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- PDB-4v3k: RNF38-UbcH5B-UB complex -

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Basic information

Entry
Database: PDB / ID: 4v3k
TitleRNF38-UbcH5B-UB complex
Components
  • E3 UBIQUITIN-PROTEIN LIGASE RNF38
  • POLYUBIQUITIN-C
  • UBIQUITIN-CONJUGATING ENZYME E2 D2
KeywordsLIGASE / RING E3 / E2 / UBIQUITIN
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / sperm flagellum / protein autoubiquitination / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / sperm flagellum / protein autoubiquitination / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Termination of translesion DNA synthesis / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Stabilization of p53 / EGFR downregulation
Similarity search - Function
Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like ...Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ring finger / Ubiquitin conserved site / Ubiquitin domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase RNF38
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBuetow, L. / Gabrielsen, M. / Anthony, N.G. / Dou, H. / Patel, A. / Aitkenhead, H. / Sibbet, G.J. / Smith, B.O. / Huang, D.T.
CitationJournal: Mol.Cell / Year: 2015
Title: Activation of a Primed Ring E3-E2-Ubiquitin Complex by Non-Covalent Ubiquitin.
Authors: Buetow, L. / Gabrielsen, M. / Anthony, N.G. / Dou, H. / Patel, A. / Aitkenhead, H. / Sibbet, G.J. / Smith, B.O. / Huang, D.T.
History
DepositionOct 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jul 31, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 1.3Jan 10, 2024Group: 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: UBIQUITIN-CONJUGATING ENZYME E2 D2
B: POLYUBIQUITIN-C
C: E3 UBIQUITIN-PROTEIN LIGASE RNF38
D: UBIQUITIN-CONJUGATING ENZYME E2 D2
E: POLYUBIQUITIN-C
F: E3 UBIQUITIN-PROTEIN LIGASE RNF38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,34021
Polymers69,5556
Non-polymers78515
Water6,630368
1
D: UBIQUITIN-CONJUGATING ENZYME E2 D2
E: POLYUBIQUITIN-C
F: E3 UBIQUITIN-PROTEIN LIGASE RNF38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,13910
Polymers34,7783
Non-polymers3617
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-38.6 kcal/mol
Surface area13840 Å2
MethodPISA
2
A: UBIQUITIN-CONJUGATING ENZYME E2 D2
B: POLYUBIQUITIN-C
C: E3 UBIQUITIN-PROTEIN LIGASE RNF38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,20111
Polymers34,7783
Non-polymers4238
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-34 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.620, 139.620, 70.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2 D2 / UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2 / UBIQUITIN-CONJUGATING ...UBIQUITIN CARRIER PROTEIN D2 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2 / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 / UBIQUITIN-PROTEIN LIGASE D2 / P53-REGULATED UBIQUITIN-CONJUGATING ENZYME 1 / UBCH5B


Mass: 16720.186 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-147 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: LYS85 IN CHAINS A AND D IS COVALENTLY LINKED TO GLY76 IN CHAINS B AND E, RESPECTIVELY.
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62837, ubiquitin-protein ligase
#2: Protein POLYUBIQUITIN-C / UBIQUITIN


Mass: 8922.141 Da / Num. of mol.: 2 / Fragment: RESIDUES 77-152
Source method: isolated from a genetically manipulated source
Details: LYS85 IN CHAINS A AND D IS COVALENTLY LINKED TO GLY76 IN CHAINS B AND E, RESPECTIVELY.
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG48
#3: Protein E3 UBIQUITIN-PROTEIN LIGASE RNF38 / RING FINGER PROTEIN 38 / RNF38


Mass: 9135.328 Da / Num. of mol.: 2 / Fragment: RESIDUES 439-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0F5, ubiquitin-protein ligase

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Non-polymers , 4 types, 383 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL METHIONINE IS CLEAVED DURING PURIFICATION. SER22 IS MUTATED TO ARGININE. CYS85 IS ...N-TERMINAL METHIONINE IS CLEAVED DURING PURIFICATION. SER22 IS MUTATED TO ARGININE. CYS85 IS MUTATED TO LYSINE. CONTAINS GSGGS AT THE N-TERMINUS FROM CLONING CONTAINS RESIDUES 389-465 AND GS AT THE N-TERMINUS DUE TO CLONING

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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: 2.48 Å3/Da / Density % sol: 50.33 % / Description: NONE
Crystal growDetails: 50 MM TRIS-HCL, PH 8.5 AND 2.3 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.04→34.9 Å / Num. obs: 44936 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 24.56 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.4
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3ZNI AND 1X4J

3zni

1x4j


Resolution: 2.04→34.905 Å / SU ML: 0.63 / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML
Details: IN CHAIN C, RESIDUES 389 AND 465 ARE DISORDERED. IN CHAIN F, RESIDUE 389 AND 460-465 ARE DISORDERED. RESIDUES WITH POOR SIDE CHAIN ELECTRON DENSITY WERE BUILT AS ALANINE.
RfactorNum. reflection% reflection
Rfree0.2234 2269 5.1 %
Rwork0.1807 --
obs0.1829 44936 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.741 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.8938 Å20 Å20 Å2
2--3.8938 Å20 Å2
3----7.7876 Å2
Refinement stepCycle: LAST / Resolution: 2.04→34.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 30 368 5040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084847
X-RAY DIFFRACTIONf_angle_d1.1846598
X-RAY DIFFRACTIONf_dihedral_angle_d14.2661839
X-RAY DIFFRACTIONf_chiral_restr0.095735
X-RAY DIFFRACTIONf_plane_restr0.007862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.08440.26211680.20092594X-RAY DIFFRACTION100
2.0844-2.13280.25331300.20072627X-RAY DIFFRACTION100
2.1328-2.18620.2891470.18632613X-RAY DIFFRACTION100
2.1862-2.24530.2661320.18512622X-RAY DIFFRACTION100
2.2453-2.31130.23181430.17182632X-RAY DIFFRACTION100
2.3113-2.38590.25341380.18672635X-RAY DIFFRACTION100
2.3859-2.47120.2551320.18382628X-RAY DIFFRACTION100
2.4712-2.57010.26091430.18762652X-RAY DIFFRACTION100
2.5701-2.6870.27821440.18882653X-RAY DIFFRACTION100
2.687-2.82860.23631350.18332666X-RAY DIFFRACTION100
2.8286-3.00570.2571510.19942642X-RAY DIFFRACTION100
3.0057-3.23770.23991270.18552688X-RAY DIFFRACTION100
3.2377-3.56320.21281560.17962677X-RAY DIFFRACTION100
3.5632-4.07810.17891460.16032682X-RAY DIFFRACTION100
4.0781-5.13540.1771500.1482747X-RAY DIFFRACTION100
5.1354-34.91010.20031270.20632909X-RAY DIFFRACTION100

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