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- PDB-4s1z: Crystal structure of TRABID NZF1 in complex with K29 linked di-Ub... -

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Basic information

Entry
Database: PDB / ID: 4s1z
TitleCrystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin
Components
  • Ubiquitin
  • Ubiquitin thioesterase ZRANB1
KeywordsHYDROLASE / zinc finger / Protease / Ubiquitin binding
Function / homology
Function and homology information


protein K33-linked deubiquitination / protein K29-linked deubiquitination / cysteine-type deubiquitinase activity => GO:0004843 / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / Ovarian tumor domain proteases / Degradation of beta-catenin by the destruction complex / regulation of cell morphogenesis / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / Peptide chain elongation ...protein K33-linked deubiquitination / protein K29-linked deubiquitination / cysteine-type deubiquitinase activity => GO:0004843 / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / Ovarian tumor domain proteases / Degradation of beta-catenin by the destruction complex / regulation of cell morphogenesis / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / positive regulation of Wnt signaling pathway / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / 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 / cytoskeleton organization / Endosomal Sorting Complex Required For Transport (ESCRT) / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / 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 / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
Similarity search - Function
Ankyrin ubiquitin-binding domain / Ankyrin ubiquitin-binding domain / OTU-like cysteine protease / OTU domain / OTU domain profile. / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily ...Ankyrin ubiquitin-binding domain / Ankyrin ubiquitin-binding domain / OTU-like cysteine protease / OTU domain / OTU domain profile. / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin thioesterase ZRANB1 / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsKristariyanto, Y.A. / Abdul Rehman, S.A. / Campbell, D.G. / Morrice, N.A. / Johnson, C. / Toth, R. / Kulathu, Y.
CitationJournal: Mol.Cell / Year: 2015
Title: K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of k29 polyubiquitin.
Authors: Kristariyanto, Y.A. / Abdul Rehman, S.A. / Campbell, D.G. / Morrice, N.A. / Johnson, C. / Toth, R. / Kulathu, Y.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: Ubiquitin
D: Ubiquitin
E: Ubiquitin
F: Ubiquitin thioesterase ZRANB1
G: Ubiquitin thioesterase ZRANB1
H: Ubiquitin thioesterase ZRANB1
J: Ubiquitin thioesterase ZRANB1
I: Ubiquitin thioesterase ZRANB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,70515
Polymers63,37810
Non-polymers3275
Water00
1
A: Ubiquitin
G: Ubiquitin thioesterase ZRANB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7413
Polymers12,6762
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
I: Ubiquitin thioesterase ZRANB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7413
Polymers12,6762
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin
J: Ubiquitin thioesterase ZRANB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7413
Polymers12,6762
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin
F: Ubiquitin thioesterase ZRANB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7413
Polymers12,6762
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ubiquitin
H: Ubiquitin thioesterase ZRANB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7413
Polymers12,6762
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.222, 123.971, 78.312
Angle α, β, γ (deg.)90.00, 103.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ubiquitin / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1 / Ubiquitin / 60S ribosomal protein L40


Mass: 8576.831 Da / Num. of mol.: 5 / Fragment: residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA52, UBCEP2, ZRANB1 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62987
#2: Protein/peptide
Ubiquitin thioesterase ZRANB1 / Zinc finger Ran-binding domain-containing protein 1


Mass: 4098.710 Da / Num. of mol.: 5 / Fragment: RanBP2-type 1 zinc finger domain residues 2-33 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: blood / References: UniProt: A6QP16, ubiquitinyl hydrolase 1
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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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: 3.69 Å3/Da / Density % sol: 66.68 %
Crystal growTemperature: 285 K / pH: 6.5
Details: 100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 10, 2014 / Details: COMPOUND REFRACTIVE LENSES
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→76.1 Å / Num. obs: 17755 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 85.71 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.64
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4869 / Mean I/σ(I) obs: 2.05 / % possible all: 95.3

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WWZ, 1UBQ

2wwz

1ubq


Resolution: 3.03→76.1 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 22.303 / SU ML: 0.382 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.866 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 957 5.4 %RANDOM
Rwork0.222 ---
obs0.225 16797 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.64 Å20 Å20.36 Å2
2--3.02 Å20 Å2
3----10.58 Å2
Refinement stepCycle: LAST / Resolution: 3.03→76.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3623 0 5 0 3628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.023680
X-RAY DIFFRACTIONr_bond_other_d0.0010.023356
X-RAY DIFFRACTIONr_angle_refined_deg0.841.9625019
X-RAY DIFFRACTIONr_angle_other_deg0.6937679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5635488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45425.038131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45715558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2941515
X-RAY DIFFRACTIONr_chiral_restr0.0490.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02767
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_it1.8938.9341982
X-RAY DIFFRACTIONr_mcbond_other1.8898.9341981
X-RAY DIFFRACTIONr_mcangle_it3.25413.3882460
X-RAY DIFFRACTIONr_mcangle_other3.25413.3882461
X-RAY DIFFRACTIONr_scbond_it1.7778.8571698
X-RAY DIFFRACTIONr_scbond_other1.7768.8581699
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.08713.2892560
X-RAY DIFFRACTIONr_long_range_B_refined5.2570.313962
X-RAY DIFFRACTIONr_long_range_B_other5.24970.3193963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.03→3.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 68 -
Rwork0.372 1161 -
obs--93.75 %

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