[English] 日本語
Yorodumi
- PDB-4wjq: Crystal Structure of SUMO1 in complex with Daxx -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wjq
TitleCrystal Structure of SUMO1 in complex with Daxx
Components
  • Daxx
  • Small ubiquitin-related modifier 1
Keywordsprotein binding/signaling protein / SUMO1 / Daxx / Homo sapiens / SUMO Interaction Motif / PhosphoSIM / protein binding-signaling protein complex
Function / homology
Function and homology information


protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / septin ring / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / 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 / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Formation of Incision Complex in GG-NER / protein tag activity / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / nuclear body / protein stabilization / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / 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
AuthorsCappadocia, L. / Mascle, X.H. / Bourdeau, V. / Tremblay-Belzile, S. / Chaker-Margot, M. / Lussier-Price, M. / Wada, J. / Sakaguchi, K. / Aubry, M. / Ferbeyre, G. / Omichinski, J.G.
CitationJournal: Structure / Year: 2015
Title: Structural and Functional Characterization of the Phosphorylation-Dependent Interaction between PML and SUMO1.
Authors: Cappadocia, L. / Mascle, X.H. / Bourdeau, V. / Tremblay-Belzile, S. / Chaker-Margot, M. / Lussier-Price, M. / Wada, J. / Sakaguchi, K. / Aubry, M. / Ferbeyre, G. / Omichinski, J.G.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,7354
Polymers22,7354
Non-polymers00
Water6,017334
1
A: Small ubiquitin-related modifier 1
B: Daxx


Theoretical massNumber of molelcules
Total (without water)11,3682
Polymers11,3682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-4 kcal/mol
Surface area5820 Å2
MethodPISA
2
C: Small ubiquitin-related modifier 1
D: Daxx


Theoretical massNumber of molelcules
Total (without water)11,3682
Polymers11,3682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-3 kcal/mol
Surface area5500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.637, 38.402, 73.691
Angle α, β, γ (deg.)90.000, 101.090, 90.000
Int Tables number4
Space group name H-MP1211

-
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 / Fragment: unp residues 17-97 / Mutation: C52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P63165
#2: Protein/peptide Daxx


Mass: 1840.919 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, 26% PEG3350, 10 mM calcium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 39759 / % possible obs: 94.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 14.52 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.1
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.4 / % possible all: 74.6

-
Processing

Software
NameVersionClassification
CBASSdata collection
XDSdata scaling
XDSdata reduction
SCALAdata scaling
Cootmodel building
PHENIXphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: dev_1555)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UYZ

2uyz


Resolution: 1.35→36.158 Å / FOM work R set: 0.8844 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 2005 5.04 %Random selection
Rwork0.1558 37743 --
obs0.1571 39748 94.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.05 Å2 / Biso mean: 24.23 Å2 / Biso min: 8.37 Å2
Refinement stepCycle: final / Resolution: 1.35→36.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 0 334 1776
Biso mean---35.69 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091460
X-RAY DIFFRACTIONf_angle_d1.2351950
X-RAY DIFFRACTIONf_chiral_restr0.071213
X-RAY DIFFRACTIONf_plane_restr0.006253
X-RAY DIFFRACTIONf_dihedral_angle_d15.142572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.38380.31361020.27291903200566
1.3838-1.42120.23761250.24862243236881
1.4212-1.4630.22931320.21312649278194
1.463-1.51030.18691480.19632692284095
1.5103-1.56420.22611510.16972735288696
1.5642-1.62690.1981370.1632737287498
1.6269-1.70090.18831470.16682784293198
1.7009-1.79060.19651590.1632814297399
1.7906-1.90280.16491420.15912821296399
1.9028-2.04970.16421480.14732831297999
2.0497-2.25590.17021470.149528533000100
2.2559-2.58230.16731550.151328563011100
2.5823-3.2530.18511530.156228803033100
3.253-36.17070.17091590.136329453104100
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)
10.9394-0.54230.19551.6422-0.08060.5818-0.0097-0.0095-0.01130.03550.0295-0.0265-0.02030.05460.00020.0874-0.00520.00740.0946-0.01240.0974-0.2367-0.860532.0441
20.5067-0.4336-0.37250.41780.3620.32190.21780.0283-0.00750.00240.0685-0.05140.1865-0.26190.13690.1338-0.0334-0.02480.16940.00170.153-18.24514.214235.0498
30.05140.02240.00310.56880.7811.1049-0.07820.09580.235-0.2043-0.1531-0.0468-0.1018-0.0144-0.14720.1506-0.01340.03070.14120.03990.1667-4.68958.733826.0197
40.6422-0.2410.27670.95450.31820.74080.00190.0148-0.01110.0231-0.002-0.01660.0124-0.0342-00.10570.0004-0.00370.1046-0.00750.095-16.4087-5.69338.0756
50.2886-0.2387-0.03780.19330.01550.00840.03510.0591-0.0161-0.2325-0.07860.15770.0467-0.2552-0.06040.1612-0.0186-0.03030.1701-0.00750.1218-24.9153-12.98791.6166
60.11190.04740.03180.03240.01460.0078-0.06530.0021-0.02290.0531-0.070.00340.0893-0.0995-01.30820.2285-0.01210.93830.07290.8211-15.9776-15.79818.1254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 20:97 )A20 - 97
2X-RAY DIFFRACTION2( CHAIN B AND RESID 4:10 )B4 - 10
3X-RAY DIFFRACTION3( CHAIN B AND RESID 11:15 )B11 - 15
4X-RAY DIFFRACTION4( CHAIN C AND RESID 18:93 )C18 - 93
5X-RAY DIFFRACTION5( CHAIN D AND RESID 7:14 )D7 - 14
6X-RAY DIFFRACTION6( CHAIN D AND RESID 15:18 )D15 - 18

+
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://pdbjlvh1.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