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- PDB-2xbb: Nedd4 HECT:Ub complex -

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Basic information

Entry
Database: PDB / ID: 2xbb
TitleNedd4 HECT:Ub complex
Components
  • E3 UBIQUITIN-PROTEIN LIGASE NEDD4
  • UBIQUITIN
KeywordsLIGASE/PROTEIN BINDING / LIGASE-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of sodium ion transport / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex ...formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of sodium ion transport / 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 / regulation of potassium ion transmembrane transporter activity / viral budding / 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
Similarity search - Function
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. ...Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / C2 domain superfamily / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / E3 ubiquitin-protein ligase NEDD4 / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
BOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsMaspero, E. / Cecatiello, V. / Musacchio, A. / Polo, S. / Pasqualato, S.
CitationJournal: Embo Rep. / Year: 2011
Title: Structure of the Hect:Ubiquitin Complex and its Role in Ubiquitin Chain Elongation
Authors: Maspero, E. / Mari, S. / Valentini, E. / Musacchio, A. / Fish, A. / Pasqualato, S. / Polo, S.
History
DepositionApr 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE NEDD4
B: E3 UBIQUITIN-PROTEIN LIGASE NEDD4
C: UBIQUITIN
D: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9026
Polymers108,7184
Non-polymers1842
Water2,432135
1
A: E3 UBIQUITIN-PROTEIN LIGASE NEDD4
C: UBIQUITIN


Theoretical massNumber of molelcules
Total (without water)54,3592
Polymers54,3592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-8.6 kcal/mol
Surface area22480 Å2
MethodPISA
2
B: E3 UBIQUITIN-PROTEIN LIGASE NEDD4
D: UBIQUITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5434
Polymers54,3592
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-8.2 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.188, 49.276, 132.627
Angle α, β, γ (deg.)90.00, 108.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND ((RESSEQ 522:699))
211CHAIN B AND ((RESSEQ 522:699))
112CHAIN A AND ((RESSEQ 724:778))
212CHAIN B AND ((RESSEQ 724:778))
113CHAIN A AND ((RESSEQ 785:828))
213CHAIN B AND ((RESSEQ 785:828))
114CHAIN A AND ((RESSEQ 850:891))
214CHAIN B AND ((RESSEQ 850:891))
115CHAIN C AND ((RESSEQ 1:76))
215CHAIN D AND ((RESSEQ 1:76))

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(0.99908, 0.01496, 0.04012), (0.01315, -0.9989, 0.04497), (0.04075, -0.0444, -0.99818)19.13558, -11.68013, 189.51556
2given(0.99198, -0.01871, -0.12498), (-0.0336, -0.99243, -0.11808), (-0.12182, 0.12134, -0.98511)27.24666, -2.15263, 189.18298
3given(0.99873, 0.04391, -0.02477), (0.04032, -0.99065, -0.13036), (-0.03027, 0.12919, -0.99116)25.07213, 2.97213, 188.38895

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE NEDD4 / NEDD-4 / NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED PROTEIN 4 / CELL ...NEDD-4 / NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED PROTEIN 4 / CELL PROLIFERATION-INDUCING GENE 53 PROTEIN


Mass: 45782.109 Da / Num. of mol.: 2 / Fragment: HECT DOMAIN, RESIDUES 519-900
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: P46934, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein UBIQUITIN /


Mass: 8576.831 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Cell: ERYTHROCYTE / References: UniProt: P0CG53, UniProt: P63048*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 % / Description: NONE
Crystal growpH: 7.5
Details: 100 MM NA-HEPES, PH 7.5, 10% PEG 2000 MME, 5 MM TCEP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 29856 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 47.17 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.2
Reflection shellResolution: 2.68→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.9 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_542)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2XBF AND 1UBI

2xbf

1ubi


Resolution: 2.68→43.59 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1515 5.1 %
Rwork0.205 --
obs0.207 29840 98.2 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.85 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.2136 Å20 Å2-5.7949 Å2
2--14.1627 Å20 Å2
3----2.9491 Å2
Refinement stepCycle: LAST / Resolution: 2.68→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7512 0 12 135 7659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037704
X-RAY DIFFRACTIONf_angle_d0.55310378
X-RAY DIFFRACTIONf_dihedral_angle_d13.6912912
X-RAY DIFFRACTIONf_chiral_restr0.0421076
X-RAY DIFFRACTIONf_plane_restr0.0021340
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1516X-RAY DIFFRACTIONPOSITIONAL
12B1516X-RAY DIFFRACTIONPOSITIONAL0.421
21A474X-RAY DIFFRACTIONPOSITIONAL
22B474X-RAY DIFFRACTIONPOSITIONAL0.323
31A386X-RAY DIFFRACTIONPOSITIONAL
32B386X-RAY DIFFRACTIONPOSITIONAL0.415
41A357X-RAY DIFFRACTIONPOSITIONAL
42B357X-RAY DIFFRACTIONPOSITIONAL0.269
51C602X-RAY DIFFRACTIONPOSITIONAL
52D602X-RAY DIFFRACTIONPOSITIONAL0.561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.684-2.77990.40221360.31462663X-RAY DIFFRACTION93
2.7799-2.89120.35291230.28152838X-RAY DIFFRACTION98
2.8912-3.02270.32741580.26072778X-RAY DIFFRACTION98
3.0227-3.1820.29711590.24092805X-RAY DIFFRACTION99
3.182-3.38130.26011410.22262840X-RAY DIFFRACTION99
3.3813-3.64230.23261590.20392831X-RAY DIFFRACTION99
3.6423-4.00860.29151490.19972848X-RAY DIFFRACTION99
4.0086-4.58810.21491510.16912885X-RAY DIFFRACTION99
4.5881-5.77840.20041640.18052859X-RAY DIFFRACTION99
5.7784-43.59910.20631750.1822978X-RAY DIFFRACTION99

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