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- PDB-7q46: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2... -

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Basic information

Entry
Database: PDB / ID: 7q46
TitleCrystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein
Components
  • E3 ubiquitin-protein ligase HERC2
  • Pericentriolar material 1 protein
KeywordsPROTEIN BINDING / 7-bladed beta-propeller HERC2 RCC1-like Domain 2 RLD2 ubiquitin ligase PCM1 pericentriolar material 1 protein DXDKDED motif
Function / homology
Function and homology information


protein-containing complex localization to centriolar satellite / intraciliary transport involved in cilium assembly / interkinetic nuclear migration / microtubule anchoring / microtubule anchoring at centrosome / ciliary transition zone / regulation of protein complex stability / neuronal stem cell population maintenance / SUMO binding / positive regulation of intracellular protein transport ...protein-containing complex localization to centriolar satellite / intraciliary transport involved in cilium assembly / interkinetic nuclear migration / microtubule anchoring / microtubule anchoring at centrosome / ciliary transition zone / regulation of protein complex stability / neuronal stem cell population maintenance / SUMO binding / positive regulation of intracellular protein transport / non-motile cilium assembly / HECT-type E3 ubiquitin transferase / centrosome cycle / protein localization to centrosome / pericentriolar material / social behavior / centriolar satellite / cilium assembly / SUMOylation of DNA damage response and repair proteins / cytoplasmic microtubule organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / ciliary basal body / guanyl-nucleotide exchange factor activity / Nonhomologous End-Joining (NHEJ) / intracellular protein transport / neuron migration / G2/M DNA damage checkpoint / negative regulation of neurogenesis / Regulation of PLK1 Activity at G2/M Transition / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / apical part of cell / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / spermatogenesis / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / protein ubiquitination / DNA repair / centrosome / ubiquitin protein ligase binding / DNA damage response / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Pericentriolar material 1 protein / Pericentriolar material 1 protein, C-terminal / Pericentriolar material 1 C terminus / 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 ...Pericentriolar material 1 protein / Pericentriolar material 1 protein, C-terminal / Pericentriolar material 1 C terminus / 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. / Galactose-binding-like domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
CITRIC ACID / E3 ubiquitin-protein ligase HERC2 / Pericentriolar material 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46002538066 Å
AuthorsDemenge, A. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / McEwen, A.G. / Trave, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of pericentriolar material 1 protein
Authors: Demenge, A. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / McEwen, A.G. / Trave, G.
History
DepositionOct 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
C: E3 ubiquitin-protein ligase HERC2
D: Pericentriolar material 1 protein
E: E3 ubiquitin-protein ligase HERC2
F: Pericentriolar material 1 protein
B: Pericentriolar material 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8557
Polymers133,6636
Non-polymers1921
Water8,305461
1
A: E3 ubiquitin-protein ligase HERC2
B: Pericentriolar material 1 protein


Theoretical massNumber of molelcules
Total (without water)44,5542
Polymers44,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E3 ubiquitin-protein ligase HERC2
D: Pericentriolar material 1 protein


Theoretical massNumber of molelcules
Total (without water)44,5542
Polymers44,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: E3 ubiquitin-protein ligase HERC2
F: Pericentriolar material 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7473
Polymers44,5542
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.660, 107.660, 241.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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: 42770.566 Da / Num. of mol.: 3
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/peptide Pericentriolar material 1 protein / PCM-1 / hPCM-1


Mass: 1783.818 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: n-terminally biotinylated peptide via 1,13-diamino-4,7,10-trioxatridecan-succinamic acid
Source: (synth.) Homo sapiens (human) / References: UniProt: Q15154
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: hanging drop 20% PEG 3350 0.18M tris amonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0000292690819 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000292690819 Å / Relative weight: 1
ReflectionResolution: 2.46→49.156 Å / Num. obs: 52438 / % possible obs: 100 % / Redundancy: 26.5269079675 % / Biso Wilson estimate: 32.7291669667 Å2 / CC1/2: 0.984 / Net I/σ(I): 6.33
Reflection shellResolution: 2.46→2.52 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3788 / CC1/2: 0.498

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KCI

3kci


Resolution: 2.46002538066→49.1559595158 Å / SU ML: 0.319425306968 / Cross valid method: FREE R-VALUE / σ(F): 1.34511025492 / Phase error: 23.1370392962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245337109543 2617 4.99980894884 %
Rwork0.178644261638 49725 -
obs0.181991702573 52342 99.9694411551 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.7000727827 Å2
Refinement stepCycle: LAST / Resolution: 2.46002538066→49.1559595158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8409 0 13 461 8883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007239178159898580
X-RAY DIFFRACTIONf_angle_d0.89201889650811580
X-RAY DIFFRACTIONf_chiral_restr0.05662142568411289
X-RAY DIFFRACTIONf_plane_restr0.00427232125941495
X-RAY DIFFRACTIONf_dihedral_angle_d19.73379354353073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46002538066-2.50480.305127435731360.2348372598442583X-RAY DIFFRACTION100
2.5048-2.55290.3113844726861330.242113631752535X-RAY DIFFRACTION99.8876825159
2.5529-2.6050.3311560548991350.2346442542012566X-RAY DIFFRACTION100
2.605-2.66170.2976874088621360.2380167385652567X-RAY DIFFRACTION99.9630177515
2.6617-2.72360.3311092722821360.2419081056362591X-RAY DIFFRACTION100
2.7236-2.79170.3557205975421360.2378906234412580X-RAY DIFFRACTION100
2.7917-2.86720.2748740272471360.2131546174762574X-RAY DIFFRACTION99.8894213048
2.8672-2.95150.3016491846761350.2064067253872567X-RAY DIFFRACTION99.9630040696
2.9515-3.04680.2751935633511380.1918775495262626X-RAY DIFFRACTION99.9638336347
3.0468-3.15570.2689780412461360.1906559619212578X-RAY DIFFRACTION100
3.1557-3.2820.2473517413191360.1900273333862588X-RAY DIFFRACTION100
3.282-3.43130.2621054055781380.1916391799982623X-RAY DIFFRACTION100
3.4313-3.61220.2272954134361370.1592400673392609X-RAY DIFFRACTION100
3.6122-3.83840.2123724122141380.1508306668822618X-RAY DIFFRACTION99.9637286906
3.8384-4.13460.2117724850451390.1377921191732631X-RAY DIFFRACTION99.9278499278
4.1346-4.55040.1938665029391390.1322173796332640X-RAY DIFFRACTION100
4.5504-5.20830.2028818500711410.1408667591592667X-RAY DIFFRACTION100
5.2083-6.55940.2086050951421430.164943348692707X-RAY DIFFRACTION100
6.5594-49.15595951580.2280506931951490.1890218948672875X-RAY DIFFRACTION99.8678996037
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)
12.22647580193-1.83931580113-0.2284847296635.289378697281.675945778892.231111640190.1010195072060.22009189835-0.0243561087853-0.328825353325-0.2209382247460.286108350904-0.0150867423096-0.2770679926580.0969849419340.1869585578630.0258206423219-0.003169093919270.2992356455030.02034316792670.180732000837-26.3760862727-33.6436897358-42.3054754855
28.301250919961.555430832080.141693846165.73807626132-1.309818401847.671963435910.09732532186930.5282487014240.8323198445260.04233097940820.02189447801350.60402690977-0.871611052169-0.56501575323-0.1183492306460.3119325204960.1205362784730.0120648596420.2881148670610.009411648943860.280173188882-29.0581072941-21.7497730898-30.9592495064
34.9519425796-2.51181572812-1.12733150672.515147589281.223974413382.026748068170.0142504392134-0.2517999053590.3187575942950.09394750726990.0676011706939-0.146485004816-0.266709324910.118592163894-0.07111448233240.295755580081-0.00528682619923-0.006506779455680.2160229561430.0171705942960.160890034607-9.80311775978-28.6393002253-25.7618008042
44.978113192751.22783939565-0.9057548745894.54613552878-0.02602065759624.143924241350.04521372453860.3989514139960.118688826066-0.240395346292-0.022057790561-0.06747282779580.008980341604670.3970789164910.0006606521503280.2515114483860.05939236750560.04187689956370.3002732330450.02922882223010.143351776061-7.54118007885-39.7020026862-44.5976741786
53.919666236580.493382260246-0.9860454311985.46575405319-1.468082007413.100034732220.001509877989550.480959385505-0.147883316149-0.470493617154-0.04532386817130.2272502678920.306224177614-0.3485824833990.03925257179750.251292137438-0.0437662620437-0.021127167850.320321229369-0.06718605482910.15913425586-20.9747771782-62.5395014071-7.9834839179
66.93415648461-0.7945297890640.8271242166661.99520032628-2.379185152168.843209541520.02298215313940.2698284206460.1741186274620.07943096874320.2087293997150.4660841001060.38857247675-0.708429893119-0.2053800213540.252902641259-0.08581166779960.01683515648880.249108417954-0.04347832011040.314155999651-33.2821546147-61.5889393876.21262483231
73.539134873290.8778911919670.5704467602654.8361360469-0.6611334901562.306901082940.126887047986-0.4142811519260.06068072156450.35876487587-0.1289327973360.303113973043-0.0823069636849-0.171580871671-0.005240594861810.240843881473-0.04280942978720.05214261386880.246371556837-0.04214203678030.15600440267-23.3242943645-51.325221663418.3772604158
83.38190190986-0.5636053415320.3537769324072.082659104871.077807280696.29462484090.1654197984270.04625591926960.232260201680.0293221532244-0.035770571227-0.257194738111-0.1561493143190.228185904824-0.1350643804940.152801483831-0.04016053105060.01664547620970.174194804826-0.006099025910390.198327032301-7.50589941736-48.58564872094.17868534283
92.987217356463.06430013226-1.778546532788.82705620671-8.687720704039.367244193020.08357220547150.2873890423970.0024516772182-0.008199627458790.09062969711130.231713778731-0.169023630637-0.10743802063-0.1748674390160.2610829109650.0272422650498-0.03038090407740.193963933571-0.05220866921650.145696742717-15.0189609716-50.3265612496-8.42320920154
108.042669289143.094306565144.505159590018.10182044075-2.347016434114.93178903481-0.0157220979345-1.627501820110.147693875846-0.0529351063014-2.040960911091.193824378881.28189638669-1.172532035672.055382496651.05797658972-0.0703590577938-0.1236790069230.986395659065-0.1460948390560.710535996203-7.8540557199-67.86172500864.67842595711
114.90990799162-1.401060417021.513940820013.02618663633-0.8000726506973.054844316150.02925147592520.5397671265320.225986855771-0.270432524567-0.101446138628-0.45414558024-0.104161781650.3266689204710.06032342778170.208312087858-0.04467191321130.04830855913540.2868135422410.03416425115990.27671086294630.1670013672-52.0059404717-26.3550521051
126.20503754271-0.439890741041-0.2711004793268.793585498450.1996439090686.90943877648-0.2469581153020.259500237033-0.4336993379590.4367549966520.176230931875-1.240570299010.2421993657080.9695756792770.06561001830990.2159161712970.0527792938954-0.05275294060010.415260260095-0.02901534074330.36488835524539.707051642-60.0982869018-15.4871732257
135.90479015558-0.5340314634811.05935743771.31149753962-0.1234419635751.884811000250.111736679002-0.483923661128-0.1654579701280.2130678964550.00576621983423-0.2131114283260.211964951889-0.12585529944-0.1090041163410.253553256451-0.0233275422317-0.03510506904150.2310950119280.04177670089770.19227546195520.345574773-62.0347392016-7.04538838382
143.73122728619-1.556097160.7648174350896.26764344481-0.7425889701633.444057881070.01069429234630.138395097946-0.0807195227962-0.1776042462070.05941288329520.2848989947250.0045839053971-0.293673454193-0.0601669191450.158910152954-0.0183767189098-0.01486502123430.266848150268-0.008386991014990.135278105668.18789085176-54.8797696648-22.8306924056
156.140818145464.614361122065.521592596324.427777238532.415489990438.149066237580.0176912998360.547513842178-0.301364986643-0.2273272026290.162291385627-0.4692665358750.2710836110610.139896740052-0.1737786403440.2338287839710.08347890604710.06530642431530.298607917134-0.02547029704580.25304550782715.1849144072-56.6181221573-30.8741818448
161.704680310950.938221050289-1.050367384740.5161952583-0.5778878282120.6468539967490.186644223032-0.5059214707031.2101748771.976773098060.0574318379593-0.384207822507-3.140030937960.298581152099-0.2450683961351.529125751870.00144045519317-0.3187997230550.631559462149-0.2385308510961.6964306727117.766939122-41.3631144015-14.4638035375
172.28489057544-0.727750848929-0.5390576903227.303451665397.326502358077.365197375381.34195288251-1.73232616576-0.8587098852332.00324859922-1.39784535245-0.1904116493242.86916124447-3.312865075490.05226200329691.00779899726-0.4219527213270.002110393728621.1709027720.2033505399440.831224431263-20.695082533-49.754963462-32.6056251492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2958 through 3082 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3083 through 3106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 3107 through 3250 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3251 through 3326 )
5X-RAY DIFFRACTION5chain 'C' and (resid 2959 through 3037 )
6X-RAY DIFFRACTION6chain 'C' and (resid 3038 through 3106 )
7X-RAY DIFFRACTION7chain 'C' and (resid 3107 through 3212 )
8X-RAY DIFFRACTION8chain 'C' and (resid 3213 through 3302 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3303 through 3326 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1737 through 1744 )
11X-RAY DIFFRACTION11chain 'E' and (resid 2959 through 3082 )
12X-RAY DIFFRACTION12chain 'E' and (resid 3083 through 3106 )
13X-RAY DIFFRACTION13chain 'E' and (resid 3107 through 3250 )
14X-RAY DIFFRACTION14chain 'E' and (resid 3251 through 3302 )
15X-RAY DIFFRACTION15chain 'E' and (resid 3303 through 3326 )
16X-RAY DIFFRACTION16chain 'F' and (resid 1737 through 1742 )
17X-RAY DIFFRACTION17chain 'B' and (resid 1737 through 1745 )

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