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- PDB-7q45: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2... -

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Basic information

Entry
Database: PDB / ID: 7q45
TitleCrystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of Myelin transcription factor 1
Components
  • E3 ubiquitin-protein ligase HERC2
  • Myelin transcription factor 1
KeywordsPROTEIN BINDING / 7-bladed beta-propeller E3 ubiquitin-protein ligase HERC2 RCC1-like Domain 2 RLD2 MYT1 Myelin transcription factor 1 DXDKDED motif
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 / nervous system development / 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 / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / DNA-binding transcription factor activity / DNA repair / ubiquitin protein ligase binding / DNA damage response / regulation of DNA-templated transcription / chromatin / DNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Myelin transcription factor 1 / Myelin transcription factor 1 / 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 ...Myelin transcription factor 1 / Myelin transcription factor 1 / 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 / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / 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 / Myelin transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09999588083 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 Myelin transcription factor 1
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

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HERC2
C: E3 ubiquitin-protein ligase HERC2
E: E3 ubiquitin-protein ligase HERC2
B: Myelin transcription factor 1
D: Myelin transcription factor 1
F: Myelin transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0149
Polymers133,4386
Non-polymers5763
Water15,133840
1
A: E3 ubiquitin-protein ligase HERC2
B: Myelin transcription factor 1


Theoretical massNumber of molelcules
Total (without water)44,4792
Polymers44,4792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E3 ubiquitin-protein ligase HERC2
D: Myelin transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6713
Polymers44,4792
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: E3 ubiquitin-protein ligase HERC2
F: Myelin transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8644
Polymers44,4792
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.390, 108.390, 242.310
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 Myelin transcription factor 1 / MyT1 / Myelin transcription factor I / MyTI / PLPB1 / Proteolipid protein-binding protein


Mass: 1708.721 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: Q01538
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / 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: 0.999985 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999985 Å / Relative weight: 1
ReflectionResolution: 2.1→48.473 Å / Num. obs: 84379 / % possible obs: 99.2 % / Redundancy: 26.794735657 % / Biso Wilson estimate: 30.3915849439 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.67
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 6077 / CC1/2: 0.456

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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: 2.09999588083→48.4734816162 Å / SU ML: 0.2737683186 / Cross valid method: FREE R-VALUE / σ(F): 1.34348031376 / Phase error: 21.8201218509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22436902922 4242 5.03089457892 %
Rwork0.184268613443 80077 -
obs0.186274376691 84319 99.3039689083 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.8498423392 Å2
Refinement stepCycle: LAST / Resolution: 2.09999588083→48.4734816162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8423 0 39 840 9302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004063653843258628
X-RAY DIFFRACTIONf_angle_d0.78839247816111653
X-RAY DIFFRACTIONf_chiral_restr0.06055684864611294
X-RAY DIFFRACTIONf_plane_restr0.003893988644391510
X-RAY DIFFRACTIONf_dihedral_angle_d19.3780982213086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.314131678671280.2800580166582616X-RAY DIFFRACTION98.4924623116
2.1239-2.14880.3517803754181530.2771653452192588X-RAY DIFFRACTION98.7391930836
2.1488-2.17510.3078636737781500.279255956382579X-RAY DIFFRACTION98.7337192475
2.1751-2.20260.3133342974621260.2647246629642617X-RAY DIFFRACTION98.7045699892
2.2026-2.23160.3028803632351360.2614616993332618X-RAY DIFFRACTION98.9224137931
2.2316-2.26210.3217893346411420.2612002451412620X-RAY DIFFRACTION98.7839771102
2.2621-2.29450.3407242545671500.2457904061712595X-RAY DIFFRACTION98.9902632528
2.2945-2.32870.2757999203121330.2390264712842634X-RAY DIFFRACTION98.8567345481
2.3287-2.36510.2702758353571470.2358511011452637X-RAY DIFFRACTION99.0747330961
2.3651-2.40390.2917948410781440.2258735427262641X-RAY DIFFRACTION99.039829303
2.4039-2.44530.2509989255511690.2250987888432576X-RAY DIFFRACTION98.9902632528
2.4453-2.48980.2746793778991370.2138049817242635X-RAY DIFFRACTION99.1771019678
2.4898-2.53770.2614607620981540.2175577943712657X-RAY DIFFRACTION99.2234380515
2.5377-2.58950.2653203541591120.2129956533112656X-RAY DIFFRACTION99.2114695341
2.5895-2.64580.2909415084461560.2159418523562630X-RAY DIFFRACTION99.2518703242
2.6458-2.70730.258784484221320.2109217095252658X-RAY DIFFRACTION99.3236027056
2.7073-2.7750.2413543482431440.2014514153382647X-RAY DIFFRACTION99.3592025632
2.775-2.850.2303428573261260.1972711783252670X-RAY DIFFRACTION99.2193044713
2.85-2.93390.2130784053151340.1878848887652668X-RAY DIFFRACTION99.5381882771
2.9339-3.02860.2612207351911500.1800670895962672X-RAY DIFFRACTION99.5063469676
3.0286-3.13680.2243630028181460.1855252082282650X-RAY DIFFRACTION99.679144385
3.1368-3.26230.2197267646761260.1770890757442731X-RAY DIFFRACTION99.6164574616
3.2623-3.41080.2424082293861380.1803217357082683X-RAY DIFFRACTION99.5764207554
3.4108-3.59060.1747218600551340.1561036662072676X-RAY DIFFRACTION99.7161107168
3.5906-3.81540.1728710448071510.142831552832708X-RAY DIFFRACTION99.8254189944
3.8154-4.10990.1548492342911340.1316818292692730X-RAY DIFFRACTION99.8257232485
4.1099-4.52320.192912657761500.1353492638032744X-RAY DIFFRACTION99.9654576857
4.5232-5.17710.1645215738111320.1454890311642777X-RAY DIFFRACTION100
5.1771-6.52010.188506919331480.1645139689232799X-RAY DIFFRACTION99.9321804001
6.5201-48.47348161620.2077012548691600.189020983292965X-RAY DIFFRACTION99.7446536866
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)
12.01442787263-2.31380127810.08004574310465.084683817920.4278465500131.746150777230.1559063066810.305785822609-0.0751507925524-0.391593670016-0.06886948655650.49906537437-0.0667420192432-0.471568240001-0.08830467028760.2179998681490.0371519236292-0.007610690819990.4868528480080.07160261274560.253122862693-25.9006606821-36.0564343024-44.9562308829
23.63112617411-0.6470331622440.172775782653.042812995210.6314962553933.19994228903-0.0817865641027-0.05600277705240.3380181738450.1442814151860.2342105272610.280846700497-0.596560671499-0.629971455194-0.1608236813260.3853492067610.2019329863740.08461638391870.4380828590740.0728375064570.287225581409-25.8037117615-24.218268052-27.0813767565
33.3193467645-1.09788939857-0.5265390180873.25067486960.2807095790292.92086160871-0.0235142206286-0.1835934916750.3181579434770.2549043972610.143320861958-0.0889136361406-0.3912441488150.0622973172545-0.1203878135870.230847250460.0380673248555-0.001961315912710.2115110899390.009590074940350.173805013775-6.43538445455-31.1053305273-27.2517482301
43.29658553251.83651639079-1.255869527975.58304035844-1.353402957024.755427177690.1164674748340.2927355730790.0470331330402-0.2292635301160.00297269334146-0.200723105195-0.02812806095020.204956130698-0.1217817393850.1837049342870.07285017508520.01813653219030.2724382173660.02187380513870.161264024164-7.6267137657-40.4356847957-44.7683401325
53.214656893551.02507451991-1.617349176012.7255179707-1.311969386572.7252413787-0.1348895603680.459209984013-0.114588352864-0.55600976891-0.04535121772170.03982332546220.268662087371-0.248238011420.1910363018110.277141738456-0.00603097032812-0.01254557275440.299744167248-0.05342765982810.159177136288-21.1023750461-63.3806057646-7.87514353523
65.18936850041-0.471129855031-0.05773842165892.09396647447-1.367440565255.50082233218-0.006140272726920.1242061898070.0736220918533-0.04264658944170.0454450858730.4496222457730.165833902345-0.483868436739-0.0233601846820.186001003547-0.0484365566869-0.004092906525390.232907522038-0.05725313111680.264332847613-33.6594387461-62.32046245236.19901104552
73.52544421717-1.20941871570.9784403818778.24038674313-2.680332167953.512806800770.0465121737862-0.238475319452-0.06357074423550.274081973408-0.02097248466220.529358699339-0.119052256161-0.2743291744-0.01191058162610.18226123708-0.03576529122510.006642526034090.217234492336-0.04286045221810.150428129576-27.8374009477-54.944142627818.0128803894
84.42325712537-0.887716326743-1.093456775532.418303869930.6485171625772.173090231980.112300760169-0.1912656956750.2255030277210.170948813262-0.0998190058164-0.0770482996441-0.1749108256230.109670289806-0.007712094929970.214262352311-0.0408211759146-0.03165512623910.16203177029-0.003327935485990.15956072998-13.3465438094-47.808491436715.1206602484
92.47224731174-0.425038876427-0.7555103991846.25723414125-1.133780026323.987770293820.1114938531760.259871661470.2373912926580.0194474612367-0.177571505817-0.219662266712-0.2440431138290.1663872411930.05660800730930.1551193335880.00974375496139-0.01131859954110.2459168288710.05719438555620.169669762041-9.97667326011-49.9605080371-3.36599353969
105.26770317619-1.398590313141.33269207111.99040939272-0.2292710525152.885315716730.09544480145740.6390115834870.34076045139-0.274428584919-0.0822760464702-0.371092718524-0.1447717191760.25873586416-0.0002996504375720.205806588851-0.01783366804560.03888836466250.2688095422310.04997329069050.26531570746928.323513474-51.4648312295-28.4770181765
113.923717972461.01844308652-0.4266168707252.73024581644-0.9605476588893.420404887740.0484345047325-0.184077705765-0.3700405641130.0264909610972-0.0187035129084-0.5304971455250.1717304996180.253841200804-0.04045203793440.2022863369880.0315211819391-0.08855733942370.2135153404350.01589904365590.35172268735533.6783086054-61.5796062317-10.0477438252
122.75785050763-0.1222089497650.5753150618722.01374625128-0.4508536244853.013433763220.0745229773102-0.0775827828714-0.2412781732230.05439173357050.06466414218570.01945608862470.11326344295-0.229093637461-0.1448192997010.131512596006-0.0118369960519-0.01138033157170.1898814015370.01110988659390.19850968371711.7712555118-59.1623900435-16.2699087883
132.037513284765.327515086655.08524185498.736982226744.574042616622.02200945160.645708989229-0.914242043122-0.8431097538361.3005558373-0.1813385324270.3404434835191.93537366053-1.85962371367-0.4123228077350.633185351792-0.1661298842710.03561448706040.8214833435140.1955886867090.662626429214-20.7250914453-50.4205264788-33.0631757068
144.06226947591-1.54736492981-2.469535593436.101615100943.847314064818.536796428280.090971697836-0.381232810375-0.2656438743941.252899488650.510326591488-1.388640843793.121997803421.39942980102-0.6755174214330.8861953446820.209608708076-0.04578379776310.5694938765640.01802299754150.721459710025-7.67604518874-68.4873051144.48662722087
156.27310460316-7.245951617076.104774888119.37942166172-7.762701644292.00177628056-0.0707750795299-0.6187654706490.4303475202971.262553677280.510613235540.519271873597-3.964184274650.954255070099-0.4533049250361.19235058192-0.00580411000604-0.1261054248120.645018551499-0.1487598162910.86355171776218.0793010153-41.1598092541-14.6393799973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2958 through 3063 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3064 through 3144 )
3X-RAY DIFFRACTION3chain 'A' and (resid 3145 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 3169 )
8X-RAY DIFFRACTION8chain 'C' and (resid 3170 through 3250 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3251 through 3326 )
10X-RAY DIFFRACTION10chain 'E' and (resid 2959 through 3063 )
11X-RAY DIFFRACTION11chain 'E' and (resid 3064 through 3169 )
12X-RAY DIFFRACTION12chain 'E' and (resid 3170 through 3326 )
13X-RAY DIFFRACTION13chain 'B' and (resid 249 through 257 )
14X-RAY DIFFRACTION14chain 'D' and (resid 248 through 257 )
15X-RAY DIFFRACTION15chain 'F' and (resid 249 through 255 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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