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- PDB-9l8y: Crystal structure of HERC2 -

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Basic information

Entry
Database: PDB / ID: 9l8y
TitleCrystal structure of HERC2
ComponentsE3 ubiquitin-protein ligase HERC2
KeywordsLIGASE / HERC2
Function / homology
Function and homology information


SUMO binding / HECT-type E3 ubiquitin transferase / negative regulation of Notch signaling pathway / SUMOylation of DNA damage response and repair proteins / centriole / guanyl-nucleotide exchange factor activity / intracellular protein transport / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / neuron differentiation ...SUMO binding / HECT-type E3 ubiquitin transferase / negative regulation of Notch signaling pathway / SUMOylation of DNA damage response and repair proteins / centriole / guanyl-nucleotide exchange factor activity / intracellular protein transport / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / neuron differentiation / 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 / nucleus / membrane / 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 ...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 / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / 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 finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / 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
E3 ubiquitin-protein ligase HERC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsLiu, H.B. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21822705 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Mechanistic insights into the iron-sulfur cluster-dependent interaction of the autophagy receptor NCOA4 with the E3 ligase HERC2.
Authors: Liu, H. / Shen, L. / Gong, X. / Zhou, X. / Huang, Y. / Zhou, Y. / Guo, Z. / Guo, H. / Wang, S. / Pan, L.
History
DepositionDec 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HERC2


Theoretical massNumber of molelcules
Total (without water)18,3521
Polymers18,3521
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.232, 99.591, 123.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z

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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: 18351.852 Da / Num. of mol.: 1
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, HECT-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane (pH 8.8), 16% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.92→49.8 Å / Num. obs: 14962 / % possible obs: 99.9 % / Redundancy: 9.1 % / Biso Wilson estimate: 39.08 Å2 / Rpim(I) all: 0.026 / Net I/σ(I): 15.2
Reflection shellResolution: 1.92→1.96 Å / Num. unique obs: 723 / Rpim(I) all: 0.356

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→28.13 Å / SU ML: 0.2273 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.2227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2061 713 4.77 %
Rwork0.1797 14239 -
obs0.181 14952 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.61 Å2
Refinement stepCycle: LAST / Resolution: 1.92→28.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 79 1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211271
X-RAY DIFFRACTIONf_angle_d1.41091726
X-RAY DIFFRACTIONf_chiral_restr0.0858185
X-RAY DIFFRACTIONf_plane_restr0.0132222
X-RAY DIFFRACTIONf_dihedral_angle_d6.3337175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-2.070.35071450.26252790X-RAY DIFFRACTION99.83
2.07-2.280.23021440.21382816X-RAY DIFFRACTION99.93
2.28-2.610.23921480.21112816X-RAY DIFFRACTION99.97
2.61-3.290.26281340.20232875X-RAY DIFFRACTION99.93
3.29-28.130.16081420.15282942X-RAY DIFFRACTION99.68
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)
15.9783057815-0.742266191348-0.7363787618058.679630629353.994913030535.4797317909-0.0500189142980.95252285550.423932115312-1.030403020330.105575448598-0.592355651116-0.1235904997320.470763451732-0.05221096716510.6030167146020.01834494956310.2098822114860.6734639461990.09444094198660.35297389008242.8599004751-11.8447823593-23.6226137265
26.62595422082-0.3610514169780.6347012253377.21774853032-1.853178446447.86566011196-0.04423707785910.343677875632-0.0546631710482-0.3177003609320.00606313994532-0.2782316915620.2254326558690.2717932506650.0428051808580.2769302862090.009936333277840.06307600141340.247779949303-0.002292600433630.30717996257138.7966686514-12.721919885-10.8683571276
35.972782444356.58928210133-6.55228014327.45029224967-7.848421277349.637578798190.148673451340.8882964289170.863397483236-1.015971349670.0695026223873-0.0518227420031-0.11775112201-0.986360850395-0.3165590673140.596508497920.118320266240.03984345402960.4639559068180.1747725501150.58560610141723.7715056102-8.31273459147-10.8791478458
46.74211477326-1.473680392550.716471915078.779218217640.1544011984186.90469023959-0.03860484145310.5320631367680.720772901177-0.4056746499990.07598308995490.860575738878-0.438313828091-0.413229439894-0.06618638406410.287389018327-0.027082136898-0.03723580999770.3111882239730.1011984254870.51232692570712.5476268508-14.4383641263-8.40832138447
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2548 through 2570 )2548 - 25701 - 23
22chain 'A' and (resid 2571 through 2629 )2571 - 262924 - 82
33chain 'A' and (resid 2630 through 2644 )2630 - 264483 - 97
44chain 'A' and (resid 2645 through 2700 )2645 - 270098 - 153

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