[English] 日本語
Yorodumi
- PDB-1wrd: Crystal structure of Tom1 GAT domain in complex with ubiquitin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wrd
TitleCrystal structure of Tom1 GAT domain in complex with ubiquitin
Components
  • Target of Myb protein 1
  • Ubiquitin
KeywordsPROTEIN TRANSPORT/SIGNALING PROTEIN / THREE-HELIX BUNDLE / UBIQUITIN-BINDING PROTEIN / PROTEIN TRANSPORT-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / : / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling ...myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / : / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Negative regulation of FLT3 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of pyruvate metabolism / SCF-beta-TrCP mediated degradation of Emi1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Ovarian tumor domain proteases / Cyclin D associated events in G1 / Regulation of BACH1 activity / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Formation of Incision Complex in GG-NER / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Inactivation of CSF3 (G-CSF) signaling / Termination of translesion DNA synthesis / Iron uptake and transport / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / G2/M Checkpoints
Similarity search - Function
Target of Myb protein 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #160 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM ...Target of Myb protein 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #160 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / ENTH/VHS / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Target of Myb1 membrane trafficking protein / Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsAkutsu, M. / Kawasaki, M. / Katoh, Y. / Shiba, T. / Yamaguchi, Y. / Kato, R. / Kato, K. / Nakayama, K. / Wakatsuki, S.
CitationJournal: Febs Lett. / Year: 2005
Title: Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain.
Authors: Akutsu, M. / Kawasaki, M. / Katoh, Y. / Shiba, T. / Yamaguchi, Y. / Kato, R. / Kato, K. / Nakayama, K. / Wakatsuki, S.
History
DepositionOct 14, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Target of Myb protein 1
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)20,3792
Polymers20,3792
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Target of Myb protein 1
B: Ubiquitin
x 24


Theoretical massNumber of molelcules
Total (without water)489,10348
Polymers489,10348
Non-polymers00
Water86548
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_665-y+1,-x+1,-z1
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_655-y+1,z+1/2,-x+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation36_654-y+1,-z+1/2,x-1/21
crystal symmetry operation41_555x,z+1/2,-y+1/21
crystal symmetry operation42_654-x+1,z+1/2,y-1/21
crystal symmetry operation43_655-x+1,-z+1/2,-y+1/21
crystal symmetry operation44_554x,-z+1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_565z+1/2,-x+1,-y+1/21
crystal symmetry operation55_564-z+1/2,-x+1,y-1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation69_555z+1/2,y,-x+1/21
crystal symmetry operation70_564z+1/2,-y+1,x-1/21
crystal symmetry operation71_554-z+1/2,y,x-1/21
crystal symmetry operation72_565-z+1/2,-y+1,-x+1/21
Buried area96140 Å2
ΔGint-362 kcal/mol
Surface area167620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.317, 168.317, 168.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-409-

HOH

-
Components

#1: Protein Target of Myb protein 1 / Tom1


Mass: 11802.447 Da / Num. of mol.: 1 / Fragment: GAT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: O60784
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: red blood cells / References: UniProt: P62990, UniProt: P0CH28*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium citrate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A10.978
SYNCHROTRONPhoton Factory AR-NW12A20.9791, 0.9794, 0.985
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 15, 2004
ADSC QUANTUM 2102CCDJun 2, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.97911
30.97941
40.9851
ReflectionResolution: 1.75→50 Å / Num. all: 21120 / Num. obs: 20997 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Redundancy: 14.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.9
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 8.2 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
CNS1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→28.45 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1059 -RANDOM
Rwork0.213 ---
all0.214 21120 --
obs0.214 20997 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.75→28.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 0 289 1677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.031

+
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