[English] 日本語
Yorodumi
- PDB-4s1z: Crystal structure of TRABID NZF1 in complex with K29 linked di-Ub... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...protein K33-linked deubiquitination / protein K29-linked deubiquitination / 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 / positive regulation of Wnt signaling pathway / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / cytoskeleton organization / cytosolic ribosome / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex
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. ...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 superfamily / Zinc finger RanBP2-type signature. / 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 (domestic 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 (domestic 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more