[English] 日本語
Yorodumi
- PDB-3c3o: ALIX Bro1-domain:CHMIP4A co-crystal structure -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of extracellular exosome assembly / plasma membrane tubulation / amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole ...proteinase activated receptor binding / membrane invagination / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / plasma membrane tubulation / amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole / extracellular exosome biogenesis / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / regulation of membrane permeability / late endosome to vacuole transport via multivesicular body sorting pathway / regulation of centrosome duplication / Sealing of the nuclear envelope (NE) by ESCRT-III / nuclear membrane reassembly / post-translational protein targeting to endoplasmic reticulum membrane / midbody abscission / multivesicular body sorting pathway / vesicle budding from membrane / bicellular tight junction assembly / membrane coat / actomyosin / membrane fission / plasma membrane repair / multivesicular body membrane / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / nervous system process / Translation of Replicase and Assembly of the Replication Transcription Complex / Flemming body / nucleus organization / RIPK1-mediated regulated necrosis / Macroautophagy / mitotic metaphase chromosome alignment / viral budding via host ESCRT complex / autophagosome maturation / autophagosome membrane / mitotic cytokinesis / Uptake and function of anthrax toxins / immunological synapse / protein polymerization / bicellular tight junction / Pyroptosis / endoplasmic reticulum exit site / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / protein homooligomerization / Budding and maturation of HIV virion / cytoplasmic side of plasma membrane / Regulation of necroptotic cell death / kinetochore / autophagy / calcium-dependent protein binding / extracellular vesicle / melanosome / protein transport / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / ATPase binding / endosome / lysosomal membrane / focal adhesion / centrosome / lipid binding / apoptotic process / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
alix/aip1 like domains / Vacuolar protein-sorting protein Bro1-like / 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 ...alix/aip1 like domains / Vacuolar protein-sorting protein Bro1-like / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more