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- PDB-6ww3: Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail -

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Basic information

Entry
Database: PDB / ID: 6ww3
TitleCrystal structure of HERC2 ZZ domain in complex with SUMO1 tail
ComponentsSUMO1 linked HERC2 ZZ domain (Small ubiquitin-related modifier 1,E3 ubiquitin-protein ligase HERC2)
KeywordsGENE REGULATION / Zn finger protein / ZZ domain / HERC2
Function / homology
Function and homology information


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 / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / SUMO binding ...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 / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / SUMO binding / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / HECT-type E3 ubiquitin transferase / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / cellular response to cadmium ion / centriole / SUMOylation of chromatin organization proteins / guanyl-nucleotide exchange factor activity / SUMOylation of transcription cofactors / positive regulation of protein-containing complex assembly / Nonhomologous End-Joining (NHEJ) / intracellular protein transport / SUMOylation of intracellular receptors / PKR-mediated signaling / G2/M DNA damage checkpoint / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / Formation of Incision Complex in GG-NER / regulation of protein localization / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / Processing of DNA double-strand break ends / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear membrane / protein stabilization / protein ubiquitination / nuclear body / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / nucleolus / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Beta-propeller repeat TECPR / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / CPH domain / Mouse development and cellular proliferation protein Cullin-7 ...HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Beta-propeller repeat TECPR / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / Small ubiquitin-related modifier 1, Ubl domain / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Galactose-binding-like domain superfamily / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ribosomal protein L2, domain 2 / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / E3 ubiquitin-protein ligase HERC2 / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsLiu, J. / Vann, K.R. / Kutateladze, T.G.
CitationJournal: Structure / Year: 2020
Title: Structural Insight into Binding of the ZZ Domain of HERC2 to Histone H3 and SUMO1.
Authors: Liu, J. / Xue, Z. / Zhang, Y. / Vann, K.R. / Shi, X. / Kutateladze, T.G.
History
DepositionMay 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUMO1 linked HERC2 ZZ domain (Small ubiquitin-related modifier 1,E3 ubiquitin-protein ligase HERC2)
B: SUMO1 linked HERC2 ZZ domain (Small ubiquitin-related modifier 1,E3 ubiquitin-protein ligase HERC2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2798
Polymers13,8202
Non-polymers4606
Water2,324129
1
A: SUMO1 linked HERC2 ZZ domain (Small ubiquitin-related modifier 1,E3 ubiquitin-protein ligase HERC2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1474
Polymers6,9101
Non-polymers2373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SUMO1 linked HERC2 ZZ domain (Small ubiquitin-related modifier 1,E3 ubiquitin-protein ligase HERC2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1334
Polymers6,9101
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.882, 47.262, 55.476
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SUMO1 linked HERC2 ZZ domain (Small ubiquitin-related modifier 1,E3 ubiquitin-protein ligase HERC2)


Mass: 6909.763 Da / Num. of mol.: 2 / Fragment: fusion protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43, HERC2 / Production host: Escherichia coli (E. coli)
References: UniProt: P63165, UniProt: O95714, HECT-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsResidues 2-7 of SUMO1 fused to the ZZ domain of HERC2

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium chloride, 0.1 M Tris, pH 8.0 and 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 7588 / % possible obs: 89.2 % / Redundancy: 3 % / Biso Wilson estimate: 13.18 Å2 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.113 / Rrim(I) all: 0.215 / Χ2: 1.062 / Net I/σ(I): 3.5 / Num. measured all: 22967
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.022.80.4767730.8280.3220.5780.95493.2
2.02-2.12.90.3987910.8190.2630.4811.08193.7
2.1-2.230.3427660.8670.2240.4120.97692.4
2.2-2.313.10.3017520.9180.1890.3581.02391.5
2.31-2.4630.2767730.9390.1750.3290.94891.6
2.46-2.653.10.2647590.9450.1630.3120.93990.4
2.65-2.913.10.1957560.9620.120.2310.95490
2.91-3.333.20.147430.9830.0830.1641.01186.9
3.33-4.23.20.1097400.9880.0640.1271.4384.8
4.2-502.90.1037350.9910.0620.121.31678.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DS6

6ds6


Resolution: 2.096→33.426 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 346 5.16 %
Rwork0.1847 6360 -
obs0.1869 6706 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 42.5 Å2 / Biso mean: 14.5705 Å2 / Biso min: 4.74 Å2
Refinement stepCycle: final / Resolution: 2.096→33.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 17 129 1091
Biso mean--23.59 20.84 -
Num. residues----118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008978
X-RAY DIFFRACTIONf_angle_d0.9611303
X-RAY DIFFRACTIONf_chiral_restr0.064127
X-RAY DIFFRACTIONf_plane_restr0.006177
X-RAY DIFFRACTIONf_dihedral_angle_d22.371371
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.64030.23741740.1891313899
2.6403-33.40.22051720.1822322297

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