[English] 日本語
Yorodumi
- PDB-2znv: Crystal structure of human AMSH-LP DUB domain in complex with Lys... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2znv
TitleCrystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer
Components
  • (Ubiquitin) x 2
  • AMSH-like protease
KeywordsHYDROLASE/Signaling Protein / protein complex / metal binding protein / Alternative splicing / Hydrolase / Metal-binding / Metalloprotease / Protease / Ubl conjugation pathway / Zinc / Cytoplasm / Nucleus / Phosphoprotein / HYDROLASE-Signaling Protein COMPLEX
Function / homology
Function and homology information


: / : / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 ...: / : / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of expression of SLITs and ROBOs / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Alpha-protein kinase 1 signaling pathway / Pexophagy / Regulation of pyruvate metabolism / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / SCF-beta-TrCP mediated degradation of Emi1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Formation of a pool of free 40S subunits / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / SRP-dependent cotranslational protein targeting to membrane / p75NTR recruits signalling complexes / Interferon alpha/beta signaling / Negative regulation of MAPK pathway / Major pathway of rRNA processing in the nucleolus and cytosol / E3 ubiquitin ligases ubiquitinate target proteins / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Termination of translesion DNA synthesis / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Ubiquitin-dependent degradation of Cyclin D / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Downregulation of ERBB2 signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Dual incision in TC-NER / Oncogene Induced Senescence / Degradation of CRY and PER proteins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Regulation of BACH1 activity / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / TNFR1-induced NF-kappa-B signaling pathway / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / EGFR downregulation / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Inactivation of CSF3 (G-CSF) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / L13a-mediated translational silencing of Ceruloplasmin expression / MAP3K8 (TPL2)-dependent MAPK1/3 activation
Similarity search - Function
STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Ribosomal L40e family / Ribosomal_L40e ...STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / MPN domain / MPN domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin-like (UB roll) / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / AMSH-like protease
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSato, Y. / Azusa, Y. / Yamagata, A. / Mimura, H. / Wang, X. / Yamashita, M. / Ookata, K. / Nureki, O. / Iwai, K. / Komada, M. / Fukai, S.
CitationJournal: Nature / Year: 2008
Title: Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains
Authors: Sato, Y. / Yoshikawa, A. / Yamagata, A. / Mimura, H. / Yamashita, M. / Ookata, K. / Nureki, O. / Iwai, K. / Komada, M. / Fukai, S.
History
DepositionMay 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AMSH-like protease
B: Ubiquitin
C: Ubiquitin
D: AMSH-like protease
E: Ubiquitin
F: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,74311
Polymers74,4266
Non-polymers3175
Water10,899605
1
A: AMSH-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0443
Polymers19,9161
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6672
Polymers8,6051
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6921
Polymers8,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AMSH-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0443
Polymers19,9161
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6051
Polymers8,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6921
Polymers8,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.089, 97.363, 87.894
Angle α, β, γ (deg.)90.00, 97.49, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 3 types, 6 molecules ADBECF

#1: Protein AMSH-like protease / AMSH-LP / STAM-binding protein-like 1


Mass: 19916.230 Da / Num. of mol.: 2 / Fragment: MPN domain, DUB domain, UNP residues 264-436 / Mutation: E292A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCold GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q96FJ0, EC: 3.1.2.15
#2: Protein Ubiquitin


Mass: 8604.845 Da / Num. of mol.: 2 / Mutation: K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P62991, UniProt: P0CG50*PLUS
#3: Protein Ubiquitin


Mass: 8691.918 Da / Num. of mol.: 2 / Mutation: M77D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P62991, UniProt: P0CG50*PLUS

-
Non-polymers , 3 types, 610 molecules

#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 180mM tri-ammonium citrate (pH 7.0), 24% PEG 3350, 3% 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→87.04 Å / Num. all: 83683 / Num. obs: 83683 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.5 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.9
Reflection shellResolution: 1.6→1.62 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 3.2 / % possible all: 90.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2ZNR and 1ubq

2znr

1ubq


Resolution: 1.6→32.47 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.629 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The depositors have noticed that 1.7 A is out of range for the link between the GLY76 C atom and the LYS63 NZ atom. However, Refmac5 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The depositors have noticed that 1.7 A is out of range for the link between the GLY76 C atom and the LYS63 NZ atom. However, Refmac5 refined the bond length up to 1.7 A, despite of the declaration of the link record. And, actually, the electron density map shows a little bit longer bonding. So, they concluded that this atypical bonding likely occurs in their structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.21522 4051 5 %RANDOM
Rwork0.1835 ---
obs0.18511 77359 97.15 %-
all-83683 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20.15 Å2
2--0.02 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5072 0 14 605 5691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225177
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9766987
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7475643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82224.955222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86315982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3071526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023756
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.22246
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23523
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2447
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8581.53291
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4825228
X-RAY DIFFRACTIONr_scbond_it2.24832040
X-RAY DIFFRACTIONr_scangle_it3.7244.51755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 285 -
Rwork0.204 5197 -
obs--89.4 %

+
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