[English] 日本語
Yorodumi
- PDB-6v7q: Crystal structure of SUMO1 in complex with phosphorylated PIAS-SIM2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v7q
TitleCrystal structure of SUMO1 in complex with phosphorylated PIAS-SIM2
Components
  • Protein PIAS
  • Small ubiquitin-related modifier 1
KeywordsPEPTIDE BINDING PROTEIN / SUMO1 / PIAS / SUMO INTERACTION MOTIF
Function / homology
Function and homology information


negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / 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 ...negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / 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 / 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 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 / cellular response to cadmium ion / roof of mouth development / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / nuclear pore / transporter activator activity / negative regulation of DNA-binding transcription factor activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PML body / PKR-mediated signaling / regulation of protein stability / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / nuclear membrane / protein stabilization / nuclear speck / nuclear body / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
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 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLussier-Price, M. / Wahba, H.M. / Mascle, X.H. / Cappadocia, L. / Sakaguchi, K. / Omichinski, J.G.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research74739 Canada
Canadian Institutes of Health Research130414 Canada
CitationJournal: Structure / Year: 2020
Title: Characterization of a C-Terminal SUMO-Interacting Motif Present in Select PIAS-Family Proteins.
Authors: Lussier-Price, M. / Mascle, X.H. / Cappadocia, L. / Kamada, R. / Sakaguchi, K. / Wahba, H.M. / Omichinski, J.G.
History
DepositionDec 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Small ubiquitin-related modifier 1
D: Protein PIAS
A: Small ubiquitin-related modifier 1
B: Protein PIAS


Theoretical massNumber of molelcules
Total (without water)21,9664
Polymers21,9664
Non-polymers00
Water5,549308
1
C: Small ubiquitin-related modifier 1
D: Protein PIAS


Theoretical massNumber of molelcules
Total (without water)10,9832
Polymers10,9832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Small ubiquitin-related modifier 1
B: Protein PIAS


Theoretical massNumber of molelcules
Total (without water)10,9832
Polymers10,9832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.315, 38.749, 121.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Small ubiquitin-related modifier 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 9526.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P63165
#2: Protein/peptide Protein PIAS


Mass: 1456.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium cacodylate pH 6.5, 19 to 31% (w/v) PEG3350 and 10 mM calcium chloride.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.35→36.91 Å / Num. obs: 38573 / % possible obs: 95.02 % / Redundancy: 5.2 % / CC1/2: 0.997 / Net I/σ(I): 19.53
Reflection shellResolution: 1.35→1.399 Å / Num. unique obs: 2743 / CC1/2: 0.927

-
Processing

Software
NameVersionClassification
PHENIX1.13-2998_1496refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UYO

6uyo


Resolution: 1.35→36.91 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.2
RfactorNum. reflection% reflection
Rfree0.1959 2004 5.2 %
Rwork0.1709 --
obs0.1721 38571 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.83 Å2 / Biso mean: 23.5525 Å2 / Biso min: 7.34 Å2
Refinement stepCycle: final / Resolution: 1.35→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 0 308 1730
Biso mean---31.64 -
Num. residues----172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3503-1.38410.2439980.2286179566
1.3841-1.42150.21091120.218215980
1.4215-1.46340.25741390.1987244891
1.4634-1.51060.24021440.1912263197
1.5106-1.56460.20941450.1827266198
1.5646-1.62720.221510.1748263698
1.6272-1.70130.20941410.182742100
1.7013-1.7910.19491520.18392713100
1.791-1.90320.21221490.17462736100
1.9032-2.05010.18251450.15972762100
2.0501-2.25640.19561580.15962762100
2.2564-2.58280.17351520.1632773100
2.5828-3.25380.22741550.17612804100
3.2538-36.910.17161630.16422945100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8710.2366-0.03750.7404-0.17071.95360.11010.02610.2314-0.0179-0.0111-0.11880.0477-0.22630.03460.15940.0070.01520.08680.0250.1788-8.48421.8587-34.8751
20.5273-0.0626-0.69110.272-0.69393.55140.03340.09730.03370.0250.11110.01790.0875-0.4310.05290.1305-0.00620.0010.06610.01840.1434-10.9101-2.3099-33.1275
30.1989-0.10120.19240.3727-0.12810.18830.0001-0.0436-0.06240.08830.03760.03620.038-0.03890.26880.1485-0.011-0.02330.0020.03530.1028-5.3383-5.6325-25.5634
41.8388-0.1824-0.31992.2296-0.7590.33910.1008-0.3979-0.0890.45980.02730.0714-0.08190.07220.1340.1916-0.0254-0.03290.10770.02210.1169-2.19620.2125-19.8906
53.05831.11140.81781.3887-0.08350.36650.1299-0.36670.29940.3563-0.07870.1474-0.2239-0.1078-0.01850.240.02650.0530.1104-0.01090.1558-12.39036.6079-23.815
60.3410.1487-0.04660.2846-0.25180.32070.07130.03310.22930.2230.21510.2661-0.1667-0.42970.01360.14950.04310.01990.14670.04380.1746-14.90485.7608-33.9112
72.08820.5314-0.60892.12760.35190.76650.1041-0.29480.02830.3367-0.1224-0.24910.03190.0964-0.07570.1622-0.0181-0.01890.0684-0.00350.1242-1.59256.0416-24.4408
82.28850.5487-0.81130.3058-0.52330.9453-0.15930.4153-0.2631-0.2025-0.0374-0.16490.3161-0.0499-0.0310.2608-0.00820.03280.1795-0.0110.2838-5.0322-7.5125-36.4294
90.8393-0.03980.44040.75070.04070.9510.09290.3688-0.176-0.1856-0.1560.06210.13980.1253-0.00540.1004-0.00280.01850.15090.01470.1414-15.82472.3488-59.8536
100.4570.21880.19710.35760.59671.57860.0745-0.1383-0.10170.0995-0.0008-0.00110.23280.12190.1560.0651-0.0034-0.00350.17550.03440.0831-11.23895.4065-52.3059
110.5225-0.4701-0.38031.52720.04780.3595-0.0783-0.40370.23350.00230.0034-0.1547-0.23860.03910.02870.1186-0.013-0.0140.1982-0.00440.1184-15.954514.4758-51.1918
120.6241-0.06910.24130.3473-0.34461.11020.0364-0.1552-0.04410.1034-0.02560.02390.0643-0.2965-0.01420.0949-0.02580.00030.16930.02620.0886-22.29624.6777-51.6137
130.67580.1046-0.30060.4135-0.07241.6253-0.1806-0.0706-0.2343-0.17230.071-0.07590.35650.0788-0.16030.1515-0.00210.02220.24540.00190.1585-9.67113.0826-64.7506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 17 through 32 )C17 - 32
2X-RAY DIFFRACTION2chain 'C' and (resid 33 through 43 )C33 - 43
3X-RAY DIFFRACTION3chain 'C' and (resid 44 through 55 )C44 - 55
4X-RAY DIFFRACTION4chain 'C' and (resid 56 through 65 )C56 - 65
5X-RAY DIFFRACTION5chain 'C' and (resid 66 through 76 )C66 - 76
6X-RAY DIFFRACTION6chain 'C' and (resid 77 through 86 )C77 - 86
7X-RAY DIFFRACTION7chain 'C' and (resid 87 through 93 )C87 - 93
8X-RAY DIFFRACTION8chain 'D' and (resid 8 through 15 )D8 - 15
9X-RAY DIFFRACTION9chain 'A' and (resid 20 through 39 )A20 - 39
10X-RAY DIFFRACTION10chain 'A' and (resid 40 through 55 )A40 - 55
11X-RAY DIFFRACTION11chain 'A' and (resid 56 through 65 )A56 - 65
12X-RAY DIFFRACTION12chain 'A' and (resid 66 through 95 )A66 - 95
13X-RAY DIFFRACTION13chain 'B' and (resid 5 through 15 )B5 - 15

+
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