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- PDB-3frs: Structure of human IST1(NTD) (residues 1-189)(p43212) -

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Basic information

Entry
Database: PDB / ID: 3frs
TitleStructure of human IST1(NTD) (residues 1-189)(p43212)
ComponentsUncharacterized protein KIAA0174
KeywordsPROTEIN BINDING / ESCRT / ESCRT-III / IST1 / Phosphoprotein
Function / homology
Function and homology information


MIT domain binding / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / midbody abscission / multivesicular body assembly / Flemming body / endoplasmic reticulum-Golgi intermediate compartment ...MIT domain binding / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / midbody abscission / multivesicular body assembly / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of proteolysis / establishment of protein localization / azurophil granule lumen / intracellular protein localization / nuclear envelope / protein transport / midbody / cadherin binding / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / chromatin / protein-containing complex binding / extracellular exosome / extracellular region / identical protein binding / cytosol
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 / Ferritin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.61 Å
AuthorsSchubert, H.L. / Hill, C.P. / Bajorek, M. / Sundquist, W.I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural basis for ESCRT-III protein autoinhibition.
Authors: Bajorek, M. / Schubert, H.L. / McCullough, J. / Langelier, C. / Eckert, D.M. / Stubblefield, W.M. / Uter, N.T. / Myszka, D.G. / Hill, C.P. / Sundquist, W.I.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein KIAA0174
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7172
Polymers21,6251
Non-polymers921
Water63135
1
A: Uncharacterized protein KIAA0174
hetero molecules

A: Uncharacterized protein KIAA0174
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4354
Polymers43,2512
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2850 Å2
ΔGint-11 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.180, 57.180, 157.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Uncharacterized protein KIAA0174 / Putative MAPK-activating protein PM28


Mass: 21625.352 Da / Num. of mol.: 1 / Fragment: UNP residues 1-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+RIL / References: UniProt: P53990
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10mM Tris-HCL, pH 8.0, 350mM NaCl, 1mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
SYNCHROTRONSSRL BL11-120.97852, 0.91837, 0.97922
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATESep 8, 2008
MARMOSAIC 325 mm CCD2CCDAug 6, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1verimax HRSINGLE WAVELENGTHMx-ray1
2Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degsMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.978521
30.918371
40.979221
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 13.47 / Number: 40152 / Rmerge(I) obs: 0.074 / Χ2: 1 / D res high: 3.4 Å / D res low: 40 Å / Num. obs: 5970 / % possible obs: 88.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.314099.410.0430.9657
5.817.3199.910.0670.8857.2
5.085.8110010.0850.9937.1
4.615.0899.610.0880.9877.1
4.284.6199.910.0981.0936.9
4.034.2895.310.1070.9116.8
3.834.0390.110.1251.0836.4
3.663.8376.110.1281.1736.1
3.523.6668.210.1670.9926.1
3.43.5256.510.181.0055.8
ReflectionResolution: 2.61→50 Å / Num. all: 8387 / Num. obs: 8387 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 84.2 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.031 / Net I/σ(I): 13.47
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.61-2.72.80.4597271.0231,288.3
2.7-2.813.50.3858140.9131,299.4
2.81-2.943.90.3338261.0041,2100
2.94-3.0940.2328361.0751,2100
3.09-3.2940.1638501.0631,2100
3.29-3.5440.1348421.1211,299.6
3.54-3.940.1048461.0391,299.4
3.9-4.463.90.0838521.0371,299.2
4.46-5.623.90.0748761.0511,298.3
5.62-503.60.0519180.9551,293.6

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97854.78-6.46
13 wavelength20.91843.38-3.2
13 wavelength30.97921.39-8.22
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.9870.3660.0260.961
2Se600.2510.5260.0340.696
3Se600.7090.9630.0630.483

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.61→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.321 / WRfactor Rwork: 0.292 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.695 / SU B: 16.758 / SU ML: 0.305 / SU R Cruickshank DPI: 0.576 / SU Rfree: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.576 / ESU R Free: 0.341
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.298 392 4.7 %RANDOM
Rwork0.259 ---
obs0.261 8360 98.15 %-
all-8360 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.21 Å2 / Biso mean: 86.846 Å2 / Biso min: 36.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20 Å20 Å2
2--2.11 Å20 Å2
3----4.21 Å2
Refinement stepCycle: LAST / Resolution: 2.61→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 6 35 1455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221446
X-RAY DIFFRACTIONr_angle_refined_deg1.1772.0061943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7715175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85823.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.77215293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6841514
X-RAY DIFFRACTIONr_chiral_restr0.1050.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211042
X-RAY DIFFRACTIONr_mcbond_it0.4081.5878
X-RAY DIFFRACTIONr_mcangle_it0.75221413
X-RAY DIFFRACTIONr_scbond_it0.623568
X-RAY DIFFRACTIONr_scangle_it1.1544.5530
LS refinement shellResolution: 2.61→2.676 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 18 -
Rwork0.427 497 -
all-515 -
obs--86.12 %

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