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- PDB-5aiu: A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink) -

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Basic information

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


regulation of spindle assembly / regulation of kinetochore assembly / SUMO polymer binding / Antigen processing: Ubiquitination & Proteasome degradation / : / response to human chorionic gonadotropin / UBC13-UEV1A complex / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity ...regulation of spindle assembly / regulation of kinetochore assembly / SUMO polymer binding / Antigen processing: Ubiquitination & Proteasome degradation / : / response to human chorionic gonadotropin / UBC13-UEV1A complex / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / DNA double-strand break processing / positive regulation of protein K63-linked ubiquitination / cellular response to hydroxyurea / protein K6-linked ubiquitination / cellular response to arsenic-containing substance / cellular response to testosterone stimulus / protein K11-linked ubiquitination / response to arsenic-containing substance / ubiquitin conjugating enzyme binding / postreplication repair / negative regulation of protein localization to chromatin / positive regulation of double-strand break repair / E2 ubiquitin-conjugating enzyme / positive regulation of intracellular signal transduction / nuclear androgen receptor binding / ubiquitin conjugating enzyme activity / cellular response to cytokine stimulus / protein K63-linked ubiquitination / antiviral innate immune response / nucleosome binding / protein K48-linked ubiquitination / regulation of DNA repair / 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 / negative regulation of TORC1 signaling / 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 / positive regulation of DNA repair / 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 / TBP-class protein binding / 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 / ubiquitin binding / 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
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
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.21 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 / Structure summary
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 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
E: UBIQUITIN-CONJUGATING ENZYME E2 N
F: POLYUBIQUITIN-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,05415
Polymers66,4195
Non-polymers63410
Water59433
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-13.7 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.190, 169.210, 52.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-2010-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21E
12C
22F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B2 - 151
2010E2 - 151
1020C1 - 76
2020F1 - 76

NCS ensembles :
ID
1
2

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Components

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Protein , 3 types, 5 molecules ABECF

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE RNF4 / RING FINGER PROTEIN 4 / SMALL NUCLEAR RING FINGER PROTEIN / PROTEIN SNURF / "RING DOMAIN / UBC13"


Mass: 14758.155 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, UNP RESIDUES 131-194,131-194 / Mutation: YES
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 / UBC13


Mass: 17253.832 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CHAIN B COVALENTLY LINKED TO CHAINS C, CHAIN E IS COVALENTLY LINKED TO CHAIN F
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
Details: CHAIN B COVALENTLY LINKED TO CHAINS C, CHAIN E IS COVALENTLY LINKED TO CHAIN F
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0CG48

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Non-polymers , 3 types, 43 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

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 ARTEFACT 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

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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: 2.32 Å3/Da / Density % sol: 46.96 % / Description: NONE
Crystal growDetails: 1,2-ETHANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: RIGAKU SATURN / Detector: IMAGE PLATE / Date: Nov 24, 2014
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.21→32.2 Å / Num. obs: 29485 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9
Reflection shellResolution: 2.21→2.26 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 7.8 / % possible all: 74.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.21→32.02 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.89 / SU B: 6.731 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.233 / 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.25541 1536 5.1 %RANDOM
Rwork0.21656 ---
obs0.21857 28823 94.94 %-
Solvent computationIon probe radii: 0.85 Å / Shrinkage radii: 0.75 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.191 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å20 Å2
2---1.18 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.21→32.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 28 33 4585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194654
X-RAY DIFFRACTIONr_bond_other_d0.0040.024567
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9846288
X-RAY DIFFRACTIONr_angle_other_deg1.0423.00310521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82924.384203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54315830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0671533
X-RAY DIFFRACTIONr_chiral_restr0.0940.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215140
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02989
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_it1.7132.2642295
X-RAY DIFFRACTIONr_mcbond_other1.7132.2642294
X-RAY DIFFRACTIONr_mcangle_it2.6813.3832857
X-RAY DIFFRACTIONr_mcangle_other2.683.3832858
X-RAY DIFFRACTIONr_scbond_it2.2142.5162359
X-RAY DIFFRACTIONr_scbond_other2.2142.5162359
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5483.6653431
X-RAY DIFFRACTIONr_long_range_B_refined4.87517.6924949
X-RAY DIFFRACTIONr_long_range_B_other4.87517.6944949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B90900.09
12E90900.09
21C48780.08
22F48780.08
LS refinement shellResolution: 2.206→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 83 -
Rwork0.232 1629 -
obs--74.43 %

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