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- PDB-3c3o: ALIX Bro1-domain:CHMIP4A co-crystal structure -

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Basic information

Entry
Database: PDB / ID: 3c3o
TitleALIX Bro1-domain:CHMIP4A co-crystal structure
Components
  • Charged multivesicular body protein 4a peptide
  • Programmed cell death 6-interacting protein
KeywordsTRANSPORT PROTEIN / CHMP4A ALIX BRO1 amphipathic-helix / Apoptosis / Host-virus interaction / Protein transport / Transport / Cytoplasmic vesicle / Lipid-binding / Membrane
Function / homology
Function and homology information


proteinase activated receptor binding / membrane invagination / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / plasma membrane tubulation / regulation of extracellular exosome assembly / extracellular exosome biogenesis / viral budding / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly ...proteinase activated receptor binding / membrane invagination / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / plasma membrane tubulation / regulation of extracellular exosome assembly / extracellular exosome biogenesis / viral budding / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / late endosome to lysosome transport / regulation of membrane permeability / ESCRT III complex / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway / post-translational protein targeting to endoplasmic reticulum membrane / regulation of centrosome duplication / nuclear membrane reassembly / bicellular tight junction assembly / multivesicular body sorting pathway / Sealing of the nuclear envelope (NE) by ESCRT-III / actomyosin / membrane coat / vesicle budding from membrane / positive regulation of exosomal secretion / midbody abscission / membrane fission / plasma membrane repair / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body membrane / multivesicular body assembly / regulation of mitotic spindle assembly / Flemming body / Translation of Replicase and Assembly of the Replication Transcription Complex / nervous system process / RIPK1-mediated regulated necrosis / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / viral budding via host ESCRT complex / endoplasmic reticulum exit site / Uptake and function of anthrax toxins / mitotic cytokinesis / autophagosome membrane / immunological synapse / protein polymerization / autophagosome maturation / bicellular tight junction / Pyroptosis / nuclear pore / multivesicular body / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / protein homooligomerization / kinetochore / Regulation of necroptotic cell death / autophagy / cytoplasmic side of plasma membrane / calcium-dependent protein binding / melanosome / protein transport / extracellular vesicle / ATPase binding / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / endosome / lysosomal membrane / focal adhesion / apoptotic process / lipid binding / centrosome / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
alix/aip1 like domains / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Snf7 family / Snf7 ...alix/aip1 like domains / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Snf7 family / Snf7 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death 6-interacting protein / Charged multivesicular body protein 4a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsMcCullough, J.B. / Fisher, R.D. / Whitby, F.G. / Sundquist, W.I. / Hill, C.P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: ALIX-CHMP4 interactions in the human ESCRT pathway.
Authors: McCullough, J. / Fisher, R.D. / Whitby, F.G. / Sundquist, W.I. / Hill, C.P.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Programmed cell death 6-interacting protein
B: Charged multivesicular body protein 4a peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3473
Polymers44,2542
Non-polymers921
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.668, 62.681, 76.124
Angle α, β, γ (deg.)90.00, 122.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Programmed cell death 6-interacting protein / PDCD6-interacting protein / ALG-2-interacting protein 1 / Hp95


Mass: 42735.789 Da / Num. of mol.: 1 / Fragment: BRO1 domain (UNP residues 1-358)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6IP, AIP1, ALIX, KIAA1375 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WUM4
#2: Protein/peptide Charged multivesicular body protein 4a peptide / Chromatin-modifying protein 4a / CHMP4a / Vacuolar protein-sorting-associated protein 7-1 / SNF7- 1 ...Chromatin-modifying protein 4a / CHMP4a / Vacuolar protein-sorting-associated protein 7-1 / SNF7- 1 / hSnf-1 / SNF7 homolog associated with Alix-2


Mass: 1518.643 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CHMP4A peptide chemically synthesized. The sequence is found naturally in Homo sapiens (humans).
References: UniProt: Q9BY43
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL7-110.97607
SYNCHROTRONSSRL BL11-120.98397
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 20, 2007
MARMOSAIC 325 mm CCD2CCDNov 27, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SSRLSINGLE WAVELENGTHMx-ray1
2SSRLSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.976071
20.983971
ReflectionResolution: 2.15→50 Å / Num. obs: 25024 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.15→2.23 Å / % possible all: 75.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2oew.pdb

2oew


Resolution: 2.15→32.22 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 17.458 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28403 1799 7.2 %RANDOM
Rwork0.21377 ---
all0.21868 23212 --
obs0.21868 23212 94.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å20.14 Å2
2--3.08 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.15→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 6 127 3043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222970
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9594007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3945368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78825.299134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8515540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2741511
X-RAY DIFFRACTIONr_chiral_restr0.1230.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022213
X-RAY DIFFRACTIONr_nbd_refined0.2230.21387
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22033
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.27
X-RAY DIFFRACTIONr_mcbond_it0.9711.51903
X-RAY DIFFRACTIONr_mcangle_it1.71122965
X-RAY DIFFRACTIONr_scbond_it2.44531204
X-RAY DIFFRACTIONr_scangle_it3.7994.51042
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 98 -
Rwork0.305 1302 -
obs--73.11 %

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