[English] 日本語
Yorodumi
- PDB-5aek: Crystal structure of the human SENP2 C548S in complex with the hu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aek
TitleCrystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W
Components
  • SENTRIN-SPECIFIC PROTEASE 2
  • SMALL UBIQUITIN-RELATED MODIFIER 1
KeywordsHYDROLASE / SUMO / SENP / FOLDING EVOLUTION
Function / homology
Function and homology information


regulation of DNA endoreduplication / SUMO-specific endopeptidase activity / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / trophoblast giant cell differentiation / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed ...regulation of DNA endoreduplication / SUMO-specific endopeptidase activity / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / 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) / negative regulation of delayed rectifier potassium channel activity / PML body organization / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / nuclear stress granule / small protein activating enzyme binding / labyrinthine layer development / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / XY body / regulation of calcium ion transmembrane transport / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of Wnt signaling pathway / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / fat cell differentiation / cellular response to cadmium ion / roof of mouth development / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / regulation of G1/S transition of mitotic cell cycle / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / mRNA transport / Regulation of IFNG signaling / postsynaptic cytosol / nuclear pore / transporter activator activity / : / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / negative regulation of protein ubiquitination / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / positive regulation of protein ubiquitination / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PML body / protein destabilization / PKR-mediated signaling / regulation of protein stability / Wnt signaling pathway / protein tag activity / Formation of Incision Complex in GG-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / heart development / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein stabilization / nuclear speck / nuclear body / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / 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: 3 Å
AuthorsGallego, P. / Grana-Montes, R. / Espargaro, A. / Castillo, V. / Torrent, J. / Lange, R. / Papaleo, E. / Lindorff-Larsend, K. / Ventura, S. / Reverter, D.
CitationJournal: To be Published
Title: Stepping Back and Forward on Sumo Folding Evolution
Authors: Grana-Montes, R. / Gallego, P. / Espargaro, A. / Castillo, V. / Torrent, J. / Lange, R. / Reverter, D. / Papaleo, E. / Lindorff-Larsend, K. / Ventura, S.
History
DepositionDec 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SENTRIN-SPECIFIC PROTEASE 2
B: SMALL UBIQUITIN-RELATED MODIFIER 1
C: SENTRIN-SPECIFIC PROTEASE 2
D: SMALL UBIQUITIN-RELATED MODIFIER 1
E: SENTRIN-SPECIFIC PROTEASE 2
F: SMALL UBIQUITIN-RELATED MODIFIER 1
G: SENTRIN-SPECIFIC PROTEASE 2
H: SMALL UBIQUITIN-RELATED MODIFIER 1
I: SENTRIN-SPECIFIC PROTEASE 2
J: SMALL UBIQUITIN-RELATED MODIFIER 1
K: SENTRIN-SPECIFIC PROTEASE 2
L: SMALL UBIQUITIN-RELATED MODIFIER 1
M: SENTRIN-SPECIFIC PROTEASE 2
N: SMALL UBIQUITIN-RELATED MODIFIER 1
O: SENTRIN-SPECIFIC PROTEASE 2
P: SMALL UBIQUITIN-RELATED MODIFIER 1
Q: SENTRIN-SPECIFIC PROTEASE 2
R: SMALL UBIQUITIN-RELATED MODIFIER 1
S: SENTRIN-SPECIFIC PROTEASE 2
T: SMALL UBIQUITIN-RELATED MODIFIER 1
U: SENTRIN-SPECIFIC PROTEASE 2
V: SMALL UBIQUITIN-RELATED MODIFIER 1
W: SENTRIN-SPECIFIC PROTEASE 2
X: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)428,19824
Polymers428,19824
Non-polymers00
Water00
1
A: SENTRIN-SPECIFIC PROTEASE 2
B: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-6.4 kcal/mol
Surface area17430 Å2
MethodPQS
2
C: SENTRIN-SPECIFIC PROTEASE 2
D: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-8.9 kcal/mol
Surface area17590 Å2
MethodPQS
3
E: SENTRIN-SPECIFIC PROTEASE 2
F: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-5.7 kcal/mol
Surface area17890 Å2
MethodPQS
4
G: SENTRIN-SPECIFIC PROTEASE 2
H: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-7.7 kcal/mol
Surface area17570 Å2
MethodPQS
5
I: SENTRIN-SPECIFIC PROTEASE 2
J: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-6.6 kcal/mol
Surface area17380 Å2
MethodPQS
6
K: SENTRIN-SPECIFIC PROTEASE 2
L: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-4.3 kcal/mol
Surface area18060 Å2
MethodPQS
7
M: SENTRIN-SPECIFIC PROTEASE 2
N: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-8.7 kcal/mol
Surface area17620 Å2
MethodPQS
8
O: SENTRIN-SPECIFIC PROTEASE 2
P: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-6.2 kcal/mol
Surface area17440 Å2
MethodPQS
9
Q: SENTRIN-SPECIFIC PROTEASE 2
R: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-4.3 kcal/mol
Surface area17340 Å2
MethodPQS
10
S: SENTRIN-SPECIFIC PROTEASE 2
T: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-7.7 kcal/mol
Surface area17390 Å2
MethodPQS
11
U: SENTRIN-SPECIFIC PROTEASE 2
V: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-9.4 kcal/mol
Surface area17990 Å2
MethodPQS
12
W: SENTRIN-SPECIFIC PROTEASE 2
X: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-7.8 kcal/mol
Surface area17960 Å2
MethodPQS
Unit cell
Length a, b, c (Å)113.721, 119.319, 199.840
Angle α, β, γ (deg.)90.00, 89.67, 90.00
Int Tables number3
Space group name H-MP121

-
Components

#1: Protein
SENTRIN-SPECIFIC PROTEASE 2 / AXAM2 / SMT3-SPECIFIC ISOPEPTIDASE 2 / SMT3IP2 / SENTRIN/SUMO-SPECIFIC PROTEASE SENP2


Mass: 26542.773 Da / Num. of mol.: 12 / Fragment: CATALYTIC DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HC62, Ulp1 peptidase
#2: Protein
SMALL UBIQUITIN-RELATED MODIFIER 1 / SUMO-1 / GAP-MODIFYING PROTEIN 1 / GMP1 / SMT3 HOMOLOG 3 / SENT RIN / UBIQUITIN-HOMOLOGY DOMAIN ...SUMO-1 / GAP-MODIFYING PROTEIN 1 / GMP1 / SMT3 HOMOLOG 3 / SENT RIN / UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1 / UBIQUITIN-LIKE PROTEI N SMT3C / SMT3C / UBIQUITIN-LIKE PROTEIN UBL1


Mass: 9140.415 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P63165

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.79 % / Description: NONE
Crystal growTemperature: 291 K
Details: 2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979491
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979491 Å / Relative weight: 1
ReflectionResolution: 3→46.76 Å / Num. obs: 101157 / % possible obs: 94.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 3.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.4 / % possible all: 87.1

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XPSdata reduction
CCP4Idata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TGZ

1tgz


Resolution: 3→47 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.835 / SU B: 24.349 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.32625 3167 3.1 %RANDOM
Rwork0.25688 ---
obs0.25935 97738 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20.33 Å2
2--1.56 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 3→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29972 0 0 0 29972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02230658
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.95341263
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21253588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39124.5091508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.02155957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.09115156
X-RAY DIFFRACTIONr_chiral_restr0.1080.24393
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02122856
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5691.517977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.094229135
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.325312681
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7724.512128
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 67 -
Rwork0.329 6330 -
obs--91.92 %

+
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