[English] 日本語
Yorodumi
- PDB-4x3g: Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x3g
TitleCrystal structure of SIAH1 SINA domain in complex with a USP19 peptide
Components
  • E3 ubiquitin-protein ligase SIAH1
  • Ubiquitin carboxyl-terminal hydrolase 19
KeywordsLIGASE / UBIQUITIN-PROTEIN LIGASE / HYDROLASE / UBIQUITIN SPECIFIC PROTEASE / PROTEIN-PEPTIDE COMPLEX / SGC
Function / homology
Function and homology information


regulation of ERAD pathway / positive regulation of cell cycle process / negative regulation of skeletal muscle tissue development / Netrin-1 signaling / regulation of cellular response to hypoxia / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / protein deubiquitination / anatomical structure morphogenesis / canonical Wnt signaling pathway ...regulation of ERAD pathway / positive regulation of cell cycle process / negative regulation of skeletal muscle tissue development / Netrin-1 signaling / regulation of cellular response to hypoxia / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / protein deubiquitination / anatomical structure morphogenesis / canonical Wnt signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / ERAD pathway / response to endoplasmic reticulum stress / axon guidance / Hsp90 protein binding / RING-type E3 ubiquitin transferase / regulation of protein stability / protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / amyloid fibril formation / protein stabilization / Ub-specific processing proteases / protein ubiquitination / positive regulation of apoptotic process / Amyloid fiber formation / endoplasmic reticulum membrane / apoptotic process / zinc ion binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Linker region of USP19 deubiquitinase / E3 ubiquitin-protein ligase SINA-like, animal / Seven-in-absentia protein, TRAF-like domain / : / Sina, TRAF-like domain / Sina, zinc finger / E3 ubiquitin-protein ligase sina/sinah, RING finger / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / CS domain ...Linker region of USP19 deubiquitinase / E3 ubiquitin-protein ligase SINA-like, animal / Seven-in-absentia protein, TRAF-like domain / : / Sina, TRAF-like domain / Sina, zinc finger / E3 ubiquitin-protein ligase sina/sinah, RING finger / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / CS domain / CS domain / CS domain profile. / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / MYND finger / : / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / TRAF-like / HSP20-like chaperone / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Papain-like cysteine peptidase superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 19 / E3 ubiquitin-protein ligase SIAH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsWalker, J.R. / Dong, A. / Zhang, Q. / Huang, X. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide
Authors: Walker, J.R. / Dong, A. / Zhang, Q. / Huang, X. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionNov 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SIAH1
B: E3 ubiquitin-protein ligase SIAH1
C: Ubiquitin carboxyl-terminal hydrolase 19
D: Ubiquitin carboxyl-terminal hydrolase 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5878
Polymers46,3254
Non-polymers2624
Water1,00956
1
A: E3 ubiquitin-protein ligase SIAH1
C: Ubiquitin carboxyl-terminal hydrolase 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2934
Polymers23,1632
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-13 kcal/mol
Surface area11050 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase SIAH1
D: Ubiquitin carboxyl-terminal hydrolase 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2934
Polymers23,1632
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-18 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.343, 88.092, 59.590
Angle α, β, γ (deg.)90.000, 103.240, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein E3 ubiquitin-protein ligase SIAH1 / Seven in absentia homolog 1 / Siah-1 / Siah-1a


Mass: 21651.742 Da / Num. of mol.: 2 / Fragment: SINA DOMAIN, RESIDUES 91-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIAH1, HUMSIAH / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): V2R-pRARE2
References: UniProt: Q8IUQ4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Ubiquitin carboxyl-terminal hydrolase 19 / Deubiquitinating enzyme 19 / Ubiquitin thioesterase 19 / Ubiquitin-specific-processing protease 19 ...Deubiquitinating enzyme 19 / Ubiquitin thioesterase 19 / Ubiquitin-specific-processing protease 19 / Zinc finger MYND domain-containing protein 9


Mass: 1510.840 Da / Num. of mol.: 2 / Fragment: SIAH1 BINDING MOTIF (SBM), RESIDUES 461-474 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O94966, ubiquitinyl hydrolase 1
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: SIAH1 AT 17.6 MG/ML WAS MIXED WITH A TWO-FOLD EXCESS OF USP19 PEPTIDE ON ICE FOR 30 MIN. BEFORE SETTING UP FOR CRYSTALLIZATION. CRYSTALS WERE GROWN AT 298K USING THE SITTING DROP METHOD BY ...Details: SIAH1 AT 17.6 MG/ML WAS MIXED WITH A TWO-FOLD EXCESS OF USP19 PEPTIDE ON ICE FOR 30 MIN. BEFORE SETTING UP FOR CRYSTALLIZATION. CRYSTALS WERE GROWN AT 298K USING THE SITTING DROP METHOD BY MIXING 0.5 UL PROTEIN:PEPTIDE MIX WITH 0.5 UL WELL SOLUTION CONSISTING OF 20% PEG6000, 0.1 M BICINE PH 9.0. THE CRYSTALS WERE CRYOPROTECTED BY FIRST IMMERSION IN WELL SOLUTION MIXED WITH 15% (FINAL) ETHYLENE GLYCOL, THEN IMMERSION IN N-PARATONE.
PH range: 9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 15818 / % possible obs: 90.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 67.92 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.007 / Net I/av σ(I): 9.631 / Net I/σ(I): 6.2 / Num. measured all: 36140
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.33-2.371.50.445130.45658.9
2.37-2.411.70.4096590.4376.3
2.41-2.461.80.3527060.37582.1
2.46-2.5120.3347320.45284.2
2.51-2.562.10.3017700.49788.4
2.56-2.622.10.2697800.44491.8
2.62-2.692.20.2438230.52893.4
2.69-2.762.30.2398150.55295.1
2.76-2.842.40.28360.66296.4
2.84-2.942.40.1678530.71497.5
2.94-3.042.40.1478320.84698.5
3.04-3.162.50.1348510.97896.8
3.16-3.312.50.1258401.49597.6
3.31-3.482.50.0998341.67296.2
3.48-3.72.40.0948451.26695.8
3.7-3.982.50.0888431.37397.2
3.98-4.382.40.0788261.45395.6
4.38-5.022.50.0838441.40395
5.02-6.322.50.0878191.46694.5
6.32-502.40.0727971.20487.9

-
Processing

Software
NameVersionClassification
HKL-3000data reduction
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I7B

4i7b


Resolution: 2.34→48.45 Å / Cor.coef. Fo:Fc: 0.9353 / Cor.coef. Fo:Fc free: 0.9303 / SU R Cruickshank DPI: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.508 / SU Rfree Blow DPI: 0.265 / SU Rfree Cruickshank DPI: 0.271
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 780 4.94 %RANDOM
Rwork0.2218 ---
obs0.2233 15802 89.68 %-
Displacement parametersBiso max: 173.92 Å2 / Biso mean: 82.59 Å2 / Biso min: 31.82 Å2
Baniso -1Baniso -2Baniso -3
1-4.7768 Å20 Å2-1.8572 Å2
2---19.3544 Å20 Å2
3---14.5776 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 2.34→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 4 58 3141
Biso mean--92.57 69.86 -
Num. residues----399
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1068SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes464HARMONIC5
X-RAY DIFFRACTIONt_it3190HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion429SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3399SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3190HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4335HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion1.97
X-RAY DIFFRACTIONt_other_torsion18.94
LS refinement shellResolution: 2.34→2.5 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.27 99 4.56 %
Rwork0.2334 2074 -
all0.235 2173 -
obs--89.68 %
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)
12.53970.7306-0.11513.5326-0.92361.0883-0.08940.50330.1379-0.10220.3811-0.0983-0.0781-0.3051-0.2917-0.1890.08770.05540.20880.027-0.2221.11131.3498.9114
21.88541.09550.99533.7359-1.27972.9621-0.0252-0.1945-0.2247-0.38830.0574-0.43020.7702-0.6147-0.0322-0.1227-0.22420.06480.06580.0391-0.20694.6407-32.139620.7236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|91 - A|602 }A91 - 602
2X-RAY DIFFRACTION2{ B|93 - B|602 }B93 - 602

+
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