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- PDB-5ait: A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide cro... -

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Basic information

Entry
Database: PDB / ID: 5ait
TitleA complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink)
Components
  • E3 UBIQUITIN-PROTEIN LIGASE RNF4
  • POLYUBIQUITIN-C
  • UBIQUITIN-CONJUGATING ENZYME E2 N
  • UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2
KeywordsLIGASE/SIGNALING PROTEIN / LIGASE-SIGNALING PROTEIN COMPLEX / COMPLEX
Function / homology
Function and homology information


regulation of spindle assembly / regulation of kinetochore assembly / SUMO polymer binding / Antigen processing: Ubiquitination & Proteasome degradation / error-free postreplication DNA repair / : / response to human chorionic gonadotropin / UBC13-UEV1A complex / UBC13-MMS2 complex / Translesion synthesis by REV1 ...regulation of spindle assembly / regulation of kinetochore assembly / SUMO polymer binding / Antigen processing: Ubiquitination & Proteasome degradation / error-free postreplication DNA repair / : / response to human chorionic gonadotropin / UBC13-UEV1A complex / UBC13-MMS2 complex / 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 / ubiquitin conjugating enzyme complex / Activation of NF-kappaB in B cells / 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 / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins
Similarity search - Function
: / RNF4, RING finger, HC subclass / Zinc finger, C3HC4 type (RING finger) / 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 ...: / RNF4, RING finger, HC subclass / Zinc finger, C3HC4 type (RING finger) / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / 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
E3 ubiquitin-protein ligase RNF4 / Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 N / Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
BOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.4 Å
AuthorsBranigan, E. / Naismith, J.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structural Basis for the Ring Catalyzed Synthesis of K63 Linked Ubiquitin Chains
Authors: Branigan, E. / Plechanovova, A. / Jaffray, E. / Naismith, J.H. / Hay, R.T.
History
DepositionFeb 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references / Other / Structure summary
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Jul 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE RNF4
B: UBIQUITIN-CONJUGATING ENZYME E2 N
C: POLYUBIQUITIN-C
D: UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2
E: UBIQUITIN-CONJUGATING ENZYME E2 N
F: POLYUBIQUITIN-C
G: UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,69911
Polymers99,4377
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-47.3 kcal/mol
Surface area52790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.580, 77.580, 328.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE RNF4 / RING FINGER PROTEIN 4 / SMALL NUCLEAR RING FINGER PROTEIN / P ROTEIN SNURF / RING DOMAIN


Mass: 14758.155 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, UNP RESIDUES 131-194,131-194
Source method: isolated from a genetically manipulated source
Details: THE RING DOMAIN IS DUPLICATED BUT AS A FUSED DIMER. THAT IS THE SEQUENCE OF THE RING DOMAIN FROM RNF4 (RESIDUES 131 TO 194) IS LINKED BY A SINGLE GLYCINE RESIDUE TO ANOTHER RING DOMAIN (RESIDUES 131 TO 194).
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O88846, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein UBIQUITIN-CONJUGATING ENZYME E2 N / BENDLESS-LIKE UBIQUITIN-CONJUGATING ENZYME / UBC13 / UBCH13 / UBIQUITIN CARRIER PROTEIN N / ...BENDLESS-LIKE UBIQUITIN-CONJUGATING ENZYME / UBC13 / UBCH13 / UBIQUITIN CARRIER PROTEIN N / UBIQUITIN-PROTEIN LIGASE N


Mass: 17253.832 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61088, ubiquitin-protein ligase
#3: Protein POLYUBIQUITIN-C


Mass: 8576.831 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0CH28
#4: Protein UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2 / DDVIT 1 / ENTEROCYTE DIFFERENTIATION-ASSOCIATED FACTOR 1 / ED AF-1 / ENTEROCYTE DIFFERENTIATION- ...DDVIT 1 / ENTEROCYTE DIFFERENTIATION-ASSOCIATED FACTOR 1 / ED AF-1 / ENTEROCYTE DIFFERENTIATION-PROMOTING FACTOR 1 / EDPF-1 / MMS2 HOMOLOG / VITAMIN D3-INDUCIBLE PROTEIN


Mass: 16508.861 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q15819
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHIS IS A HEAD TO TAIL FUSION OF TWO RING DOMAINS. THE GAMG AT THE N-TERMINUS IS A CLONING ARTEFACT ...THIS IS A HEAD TO TAIL FUSION OF TWO RING DOMAINS. THE GAMG AT THE N-TERMINUS IS A CLONING ARTEFACT THE ACTIVE SITE C87 HAS BEEN MUTATED TO K87 FOR ATTACHMENT OF UBIQUITIN (MOLECULES IN CHAIN C AND F). SECOND MUTATION K92 TO A. THE N-TERMINAL GA IS A CLONING ARTIFACT NOTE TERMINAL GLY OF CHAIN C IS ATTACHED TO LYS 87 OF CHAIN B CHAIN F TERMINAL GLY IS ATTACHED TO CHAIN E LYS 87 THE GA ARE CLONING ARTEFACTS

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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: 2.87 Å3/Da / Density % sol: 60 %
Description: DATA ARE 96 TO 3.5. THE DETECTOR WAS POSITION TO AVOID OVERLAP, DATA IN CORNERS 3.49 TO 3.4 ARE INCOMPLETE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.4→67 Å / Num. obs: 14922 / % possible obs: 88.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 25.7
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / % possible all: 35

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.4→67.19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 37.502 / SU ML: 0.575 / Cross valid method: THROUGHOUT / ESU R Free: 0.711 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. THE ISOPEPTIDE LINKAGE WAS INCLUDED AS A RESTRAINT. THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. THE ISOPEPTIDE LINKAGE WAS INCLUDED AS A RESTRAINT. THE PDB FILE CANONOCAL PDB SHOWS THE BIOLOGICAL CONTEXT, HOWEVER DUE TO THE CHEMICAL CROSS LINK CANONICAL IS NOT FOUND IN THE CRYSTAL PER SE.
RfactorNum. reflection% reflectionSelection details
Rfree0.28617 753 5.1 %RANDOM
Rwork0.20771 ---
obs0.21156 14864 89.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 139.669 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20.44 Å20 Å2
2--0.88 Å20 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 3.4→67.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6738 0 4 0 6742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196893
X-RAY DIFFRACTIONr_bond_other_d0.0020.026717
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9839332
X-RAY DIFFRACTIONr_angle_other_deg2.343.00215497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5845844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25724.314306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.832151248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8241552
X-RAY DIFFRACTIONr_chiral_restr0.0720.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217678
X-RAY DIFFRACTIONr_gen_planes_other0.010.021478
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it11.75213.2313397
X-RAY DIFFRACTIONr_mcbond_other11.74913.2313396
X-RAY DIFFRACTIONr_mcangle_it17.50419.854234
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it13.814.4413494
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 23 -
Rwork0.349 407 -
obs--35.51 %

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