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- PDB-6t7f: RCR E3 ligase E2-Ubiquitin transthiolation intermediate -

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Basic information

Entry
Database: PDB / ID: 6t7f
TitleRCR E3 ligase E2-Ubiquitin transthiolation intermediate
Components
  • E3 ubiquitin-protein ligase MYCBP2
  • Polyubiquitin-C
  • Ubiquitin-conjugating enzyme E2 D3
KeywordsLIGASE / RING-Cys-Relay / RCR / Activity based probe / Ubiquitination / threonine E3 ligase.
Function / homology
Function and homology information


RCR-type E3 ubiquitin transferase / regulation of axon guidance / regulation of synaptic assembly at neuromuscular junction / branchiomotor neuron axon guidance / central nervous system projection neuron axonogenesis / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion ...RCR-type E3 ubiquitin transferase / regulation of axon guidance / regulation of synaptic assembly at neuromuscular junction / branchiomotor neuron axon guidance / central nervous system projection neuron axonogenesis / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / neuromuscular process / regulation of cytoskeleton organization / protein monoubiquitination / ubiquitin conjugating enzyme activity / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / 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 / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / 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 / Pexophagy / InlA-mediated entry of Listeria monocytogenes into host cells / 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 / NF-kB is activated and signals survival / Regulation of PTEN localization / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Gap-filling DNA repair synthesis and ligation in GG-NER / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / guanyl-nucleotide exchange factor activity / 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 / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / axon guidance / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / 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 / Recognition of DNA damage by PCNA-containing replication complex
Similarity search - Function
PHR / PHR domain superfamily / PHR domain / Bacterial SH3 domain / Regulator of chromosome condensation (RCC1) repeat / SH3-like domain, bacterial-type / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. ...PHR / PHR domain superfamily / PHR domain / Bacterial SH3 domain / Regulator of chromosome condensation (RCC1) repeat / SH3-like domain, bacterial-type / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Ring finger domain / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / 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 / Ubiquitin conserved site / Ubiquitin domain / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Immunoglobulin E-set / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-LWZ / E3 ubiquitin-protein ligase MYCBP2 / Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsMabbitt, P.D. / Virdee, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UU_12016/8 United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural basis for RING-Cys-Relay E3 ligase activity and its role in axon integrity.
Authors: Mabbitt, P.D. / Loreto, A. / Dery, M.A. / Fletcher, A.J. / Stanley, M. / Pao, K.C. / Wood, N.T. / Coleman, M.P. / Virdee, S.
History
DepositionOct 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase MYCBP2
B: Ubiquitin-conjugating enzyme E2 D3
C: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,22210
Polymers54,6123
Non-polymers6117
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, cross-linking, Three way crosslink between MYCBP2, UBE2D3 and Ubiquitin
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-13 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.008, 179.008, 87.276
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein E3 ubiquitin-protein ligase MYCBP2 / Myc-binding protein 2 / Protein associated with Myc


Mass: 29410.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYCBP2, KIAA0916, PAM / Production host: Escherichia coli (E. coli)
References: UniProt: O75592, Transferases; Acyltransferases; Aminoacyltransferases
#2: Protein Ubiquitin-conjugating enzyme E2 D3 / (E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


Mass: 16895.154 Da / Num. of mol.: 1 / Mutation: C21S, S22R, C107S, C111S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D3, UBC5C, UBCH5C / Production host: Escherichia coli (E. coli)
References: UniProt: P61077, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#3: Protein Polyubiquitin-C


Mass: 8305.532 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chemically modified ubiquitin residues 1-73 / Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48

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Non-polymers , 3 types, 48 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-LWZ / 3,3-bis(sulfanyl)-~{N}-(1~{H}-1,2,3-triazol-4-ylmethyl)propanamide


Mass: 218.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N4OS2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.85 M sodium citrate, 100 mM sodium chloride, 100 mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2737 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2737 Å / Relative weight: 1
ReflectionResolution: 2.58→48.69 Å / Num. obs: 16676 / % possible obs: 98.4 % / Redundancy: 17.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.025 / Rrim(I) all: 0.106 / Net I/σ(I): 20.7
Reflection shellResolution: 2.58→2.69 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1868 / CC1/2: 0.434 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O6C, 5EGG, 1UBQ

5o6c

5egg

1ubq


Resolution: 2.58→48.69 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 14.324 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.042 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 895 5.4 %RANDOM
Rwork0.1951 ---
obs0.1983 15778 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.19 Å2 / Biso mean: 78.285 Å2 / Biso min: 40.22 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å2-1.31 Å20 Å2
2---2.62 Å20 Å2
3---8.52 Å2
Refinement stepCycle: final / Resolution: 2.58→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 19 41 3717
Biso mean--105.62 62.73 -
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123789
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.6555139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7965468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.45621.443194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.10615597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.621527
X-RAY DIFFRACTIONr_chiral_restr0.1060.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022939
LS refinement shellResolution: 2.58→2.647 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 59 -
Rwork0.345 1038 -
all-1097 -
obs--89.41 %

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