[English] 日本語
Yorodumi
- PDB-4mvt: Crystal structure of SUMO E3 Ligase PIAS3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mvt
TitleCrystal structure of SUMO E3 Ligase PIAS3
ComponentsE3 SUMO-protein ligase PIAS3
KeywordsLIGASE / SUMO / E3 Ligase / PINIT domain / SP-RING domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / SUMO ligase activity / positive regulation of membrane potential / : / : / positive regulation of protein sumoylation / SUMOylation of immune response proteins / negative regulation of protein sumoylation / Transferases; Acyltransferases; Aminoacyltransferases ...: / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / SUMO ligase activity / positive regulation of membrane potential / : / : / positive regulation of protein sumoylation / SUMOylation of immune response proteins / negative regulation of protein sumoylation / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / negative regulation of osteoclast differentiation / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / potassium channel regulator activity / SUMOylation of transcription cofactors / response to hormone / transcription coregulator activity / SUMOylation of intracellular receptors / Formation of Incision Complex in GG-NER / nuclear speck / synapse / dendrite / positive regulation of gene expression / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
PINIT domain / PINIT domain / PINIT domain superfamily / PINIT domain / PINIT domain profile. / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / SAP domain superfamily / SAP motif profile. ...PINIT domain / PINIT domain / PINIT domain superfamily / PINIT domain / PINIT domain profile. / MIZ/SP-RING zinc finger / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / SAP domain superfamily / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
E3 SUMO-protein ligase PIAS3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDong, A. / Hu, J. / Li, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of SUMO E3 Ligase PIAS3
Authors: Hu, J. / Dong, a. / Li, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionSep 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: E3 SUMO-protein ligase PIAS3
B: E3 SUMO-protein ligase PIAS3
C: E3 SUMO-protein ligase PIAS3
D: E3 SUMO-protein ligase PIAS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,04842
Polymers167,7164
Non-polymers33338
Water2,630146
1
A: E3 SUMO-protein ligase PIAS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,03013
Polymers41,9291
Non-polymers10112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 SUMO-protein ligase PIAS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9949
Polymers41,9291
Non-polymers658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: E3 SUMO-protein ligase PIAS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,03012
Polymers41,9291
Non-polymers10111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: E3 SUMO-protein ligase PIAS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9948
Polymers41,9291
Non-polymers657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.450, 85.440, 89.530
Angle α, β, γ (deg.)83.080, 86.570, 86.140
Int Tables number1
Space group name H-MP1
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

-
Components

#1: Protein
E3 SUMO-protein ligase PIAS3 / Protein inhibitor of activated STAT protein 3


Mass: 41928.980 Da / Num. of mol.: 4 / Fragment: UNP residues 112-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIAS3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R
References: UniProt: Q9Y6X2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 32 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 20% PEG 8000, 0.2 M Magnesium Chloride, 0.1 M Tris pH8.5,(1:800-1:1300) w/w chymotrypsin, vapor diffusion hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 71156 / % possible obs: 98.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 47.58 Å2 / Rmerge(I) obs: 0.137 / Χ2: 1.635 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3450.9534860.878197.6
2.34-2.3850.78635460.911197.6
2.38-2.4350.69835430.898197.7
2.43-2.485.10.65935230.91197.8
2.48-2.535.10.58135680.955197.9
2.53-2.595.10.51835120.964198
2.59-2.665.10.45235500.976198
2.66-2.735.10.36335381.022198.2
2.73-2.815.10.31835651.068198.1
2.81-2.95.20.26735831.127198.6
2.9-35.20.22335591.201198.3
3-3.125.10.17535491.387198.6
3.12-3.265.20.15435971.53198.6
3.26-3.445.20.12935551.783198.6
3.44-3.655.20.11335742.141198.8
3.65-3.935.10.09835812.452198.8
3.93-4.3350.08935842.878199
4.33-4.9550.08735883.089199
4.95-6.244.90.08535772.801199.3
6.24-504.90.0835783.798198.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
JBluIce-EPICSdata collection
HKL-3000data reduction
MOLREP11phasing
BUSTER2.10.0refinement
Coot0.6.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4FO9

4fo9


Resolution: 2.3→48.04 Å / Cor.coef. Fo:Fc: 0.9137 / Cor.coef. Fo:Fc free: 0.8947 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: AUTHOR NOTE UNEXPLAINED DENSITY AT L341 IN CHAIN A AND B THE ELECTRON DENSITY FOR RESIDUES 316 TO 319 IN ALL CHAINS ARE WITH VERY POOR QUALITY. THE RESIDUES 316 TO 319 IN CHAIN A AND C ARE ...Details: AUTHOR NOTE UNEXPLAINED DENSITY AT L341 IN CHAIN A AND B THE ELECTRON DENSITY FOR RESIDUES 316 TO 319 IN ALL CHAINS ARE WITH VERY POOR QUALITY. THE RESIDUES 316 TO 319 IN CHAIN A AND C ARE MODELED BUT WITH QUESTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 1427 2.01 %RANDOM
Rwork0.2383 ---
obs0.239 71154 97.26 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 48.5626 Å2 / Biso min: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.7299 Å2-1.0601 Å21.391 Å2
2---1.31 Å2-6.6239 Å2
3---0.58 Å2
Refine analyzeLuzzati coordinate error obs: 0.398 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7709 0 38 146 7893
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 84 1.88 %
Rwork0.2384 4374 -
all0.2387 4458 -
obs--97.26 %
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)
10.99181.32720.39472.60030.22690.67170.109-0.05480.19420.1835-0.10330.2329-0.1779-0.0355-0.0057-0.15490.0010.0586-0.05070.0814-0.026165.600794.2785.6202
20.955-0.5478-0.91310.77280.42032.16660.1083-0.15590.04760.1661-0.0108-0.0573-0.18940.2246-0.0975-0.1461-0.05310.00910.00160.0723-0.088568.526676.1157107.9817
30.88370.54221.17360.81740.67462.81530.11570.166-0.1014-0.16810.0463-0.03150.1420.2506-0.1621-0.16230.0596-0.02950.0080.0689-0.091241.471133.191642.3787
41.2179-1.6136-0.39773.37940.29060.59260.11560.0433-0.1708-0.1171-0.090.34290.1954-0.0355-0.0256-0.17330.0089-0.0622-0.07010.0945-0.024338.3607114.020964.1015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A126 - 1000
2X-RAY DIFFRACTION2{ B|* }B126 - 1000
3X-RAY DIFFRACTION3{ C|* }C126 - 1000
4X-RAY DIFFRACTION4{ D|* }D126 - 1000

+
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