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- PDB-2xze: Structural basis for AMSH-ESCRT-III CHMP3 interaction -

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Basic information

Entry
Database: PDB / ID: 2xze
TitleStructural basis for AMSH-ESCRT-III CHMP3 interaction
Components
  • CHARGED MULTIVESICULAR BODY PROTEIN 3
  • STAM-BINDING PROTEIN
KeywordsHYDROLASE/PROTEIN TRANSPORT / HYDROLASE-PROTEIN TRANSPORT COMPLEX
Function / homology
Function and homology information


negative regulation of hippocampal neuron apoptotic process / regulation of endosome size / hippocampal neuron apoptotic process / amphisome membrane / multivesicular body-lysosome fusion / suppression of viral release by host / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule ...negative regulation of hippocampal neuron apoptotic process / regulation of endosome size / hippocampal neuron apoptotic process / amphisome membrane / multivesicular body-lysosome fusion / suppression of viral release by host / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication / Sealing of the nuclear envelope (NE) by ESCRT-III / deubiquitinase activity / nuclear membrane reassembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / midbody abscission / multivesicular body sorting pathway / membrane fission / plasma membrane repair / phosphatidylcholine binding / late endosome to vacuole transport / multivesicular body membrane / negative regulation of Ras protein signal transduction / metal-dependent deubiquitinase activity / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / nucleus organization / regulation of early endosome to late endosome transport / K63-linked deubiquitinase activity / Macroautophagy / mitotic metaphase chromosome alignment / molecular function inhibitor activity / ubiquitin-specific protease binding / protein deubiquitination / viral budding via host ESCRT complex / positive regulation of cytokinesis / autophagosome maturation / autophagosome membrane / cleavage furrow / cell surface receptor signaling pathway via JAK-STAT / mitotic cytokinesis / protein polymerization / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / viral release from host cell / Pyroptosis / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol-4,5-bisphosphate binding / multivesicular body / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / Metalloprotease DUBs / kinetochore / autophagy / protein transport / late endosome / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / cytoplasmic vesicle / early endosome / endosome / lysosomal membrane / protein domain specific binding / apoptotic process / positive regulation of cell population proliferation / proteolysis / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Snf7 family / Snf7 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain ...STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Snf7 family / Snf7 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
STAM-binding protein / Charged multivesicular body protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsSolomons, J. / Sabin, C. / Weissenhorn, W.
Citation
Journal: Structure / Year: 2011
Title: Structural Basis for Escrt-III Chmp3 Recruitment of Amsh.
Authors: Solomons, J. / Sabin, C. / Poudevigne, E. / Usami, Y. / Hulsik, D.L. / Macheboeuf, P. / Hartlieb, B. / Gottlinger, H. / Weissenhorn, W.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: Structural Basis for Autoinhibition of Escrt-III Chmp3.
Authors: Lata, S. / Roessle, M. / Solomons, J. / Jamin, M. / Gottlinger, H.G. / Svergun, D.I. / Weissenhorn, W.
History
DepositionNov 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STAM-BINDING PROTEIN
B: STAM-BINDING PROTEIN
Q: CHARGED MULTIVESICULAR BODY PROTEIN 3
R: CHARGED MULTIVESICULAR BODY PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)42,9894
Polymers42,9894
Non-polymers00
Water6,954386
1
B: STAM-BINDING PROTEIN
R: CHARGED MULTIVESICULAR BODY PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)21,4942
Polymers21,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-7.2 kcal/mol
Surface area9710 Å2
MethodPISA
2
A: STAM-BINDING PROTEIN
Q: CHARGED MULTIVESICULAR BODY PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)21,4942
Polymers21,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-4.7 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.970, 45.970, 206.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein STAM-BINDING PROTEIN / ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM / ENDOSOME-ASSOCIATED UBIQUITIN ISOPEPTIDASE


Mass: 17162.611 Da / Num. of mol.: 2 / Fragment: MIT DOMAIN, RESIDUES 1-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O95630, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Protein/peptide CHARGED MULTIVESICULAR BODY PROTEIN 3 / CHROMATIN-MODIFYING PROTEIN 3 / NEUROENDOCRINE DIFFERENTIATION FACTOR / VACUOLAR PROTEIN SORTING- ...CHROMATIN-MODIFYING PROTEIN 3 / NEUROENDOCRINE DIFFERENTIATION FACTOR / VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 24 / HVPS24 / CHMP3


Mass: 4331.674 Da / Num. of mol.: 2 / Fragment: C-TERM FRAGMENT, RESIDUES 183-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9Y3E7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 6
Details: 3.3 MG/ML OF AMSH PROTEIN IN 10 MM HEPES PH 8.0, 100 MM NACL WAS MIXED WITH AN EQUAL VOLUME WELL CONDITION: 2.2 M SODIUM MALONATE,WITH 30 % GLYCEROL AS CRYO-PROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9760, 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2009 / Details: TORODIAL FOCUSING MIRROR
RadiationMonochromator: U35 UNDULATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
20.97951
ReflectionResolution: 1.75→44.85 Å / Num. obs: 141404 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.75→51.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.52 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22694 2164 5 %RANDOM
Rwork0.19163 ---
obs0.19333 40725 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 0 386 3029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9953686
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6995329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88424.366142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39415556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9981525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022069
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21376
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21901
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2320
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1361.51712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81722660
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.06431164
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9614.51024
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 171 -
Rwork0.305 3014 -
obs--99.97 %

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