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- PDB-9l93: Crystal structure of NCOA4 in complex with HERC2 -

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Basic information

Entry
Database: PDB / ID: 9l93
TitleCrystal structure of NCOA4 in complex with HERC2
Components
  • E3 ubiquitin-protein ligase HERC2
  • Nuclear receptor coactivator 4
KeywordsLIGASE / NCOA4 / HERC2 / Iron-Sulfur Cluster
Function / homology
Function and homology information


cellular response to testosterone stimulus / SUMO binding / protein targeting to lysosome / HECT-type E3 ubiquitin transferase / autolysosome / cellular response to estrogen stimulus / negative regulation of Notch signaling pathway / SUMOylation of DNA damage response and repair proteins / estrogen receptor signaling pathway / response to hormone ...cellular response to testosterone stimulus / SUMO binding / protein targeting to lysosome / HECT-type E3 ubiquitin transferase / autolysosome / cellular response to estrogen stimulus / negative regulation of Notch signaling pathway / SUMOylation of DNA damage response and repair proteins / estrogen receptor signaling pathway / response to hormone / centriole / autophagosome / guanyl-nucleotide exchange factor activity / intracellular protein transport / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / male gonad development / 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 / chromosome / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / cytoplasmic vesicle / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular iron ion homeostasis / transcription coactivator activity / protein ubiquitination / DNA repair / DNA damage response / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nuclear coactivator / Nuclear receptor coactivator 4 / Nuclear coactivator / 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 ...Nuclear coactivator / Nuclear receptor coactivator 4 / Nuclear coactivator / 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
FE2/S2 (INORGANIC) CLUSTER / E3 ubiquitin-protein ligase HERC2 / Nuclear receptor coactivator 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 29, 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

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HERC2
B: E3 ubiquitin-protein ligase HERC2
C: Nuclear receptor coactivator 4
D: Nuclear receptor coactivator 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6176
Polymers48,2654
Non-polymers3522
Water9,098505
1
A: E3 ubiquitin-protein ligase HERC2
C: Nuclear receptor coactivator 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3083
Polymers24,1322
Non-polymers1761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase HERC2
D: Nuclear receptor coactivator 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3083
Polymers24,1322
Non-polymers1761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.456, 41.886, 86.258
Angle α, β, γ (deg.)90.000, 95.930, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,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.: 2
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: Protein Nuclear receptor coactivator 4 / NCoA-4 / Androgen receptor coactivator 70 kDa protein / 70 kDa AR-activator / 70 kDa androgen ...NCoA-4 / Androgen receptor coactivator 70 kDa protein / 70 kDa AR-activator / 70 kDa androgen receptor coactivator / Androgen receptor-associated protein of 70 kDa / Ferritin cargo receptor NCOA4 / Ret-activating protein ELE1


Mass: 5780.626 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA4, ARA70, ELE1, RFG / Production host: Escherichia coli (E. coli) / References: UniProt: Q13772
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate (pH 5.5), 20% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.73→56.24 Å / Num. obs: 51268 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 23.57 Å2 / Rpim(I) all: 0.035 / Net I/σ(I): 13
Reflection shellResolution: 1.73→1.76 Å / Num. unique obs: 2561 / Rpim(I) all: 0.35

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→28.6 Å / SU ML: 0.1829 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2071 2618 5.11 %
Rwork0.166 48633 -
obs0.1681 51251 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.14 Å2
Refinement stepCycle: LAST / Resolution: 1.73→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 8 505 3663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01233226
X-RAY DIFFRACTIONf_angle_d1.16834356
X-RAY DIFFRACTIONf_chiral_restr0.0749464
X-RAY DIFFRACTIONf_plane_restr0.009560
X-RAY DIFFRACTIONf_dihedral_angle_d5.2063438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.760.31481500.25562543X-RAY DIFFRACTION99.74
1.76-1.790.2971230.22972533X-RAY DIFFRACTION99.92
1.79-1.830.22021390.20812556X-RAY DIFFRACTION99.89
1.83-1.870.23261420.20212507X-RAY DIFFRACTION99.92
1.87-1.910.23381430.19242568X-RAY DIFFRACTION100
1.91-1.960.23781370.19082524X-RAY DIFFRACTION99.96
1.96-2.020.25181270.17652574X-RAY DIFFRACTION100
2.02-2.070.23111430.1732530X-RAY DIFFRACTION99.96
2.08-2.140.22191290.17162539X-RAY DIFFRACTION99.96
2.14-2.220.19711380.16432568X-RAY DIFFRACTION99.89
2.22-2.310.20211280.16922559X-RAY DIFFRACTION99.93
2.31-2.410.24211360.17012544X-RAY DIFFRACTION100
2.41-2.540.21941350.17772556X-RAY DIFFRACTION99.93
2.54-2.70.23781480.18062557X-RAY DIFFRACTION99.93
2.7-2.910.21771540.17792548X-RAY DIFFRACTION99.67
2.91-3.20.20781240.1662600X-RAY DIFFRACTION99.78
3.2-3.660.1831390.15342558X-RAY DIFFRACTION99.59
3.66-4.610.16421440.13412604X-RAY DIFFRACTION99.42
4.61-28.60.19681390.15582665X-RAY DIFFRACTION99.29
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)
15.325253823121.291758222240.7523976510096.56913084801-0.1348779937694.43673724434-0.1112445759170.2978477754520.467547597838-0.5235766806190.1471309060060.0584589405083-0.7166181066150.251099259593-0.05405764035010.3531031853310.0370597316810.04853996648250.257480565740.05594369624350.211273253862-15.188060597713.4865307426-4.54052039851
24.047578238130.1331630489830.7307154161834.577274802160.3557918012353.818731565520.02731824664910.1216262189930.0157321532242-0.1206889917990.0644779475312-0.08983323817-0.0703699009320.203595657999-0.1298443221520.1855891744820.01777176802210.01900095503790.1840598110210.005437818698640.168168247264-10.97673196752.221947048382.11423836689
36.297029062351.84842593408-1.112726776149.110221918435.354414167416.827794650320.2819666735841.32483793733-1.42954033936-0.004423996191770.184727507689-1.029790126310.7606827332181.56779175739-0.4778037624910.4075451580840.08636857903430.009671398753210.517580221558-0.1145664864450.533945787349-21.237134632-9.84801641378-15.22448198
45.781717120.182210986551-0.9762814693194.15237648519-0.7808535361863.08210816928-0.01160950605060.111430557049-0.127481454875-0.2625584585330.0317622586767-0.177693085210.265640504131-0.00960230426037-0.02176839231730.205652822683-0.00805654217208-0.02574877432160.1032409093870.0001677875507890.160690848296-31.7957054325-11.8782781614-6.85209961904
53.970223716910.179209271103-2.21464183963.95725816197-0.02325237289393.695890570480.0480543571124-0.400498651316-0.05934738607250.1753019269430.0381666708103-0.2339809714970.05473732883650.553531802848-0.06692089760090.181856500338-0.002365734589640.002408511730620.2998742238640.002364426065780.1708980656570.641105481395-30.916798139821.0993421631
64.88385965699-0.145322673739-0.1844964551824.502389745690.722046764175.655091886180.02090540381220.1875187527170.0546495822551-0.298837428565-0.0182041084784-0.432404533278-0.03392890449590.4106548384370.01236450604010.245362155848-0.0007595311552520.002399803728420.1977148156710.01873752760230.1788849454044.89155152058-13.688616008940.7299328817
72.267621711353.069181019272.662487416514.523549385363.955053023923.46180716330.286770976788-2.710520704130.6608998115271.93840745463-0.390110772079-0.094217717565-1.215665149610.2737988776930.04735410446790.7456830519520.0181469290844-0.1020677692610.806464271367-0.1538394250590.498394741092-30.1958121431-8.2661432958617.8475947926
87.83272160541-5.643414591845.413085690555.69454665608-4.390478103993.88837040075-0.219265743890.04185284764530.1287137953580.4466430779120.0311994355976-0.239307276648-0.2376942113980.1297752331110.1715558339950.229261718902-0.00510925578464-0.03357768851930.163957196482-0.01194167651720.178091229822-29.8522643239-14.90672119579.21185190863
94.482328217881.822076667035.446071907792.020110028111.991893689226.654740347890.09785767436260.3164962492270.122244265774-0.0208327964640.0370956273838-0.04619352412030.1154596318560.541894650769-0.08775855184040.419447839884-0.0503210198842-0.07336399622840.331759559270.02826061869480.28425791593-19.4637566151-7.3327209003118.2639877145
103.13776634186-5.24852381285-3.63906407139.733414988144.501377397727.3991135495-0.0229431897537-0.09116706179280.3776209845530.5284996440810.0614229382735-0.1844219209260.8389763281730.6879633062320.01329367796540.280472191696-0.0216966129405-0.006385268886860.3673332237130.03645446438160.289950675872-11.54637287810.46809796878618.1382782485
118.128241702254.41421018376.375389266344.119882524412.361142029565.703804823790.4804136010750.509916955604-2.01883112119-0.430993289576-0.390675579091.293418397371.80212628017-2.34488427705-0.3399793700150.622207859916-0.15747342662-0.151415807480.744425627542-0.1244959127020.826864316277-20.0050263041-18.154346360133.3526177035
127.78212367302-2.405596771075.523625985418.18798598021-6.955672934517.62192760380.1355223806170.138189712878-0.05068675681-0.4986562885240.1129039299410.3412374774280.3250413132160.250294488708-0.2184125055820.2698406196680.00657688336788-0.04353984040820.199841659096-0.057790289660.208401375107-11.7887315734-10.080033625736.269805279
139.641712450314.985516893486.884218671818.542613732037.657649511139.38142264565-0.2393877386610.185998976469-0.08991710885290.2007075625890.430959483704-0.183815196891-0.124604445640.204100555571-0.1998169081910.3314563417080.0716621998301-0.04911654899010.266671388946-0.03322617930080.242266541361-18.5347209011-16.990477243723.4547096192
143.83462315684-2.86219139126-4.339271448732.424830696243.449811981975.18952837896-0.484605928660.212732228472-0.5659050111360.05962773428870.1310093559570.438019330053-0.0865209625734-0.4911039870440.4701509021390.2795906538320.01189544215110.03614609471790.2567233940560.0212580614490.343725807676-15.0155345582-24.957926428316.4857060706
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2550 through 2570 )AA2550 - 25701 - 21
22chain 'A' and (resid 2571 through 2630 )AA2571 - 263022 - 81
33chain 'A' and (resid 2631 through 2644 )AA2631 - 264482 - 95
44chain 'A' and (resid 2645 through 2700 )AA2645 - 270096 - 151
55chain 'B' and (resid 2550 through 2630 )BB2550 - 26301 - 81
66chain 'B' and (resid 2631 through 2700 )BB2631 - 270082 - 151
77chain 'C' and (resid 396 through 403 )CC396 - 4031 - 8
88chain 'C' and (resid 404 through 421 )CC404 - 4219 - 26
99chain 'C' and (resid 422 through 434 )CC422 - 43427 - 39
1010chain 'C' and (resid 435 through 442 )CC435 - 44240 - 47
1111chain 'D' and (resid 396 through 403 )DE396 - 4031 - 8
1212chain 'D' and (resid 404 through 421 )DE404 - 4219 - 26
1313chain 'D' and (resid 422 through 435 )DE422 - 43527 - 40
1414chain 'D' and (resid 436 through 442 )DE436 - 44241 - 47

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