basic information

Entry
Database: PDB / ID: 5fd7
TitleX-ray Crystal Structure of ESCRT-III Snf7 core domain (conformation A)
ComponentsVacuolar-sorting protein SNF7
KeywordsPROTEIN TRANSPORT / ESCRT / Snf7 / Active / Core
Function / homology
Function and homology information


ESCRT III complex assembly / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Macroautophagy / ATP export / ESCRT III complex / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / vesicle budding from membrane / late endosome to vacuole transport ...ESCRT III complex assembly / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Macroautophagy / ATP export / ESCRT III complex / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / 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 / protein transport / nuclear envelope / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Vacuolar-sorting protein SNF7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsTang, S. / Henne, W.M. / Borbat, P.P. / Buchkovich, N.J. / Freed, J.H. / Mao, Y. / Fromme, J.C. / Emr, S.D.
Funding support United States, 4items
OrganizationGrant numberCountry
Cornell UniversityCU3704 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098621 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094347 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007273 United States
CitationJournal: 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
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_detector / pdbx_struct_oper_list / software
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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)15,8601
Polymers15,8601
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.451, 52.196, 54.486
Angle α, β, γ (deg.)90.000, 97.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vacuolar-sorting protein SNF7 / DOA4-independent degradation protein 1 / Vacuolar protein-sorting-associated protein 32


Mass: 15860.185 Da / Num. of mol.: 1
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 / Plasmid: pET28a His6-Sumo-Snf7N12-P150 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P39929
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100mM NaCl, 100mM MES:NaOH pH5.5, 3% PEG20,000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 6376 / % possible obs: 97.99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.0884 / Net I/σ(I): 8.04
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.91 / % possible all: 93.72

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RESOLVEmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ABM

4abm


Resolution: 2.4→27.009 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 315 4.99 %
Rwork0.2591 5996 -
obs0.2593 6311 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 218.02 Å2 / Biso mean: 91.0538 Å2 / Biso min: 40.74 Å2
Refinement stepCycle: final / Resolution: 2.4→27.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 0 7 982
Biso mean---69.2 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015980
X-RAY DIFFRACTIONf_angle_d1.2391306
X-RAY DIFFRACTIONf_chiral_restr0.088154
X-RAY DIFFRACTIONf_plane_restr0.006167
X-RAY DIFFRACTIONf_dihedral_angle_d16.387396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 97 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4002-3.02340.3651570.31629773134
3.0234-27.01020.23861580.244930193177
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)
13.36971.41173.43733.98321.52037.29830.85830.2058-2.008-0.5610.20390.61851.0025-0.0099-0.8180.54320.0726-0.06880.6641-0.16190.7876-19.7799-15.5377-2.6062
22.8157-2.13460.9241.1716-0.77622.0837-0.124-0.51660.3206-0.01130.0818-0.12-0.0335-0.0238-0.01890.32720.03140.10370.5133-0.02980.6036-3.6101-7.28025.2759
33.35940.72013.56571.0732-0.05134.479-0.7006-0.39154.56770.6659-1.0445-0.1183-1.6691-1.76151.36933.08740.9324-0.31941.3345-0.16752.093744.0364-6.551923.6775
42.2711.22083.35379.8343.9489.3006-0.14281.83581.2158-1.7599-0.43340.425-0.18541.2160.84510.7087-0.0001-0.1860.9277-0.00280.977949.1662-1.047537.4111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 59 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 119 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 125 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 140 )A0

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