[English] 日本語
Yorodumi
- PDB-3obq: Crystal Structure of the Tsg101 UEV domain in complex with a huma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3obq
TitleCrystal Structure of the Tsg101 UEV domain in complex with a human HRS PSAP peptide
Components
  • Hepatocyte growth factor-regulated tyrosine kinase substrate
  • Tumor susceptibility gene 101 protein
KeywordsPROTEIN TRANSPORT / Protein Transprot / Ubiquitin Binding
Function / homology
Function and homology information


Inhibition of membrane repair / ESCRT-0 complex / positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / membrane invagination / ESCRT I complex / regulation of extracellular exosome assembly / negative regulation of epidermal growth factor-activated receptor activity / viral budding ...Inhibition of membrane repair / ESCRT-0 complex / positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / membrane invagination / ESCRT I complex / regulation of extracellular exosome assembly / negative regulation of epidermal growth factor-activated receptor activity / viral budding / regulation of MAP kinase activity / phagocytic vesicle lumen / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to lysosome / RHOBTB3 ATPase cycle / membrane fission / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body membrane / multivesicular body assembly / protein localization to membrane / endocytic recycling / Flemming body / virion binding / negative regulation of platelet-derived growth factor receptor signaling pathway / endosomal transport / Lysosome Vesicle Biogenesis / endosome to lysosome transport / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / regulation of protein catabolic process / viral budding via host ESCRT complex / ubiquitin-like protein ligase binding / viral release from host cell / RHOU GTPase cycle / autophagosome maturation / keratinocyte differentiation / Prevention of phagosomal-lysosomal fusion / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / negative regulation of angiogenesis / phosphatidylinositol binding / InlB-mediated entry of Listeria monocytogenes into host cell / HCMV Late Events / ubiquitin binding / regulation of cell growth / macroautophagy / EGFR downregulation / Late endosomal microautophagy / Budding and maturation of HIV virion / protein modification process / Negative regulation of MET activity / receptor internalization / transcription corepressor activity / calcium-dependent protein binding / late endosome / Cargo recognition for clathrin-mediated endocytosis / late endosome membrane / Clathrin-mediated endocytosis / early endosome membrane / early endosome / lysosome / regulation of cell cycle / endosome membrane / Ub-specific processing proteases / endosome / negative regulation of cell population proliferation / protein domain specific binding / cell division / centrosome / ubiquitin protein ligase binding / positive regulation of gene expression / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / DNA binding / extracellular exosome / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Hepatocyte growth factor-regulated tyrosine kinase substrate, helical domain / Hepatocyte growth factor-regulated tyrosine kinase substrate / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / : / UEV domain / UEV domain profile. ...Hepatocyte growth factor-regulated tyrosine kinase substrate, helical domain / Hepatocyte growth factor-regulated tyrosine kinase substrate / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / : / UEV domain / UEV domain profile. / ESCRT assembly domain / FYVE zinc finger / VHS domain / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / ENTH/VHS / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor-regulated tyrosine kinase substrate / Tumor susceptibility gene 101 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsIm, Y.J. / Hurley, J.H.
CitationJournal: Structure / Year: 2010
Title: Crystallographic and Functional Analysis of the ESCRT-I /HIV-1 Gag PTAP Interaction.
Authors: Im, Y.J. / Kuo, L. / Ren, X. / Burgos, P.V. / Zhao, X.Z. / Liu, F. / Burke, T.R. / Bonifacino, J.S. / Freed, E.O. / Hurley, J.H.
History
DepositionAug 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 27, 2015Group: Source and taxonomy
Revision 1.3Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tumor susceptibility gene 101 protein
B: Hepatocyte growth factor-regulated tyrosine kinase substrate


Theoretical massNumber of molelcules
Total (without water)17,3792
Polymers17,3792
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.654, 45.126, 87.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Tumor susceptibility gene 101 protein / ESCRT-I complex subunit TSG101


Mass: 16501.195 Da / Num. of mol.: 1 / Fragment: N-terminal UEV domain (UNP residues 2 to 145) / Mutation: 43VFNDGS48 -> GTG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: pGST-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q99816
#2: Protein/peptide Hepatocyte growth factor-regulated tyrosine kinase substrate / Protein pp110 / Hrs


Mass: 878.022 Da / Num. of mol.: 1 / Fragment: PSAP sequence (nonapeptide) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14964
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsENGINEERED MUTATION 43VFNDGS48 -> GTG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-NaOH (pH 7.5), 25% PEG 3350, 0.2M Sodium Nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 26634 / Num. obs: 25924 / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 28.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1265 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F0R

2f0r


Resolution: 1.4→31.42 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 815094.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1289 5 %RANDOM
Rwork0.207 ---
all0.21 27186 --
obs0.207 25897 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.5815 Å2 / ksol: 0.34091 e/Å3
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.77 Å20 Å2
3---0.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.4→31.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 0 198 1393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 218 5.2 %
Rwork0.242 3965 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

+
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