[English] 日本語
Yorodumi
- PDB-1tgz: Structure of human Senp2 in complex with SUMO-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tgz
TitleStructure of human Senp2 in complex with SUMO-1
Components
  • Sentrin-specific protease 2
  • Ubiquitin-like protein SMT3C
KeywordsCELL CYCLE / HYDROLASE / SUMO / AXAM / SENP / ULP / PROTEASE
Function / homology
Function and homology information


regulation of DNA endoreduplication / SUMO-specific endopeptidase activity / trophoblast giant cell differentiation / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / labyrinthine layer development ...regulation of DNA endoreduplication / SUMO-specific endopeptidase activity / trophoblast giant cell differentiation / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / labyrinthine layer development / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of transcription initiation by RNA polymerase II / negative regulation of action potential / nuclear stress granule / small protein activating enzyme binding / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / Maturation of nucleoprotein / XY body / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / regulation of Wnt signaling pathway / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / roof of mouth development / Maturation of DENV proteins / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / cellular response to cadmium ion / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / ubiquitin-like protein ligase binding / protein sumoylation / nuclear pore / potassium channel regulator activity / Regulation of IFNG signaling / transporter activator activity / fat cell differentiation / mRNA transport / postsynaptic cytosol / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / regulation of G1/S transition of mitotic cell cycle / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / negative regulation of protein ubiquitination / positive regulation of protein ubiquitination / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / regulation of protein stability / positive regulation of protein-containing complex assembly / PML body / PKR-mediated signaling / protein destabilization / Wnt signaling pathway / Formation of Incision Complex in GG-NER / protein tag activity / heart development / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / protein transport / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / nuclear speck / nuclear body / protein stabilization / negative regulation of DNA-templated transcription / DNA repair / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily ...Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 1 / Sentrin-specific protease 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsReverter, D. / Lima, C.D.
CitationJournal: Structure / Year: 2004
Title: A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex
Authors: Reverter, D. / Lima, C.D.
History
DepositionMay 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref / 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_ref.pdbx_seq_one_letter_code / _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: Sentrin-specific protease 2
B: Ubiquitin-like protein SMT3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5537
Polymers36,0732
Non-polymers4805
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-56 kcal/mol
Surface area14750 Å2
MethodPISA
2
A: Sentrin-specific protease 2
B: Ubiquitin-like protein SMT3C
hetero molecules

A: Sentrin-specific protease 2
B: Ubiquitin-like protein SMT3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,10614
Polymers72,1454
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area5340 Å2
ΔGint-127 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.163, 111.163, 143.106
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522

-
Components

#1: Protein Sentrin-specific protease 2 / E.C.3.4.22.- / Sentrin/SUMO-specific protease SENP2 / SMT3-specific isopeptidase 2 / Smt3ip2 / Axam2


Mass: 26787.084 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Details: CHEMICALLY MODIFIED TO PROMOTE BOND BETWEEN CYS548 AND SUMO-1 GLY97
Source: (gene. exp.) Homo sapiens (human) / Gene: SENP2, KIAA1331 / Plasmid: T7 BASED / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CP RIL
References: UniProt: Q9HC62, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Ubiquitin-like protein SMT3C / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein UBL1 / Ubiquitin-related protein ...Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein UBL1 / Ubiquitin-related protein SUMO-1 / GAP modifying protein 1 / GMP1 / Sentrin


Mass: 9285.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBL1, SMT3H3, SMT3C / Plasmid: T7 BASED / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CP RIL / References: UniProt: P63165
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 15, 2004
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 16622 / Num. obs: 15675 / % possible obs: 94.3 % / Observed criterion σ(I): -2 / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.93 Å / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 0.9 / % possible all: 84.8

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1814230.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 612 5 %RANDOM
Rwork0.226 ---
obs0.2261 12149 90.8 %-
all-13430 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.7793 Å2 / ksol: 0.34907 e/Å3
Displacement parametersBiso mean: 54.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å28.16 Å20 Å2
2--0.1 Å20 Å2
3----0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 25 81 2608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.434 81 5.1 %
Rwork0.391 1495 -
obs--72.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

+
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