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- PDB-1wrd: Crystal structure of Tom1 GAT domain in complex with ubiquitin -

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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 / SCF-beta-TrCP mediated degradation of Emi1 / 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 / PINK1-PRKN Mediated Mitophagy / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / 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 / Cyclin D associated events in G1 / 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 / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / 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 / Activation of NF-kappaB in B cells / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / SRP-dependent cotranslational protein targeting to membrane / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling
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 conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / 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 (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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 (cattle) / Tissue: red blood cellsRed blood cell / References: UniProt: P62990, UniProt: P0CH28*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2

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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

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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

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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

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