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- PDB-7rgw: Crystal structure of HERC2 DOC domain -

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Basic information

Entry
Database: PDB / ID: 7rgw
TitleCrystal structure of HERC2 DOC domain
ComponentsE3 ubiquitin-protein ligase HERC2
KeywordsCELL CYCLE / DOC domain of E3 ubiquitin ligase HERC2
Function / homology
Function and homology information


SUMO binding / HECT-type E3 ubiquitin transferase / SUMOylation of DNA damage response and repair proteins / centriole / guanyl-nucleotide exchange factor activity / Nonhomologous End-Joining (NHEJ) / intracellular protein transport / G2/M DNA damage checkpoint / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation ...SUMO binding / HECT-type E3 ubiquitin transferase / SUMOylation of DNA damage response and repair proteins / centriole / guanyl-nucleotide exchange factor activity / Nonhomologous End-Joining (NHEJ) / intracellular protein transport / G2/M DNA damage checkpoint / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA repair / DNA damage response / ubiquitin protein ligase 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 / 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. / Galactose-binding-like domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / E3 ubiquitin-protein ligase HERC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLiu, J. / Tencer, A.H. / Kutateladze, T.G.
CitationJournal: Sci Rep / Year: 2022
Title: The ZZ domain of HERC2 is a receptor of arginylated substrates.
Authors: Tencer, A.H. / Liu, J. / Zhu, J. / Burkholder, N.T. / Zhang, Y. / Wu, W. / Strahl, B.D. / Ohta, T. / Kutateladze, T.G.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HERC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6952
Polymers19,5881
Non-polymers1061
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint3 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.365, 89.365, 52.845
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein E3 ubiquitin-protein ligase HERC2 / HECT domain and RCC1-like domain-containing protein 2 / HECT-type E3 ubiquitin transferase HERC2


Mass: 19588.459 Da / Num. of mol.: 1 / Fragment: DOC domain (UNP residues 2759-2914)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HERC2 / Production host: Escherichia coli (E. coli) / References: UniProt: O95714
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.11 Å3/Da / Density % sol: 60.45 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 25% PEG3350

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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: Jan 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 16667 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 18.88 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.042 / Rrim(I) all: 0.095 / Χ2: 1.217 / Net I/σ(I): 9.8 / Num. measured all: 79108
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.99-2.0630.32516530.7950.2280.3991.36499.8
2.06-2.143.40.27316430.8290.1770.3271.47999.2
2.14-2.243.90.21916600.930.1310.2571.14899.9
2.24-2.364.50.19216560.9680.1020.2181.072100
2.36-2.515.50.17216440.9830.080.191.15199.9
2.51-2.75.70.13316720.9880.060.1461.065100
2.7-2.975.60.10616770.9920.0490.1181.179100
2.97-3.45.60.07416560.9960.0340.0811.218100
3.4-4.285.40.06416780.9940.030.0711.34599.6
4.28-3050.04217280.9980.020.0471.31899.6

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JHJ

1jhj


Resolution: 1.99→29.25 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 1653 9.96 %
Rwork0.1814 14948 -
obs0.1847 16601 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.86 Å2 / Biso mean: 22.5697 Å2 / Biso min: 9.15 Å2
Refinement stepCycle: final / Resolution: 1.99→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 17 183 1297
Biso mean--39.26 31.61 -
Num. residues----141
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.050.27811370.20121228136599
2.05-2.110.22271360.19921255139199
2.11-2.190.21661410.172812331374100
2.19-2.280.23291330.19512321365100
2.28-2.380.18831380.195712371375100
2.38-2.510.25661350.210212411376100
2.51-2.660.23751430.208812691412100
2.66-2.870.27191330.21671232136599
2.87-3.160.26571330.20931231136498
3.16-3.610.19531390.166912481387100
3.61-4.540.17051390.15091254139399
4.55-29.250.18651460.157912881434100

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