[English] 日本語
Yorodumi
- PDB-3c3q: ALIX Bro1-domain:CHMIP4B co-crystal structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c3q
TitleALIX Bro1-domain:CHMIP4B co-crystal structure
Components
  • Charged multivesicular body protein 4b peptide
  • Programmed cell death 6-interacting protein
KeywordsTRANSPORT PROTEIN / ALIX CHMP4B BRO1 amphipathic-helix / Cataract / Disease mutation / Protein transport / Transport / Apoptosis / Host-virus interaction
Function / homology
Function and homology information


proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / maintenance of lens transparency / regulation of extracellular exosome assembly / multivesicular body-lysosome fusion / amphisome membrane / extracellular exosome biogenesis / viral budding / vesicle fusion with vacuole ...proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / maintenance of lens transparency / regulation of extracellular exosome assembly / multivesicular body-lysosome fusion / amphisome membrane / extracellular exosome biogenesis / viral budding / vesicle fusion with vacuole / 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 / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / post-translational protein targeting to endoplasmic reticulum membrane / midbody abscission / multivesicular body sorting pathway / bicellular tight junction assembly / actomyosin / plasma membrane repair / membrane coat / membrane fission / vesicle budding from membrane / positive regulation of exosomal secretion / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of mitotic spindle assembly / multivesicular body assembly / nervous system process / Flemming body / Translation of Replicase and Assembly of the Replication Transcription Complex / exit from mitosis / RIPK1-mediated regulated necrosis / mitotic metaphase chromosome alignment / nucleus organization / Macroautophagy / viral budding via host ESCRT complex / endoplasmic reticulum exit site / Uptake and function of anthrax toxins / mitotic cytokinesis / autophagosome membrane / immunological synapse / autophagosome maturation / Pyroptosis / protein polymerization / bicellular tight junction / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / regulation of autophagy / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / protein homooligomerization / Regulation of necroptotic cell death / kinetochore / autophagy / cytoplasmic side of plasma membrane / calcium-dependent protein binding / extracellular vesicle / melanosome / protein transport / nuclear envelope / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / vesicle / endosome / cadherin binding / lysosomal membrane / focal adhesion / centrosome / apoptotic process / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
alix/aip1 like domains / ALIX V-shaped domain / Vacuolar protein-sorting protein Bro1-like / 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 / ALIX V-shaped domain / Vacuolar protein-sorting protein Bro1-like / 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 4b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 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 1.2Feb 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death 6-interacting protein
B: Charged multivesicular body protein 4b peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9863
Polymers44,8942
Non-polymers921
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.515, 62.586, 76.053
Angle α, β, γ (deg.)90.00, 121.51, 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 1-359)
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 4b peptide / Chromatin-modifying protein 4b / CHMP4b / Vacuolar protein-sorting-associated protein 7-2 / SNF7- 2 ...Chromatin-modifying protein 4b / CHMP4b / Vacuolar protein-sorting-associated protein 7-2 / SNF7- 2 / hSnf7-2 / SNF7 homolog associated with Alix 1 / hVps32


Mass: 2158.277 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CHMP4B peptide chemically synthesized. This sequence is found naturally in Homo sapiens (humans).
References: UniProt: Q9H444
#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.: 90 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2008 / Details: VARIMAX-HR Confocal Optic
RadiationMonochromator: Copper anode, varimax confocal optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 26458 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 67.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→36.64 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.881 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29024 1899 7.2 %RANDOM
Rwork0.22801 ---
all0.23238 ---
obs0.23238 24386 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.926 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20.25 Å2
2--3.35 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 6 90 3048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9594060
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7445373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.11625.435138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.63515552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.291511
X-RAY DIFFRACTIONr_chiral_restr0.120.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022249
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21431
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22047
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9381.51937
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57623002
X-RAY DIFFRACTIONr_scbond_it2.17831221
X-RAY DIFFRACTIONr_scangle_it3.314.51058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 93 -
Rwork0.326 1325 -
obs--68.11 %

+
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