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- PDB-6ww4: Crystal structure of HERC2 ZZ domain in complex with histone H3 tail -

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Basic information

Entry
Database: PDB / ID: 6ww4
TitleCrystal structure of HERC2 ZZ domain in complex with histone H3 tail
ComponentsHistone H3.1,E3 ubiquitin-protein ligase HERC2
KeywordsGENE REGULATION / Zinc finger protein / histone reader / HERC2 / ZZ domain
Function / homology
Function and homology information


SUMO binding / HECT-type E3 ubiquitin transferase / Chromatin modifying enzymes / epigenetic regulation of gene expression / SUMOylation of DNA damage response and repair proteins / telomere organization / centriole / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication ...SUMO binding / HECT-type E3 ubiquitin transferase / Chromatin modifying enzymes / epigenetic regulation of gene expression / SUMOylation of DNA damage response and repair proteins / telomere organization / centriole / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / guanyl-nucleotide exchange factor activity / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / intracellular protein transport / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / Antigen processing: Ubiquitination & Proteasome degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein ubiquitination / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / DNA repair / DNA damage response / ubiquitin protein ligase binding / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / CPH domain / Mouse development and cellular proliferation protein Cullin-7 ...HERC2, APC10 domain / HERC2, zinc finger, ZZ-type / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / Mib-herc2 / Mib/herc2 domain superfamily / Mib_herc2 / MIB/HERC2 domain profile. / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / 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 / 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. / Histone H3 signature 1. / Histone H3 signature 2. / Galactose-binding-like domain superfamily / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HERC2 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.252 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

Downloads & links

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Assembly

Deposited unit
B: Histone H3.1,E3 ubiquitin-protein ligase HERC2
A: Histone H3.1,E3 ubiquitin-protein ligase HERC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4998
Polymers13,0532
Non-polymers4466
Water95553
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B: Histone H3.1,E3 ubiquitin-protein ligase HERC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7494
Polymers6,5261
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histone H3.1,E3 ubiquitin-protein ligase HERC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7494
Polymers6,5261
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.933, 76.439, 33.012
Angle α, β, γ (deg.)90.000, 102.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone H3.1,E3 ubiquitin-protein ligase HERC2


Mass: 6526.476 Da / Num. of mol.: 2 / Fragment: fusion protein
Source method: isolated from a genetically manipulated source
Details: Residues 1-6 of this construct belong to histone H3
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J, HERC2
Production host: Escherichia coli (E. coli)
References: UniProt: P68431, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsResidues 2-7 of histone H3 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.28 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 5256 / % possible obs: 91 % / Redundancy: 5.9 % / Biso Wilson estimate: 29.59 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Χ2: 0.833 / Net I/σ(I): 13.6 / Num. measured all: 31141
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.333.20.1573140.9630.0930.1840.78554.7
2.33-2.4240.1554100.9540.0820.1770.76372.3
2.42-2.534.80.1535450.960.0740.1710.78192.4
2.53-2.676.30.1375620.9860.0580.1490.74199.6
2.67-2.836.70.1175770.9870.0490.1270.755100
2.83-3.056.90.15810.9890.0410.1080.8799.7
3.05-3.3670.0855620.9920.0350.0920.87899.5
3.36-3.856.70.0745700.9910.0310.080.93398.6
3.85-4.8560.0595520.9920.0270.0650.89195.2
4.85-505.90.0615830.9940.0280.0670.83197.3

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Processing

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

6ds6


Resolution: 2.252→38.219 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 520 10.02 %
Rwork0.1985 4672 -
obs0.2032 5192 90.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.62 Å2 / Biso mean: 29.9424 Å2 / Biso min: 15.36 Å2
Refinement stepCycle: final / Resolution: 2.252→38.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 32 53 989
Biso mean--46.37 31.15 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007934
X-RAY DIFFRACTIONf_angle_d0.851244
X-RAY DIFFRACTIONf_chiral_restr0.047126
X-RAY DIFFRACTIONf_plane_restr0.005164
X-RAY DIFFRACTIONf_dihedral_angle_d21.114558
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2522-2.47880.3044960.210986867
2.4788-2.83740.25421410.2062126498
2.8374-3.57440.22871430.1898128599
3.5744-38.210.23861400.1988125596

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