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- PDB-3ggz: Crystal Structure of S.cerevisiae Ist1 N-terminal domain in compl... -

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Basic information

Entry
Database: PDB / ID: 3ggz
TitleCrystal Structure of S.cerevisiae Ist1 N-terminal domain in complex with Did2 MIM motif
Components
  • Increased sodium tolerance protein 1
  • Vacuolar protein-sorting-associated protein 46
KeywordsPROTEIN TRANSPORT / ENDOCYTOSIS / novel MIM binding mode / Phosphoprotein / Coiled coil / Endosome / Membrane / Transport
Function / homology
Function and homology information


ESCRT III complex assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / ESCRT III complex / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / endosome to plasma membrane protein transport / protein targeting to vacuole / late endosome to vacuole transport / ATPase inhibitor activity / multivesicular body ...ESCRT III complex assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / ESCRT III complex / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / endosome to plasma membrane protein transport / protein targeting to vacuole / late endosome to vacuole transport / ATPase inhibitor activity / multivesicular body / Neutrophil degranulation / intracellular protein localization / late endosome / protein transport / endosome / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein Ist1 / Vacuolar protein sorting-associated protein Ist1 / Vacuolar protein sorting-associated protein IST1-like / Regulator of Vps4 activity in the MVB pathway / Snf7 family / Snf7 / Ferritin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein IST1 / Vacuolar protein-sorting-associated protein 46
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsXiao, J. / Xu, Z.
CitationJournal: MOLECULAR BIOLOGY OF THE CELL / Year: 2009
Title: Structural basis of Ist1 function and Ist1-Did2 interaction in the multivesicular body pathway and cytokinesis.
Authors: Xiao, J. / Chen, X.W. / Davies, B.A. / Saltiel, A.R. / Katzmann, D.J. / Xu, Z.
History
DepositionMar 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Increased sodium tolerance protein 1
B: Increased sodium tolerance protein 1
C: Increased sodium tolerance protein 1
D: Increased sodium tolerance protein 1
E: Vacuolar protein-sorting-associated protein 46
F: Vacuolar protein-sorting-associated protein 46
G: Vacuolar protein-sorting-associated protein 46
H: Vacuolar protein-sorting-associated protein 46


Theoretical massNumber of molelcules
Total (without water)102,8888
Polymers102,8888
Non-polymers00
Water00
1
A: Increased sodium tolerance protein 1
E: Vacuolar protein-sorting-associated protein 46


Theoretical massNumber of molelcules
Total (without water)25,7222
Polymers25,7222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-5 kcal/mol
Surface area11850 Å2
MethodPISA
2
B: Increased sodium tolerance protein 1
F: Vacuolar protein-sorting-associated protein 46


Theoretical massNumber of molelcules
Total (without water)25,7222
Polymers25,7222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-5 kcal/mol
Surface area11500 Å2
MethodPISA
3
C: Increased sodium tolerance protein 1
G: Vacuolar protein-sorting-associated protein 46


Theoretical massNumber of molelcules
Total (without water)25,7222
Polymers25,7222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-7 kcal/mol
Surface area11370 Å2
MethodPISA
4
D: Increased sodium tolerance protein 1
H: Vacuolar protein-sorting-associated protein 46


Theoretical massNumber of molelcules
Total (without water)25,7222
Polymers25,7222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-5 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.916, 165.916, 121.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
12B
13C
14D

NCS domain segments:

Dom-ID: 1 / Component-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 8 - 180 / Label seq-ID: 8 - 180

Ens-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Increased sodium tolerance protein 1


Mass: 22380.164 Da / Num. of mol.: 4 / Fragment: N-terminal domain, UNP residues 1-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IST1, N0809, YNL265C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53843
#2: Protein/peptide
Vacuolar protein-sorting-associated protein 46 / Charged multivesicular body protein 1 / DOA4-independent degradation protein 2 / Fifty two inhibitor 1


Mass: 3341.793 Da / Num. of mol.: 4 / Fragment: MIM motif, UNP residues 176-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CHM1, DID2, FTI1, VPS46, YKR035W-A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P69771

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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: 4.08 Å3/Da / Density % sol: 69.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Sodium Citrate, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9793 Å
DetectorDetector: CCD / Date: Apr 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 17219 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.617
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
3.8-3.876.20.658100
3.87-3.946.10.532100
3.94-4.016.20.464100
4.01-4.096.20.374100
4.09-4.186.20.327100
4.18-4.286.20.30399.9
4.28-4.396.20.252100
4.39-4.56.10.191100
4.5-4.646.20.177100
4.64-4.796.10.165100
4.79-4.966.10.136100
4.96-5.166.10.128100
5.16-5.396.10.157100
5.39-5.676.10.147100
5.67-6.0360.1399.9
6.03-6.4960.11299.7
6.49-7.155.90.07299.7
7.15-8.185.90.04399.3
8.18-10.295.70.03599
10.29-505.10.03594.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.32 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.8 Å49.03 Å
Translation3.8 Å49.03 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→49.03 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 5432034.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.307 869 5.1 %RANDOM
Rwork0.289 ---
obs0.289 17200 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 104.977 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 146.1 Å2
Baniso -1Baniso -2Baniso -3
1-9.17 Å20 Å20 Å2
2--9.17 Å20 Å2
3----18.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.71 Å0.69 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 3.8→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6595 0 0 0 6595
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.682.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 151 5.4 %
Rwork0.397 2658 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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