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- PDB-7q41: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2... -

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Basic information

Entry
Database: PDB / ID: 7q41
TitleCrystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP)
Components
  • E3 ubiquitin-protein ligase HERC2
  • Ubiquitin-protein ligase E3A (E6AP) peptide
KeywordsPROTEIN BINDING / 7-bladed beta-propeller E3 ubiquitin-protein ligase HERC2 RCC1-like Domain 2 RLD2 ubiquitin ligase ubiquitin-protein ligase E3A UBE3A E6AP DXDKDED motif
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 / ubiquitin protein ligase binding / DNA damage response / zinc ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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
CITRIC ACID / E3 ubiquitin-protein ligase HERC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01478056714 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 ubiquitin-protein ligase E3A (E6AP)
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
B: Ubiquitin-protein ligase E3A (E6AP) peptide
D: Ubiquitin-protein ligase E3A (E6AP) peptide
A: E3 ubiquitin-protein ligase HERC2
C: E3 ubiquitin-protein ligase HERC2
E: E3 ubiquitin-protein ligase HERC2
F: Ubiquitin-protein ligase E3A (E6AP) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8708
Polymers133,4866
Non-polymers3842
Water93752
1
B: Ubiquitin-protein ligase E3A (E6AP) peptide
A: E3 ubiquitin-protein ligase HERC2


Theoretical massNumber of molelcules
Total (without water)44,4952
Polymers44,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ubiquitin-protein ligase E3A (E6AP) peptide
C: E3 ubiquitin-protein ligase HERC2


Theoretical massNumber of molelcules
Total (without water)44,4952
Polymers44,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: E3 ubiquitin-protein ligase HERC2
F: Ubiquitin-protein ligase E3A (E6AP) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8804
Polymers44,4952
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.952, 108.952, 243.160
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/peptide Ubiquitin-protein ligase E3A (E6AP) peptide


Mass: 1724.774 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)
#2: 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
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 293.1500 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: 0.999882 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999882 Å / Relative weight: 1
ReflectionResolution: 3.01→48.725 Å / Num. obs: 54825 / % possible obs: 99.2 % / Redundancy: 5.91558595531 % / Biso Wilson estimate: 58.2859737188 Å2 / CC1/2: 0.968 / Net I/σ(I): 5.81
Reflection shellResolution: 3.01→3.2 Å / Num. unique obs: 8710 / CC1/2: 0.401

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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: 3.01478056714→48.7248156569 Å / SU ML: 0.427298477345 / Cross valid method: FREE R-VALUE / σ(F): 1.34693515008 / Phase error: 25.685611377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.255047390534 2747 5.01460387003 %
Rwork0.198473603185 52033 -
obs0.201297269544 54780 99.3200979059 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.9796357813 Å2
Refinement stepCycle: LAST / Resolution: 3.01478056714→48.7248156569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8406 0 26 52 8484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009398139584038599
X-RAY DIFFRACTIONf_angle_d1.0939256511911611
X-RAY DIFFRACTIONf_chiral_restr0.06512481797271289
X-RAY DIFFRACTIONf_plane_restr0.005473781815831504
X-RAY DIFFRACTIONf_dihedral_angle_d7.318805430326205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0148-3.06680.3444369617991330.3421680719422448X-RAY DIFFRACTION94.12837345
3.0668-3.12250.3633807591371340.3243010600522634X-RAY DIFFRACTION99.3182633656
3.1225-3.18260.3188092989811390.2994618929522573X-RAY DIFFRACTION99.4499449945
3.1826-3.24750.3588851387381360.2782106935672595X-RAY DIFFRACTION99.2729916394
3.2475-3.31810.2976859755491370.2831005849862601X-RAY DIFFRACTION99.4912790698
3.3181-3.39530.3606132358831380.2718434701062628X-RAY DIFFRACTION99.4248741912
3.3953-3.48020.3452459668281350.2611998952912617X-RAY DIFFRACTION99.3143269578
3.4802-3.57420.3574555444461370.237762505622599X-RAY DIFFRACTION99.5633187773
3.5742-3.67940.2834194335041390.2279638385372594X-RAY DIFFRACTION99.4541484716
3.6794-3.79810.241471497311430.2155072766272589X-RAY DIFFRACTION99.5626822157
3.7981-3.93380.272039652771330.2116981611622614X-RAY DIFFRACTION99.4209192906
3.9338-4.09120.2440514187611380.1769341850612629X-RAY DIFFRACTION99.7836278399
4.0912-4.27730.2236351935881390.1586963503522618X-RAY DIFFRACTION99.782844734
4.2773-4.50270.1997860202991450.153536285992597X-RAY DIFFRACTION99.636627907
4.5027-4.78450.187638600111370.1421897516472622X-RAY DIFFRACTION99.7469269704
4.7845-5.15360.2120009180861330.1376413944812607X-RAY DIFFRACTION99.7815003642
5.1536-5.67150.2157305172031390.1461084487492638X-RAY DIFFRACTION99.8561668465
5.6715-6.49050.222655100241320.1648232357162609X-RAY DIFFRACTION99.9635302699
6.4905-8.17110.2039212295521410.1611481150582612X-RAY DIFFRACTION99.9274047187
8.1711-48.72481565690.2404986905571390.1851550723952609X-RAY DIFFRACTION99.5652173913
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)
13.34640292961-1.67988558796-2.883507640151.003289816551.37890960642.91908875482-0.02741266650180.561449164112-1.024018172090.287749205870.217060980707-0.421744070346-0.6651943789870.483890631048-0.011027288580.960257185237-0.4359650867550.1104933553141.03966870506-0.2108666748830.91732208420519.523547231950.6878904685-31.0771127519
25.858196096020.945366845773-2.641408676415.22637568606-6.20748467868.252528315750.4519270198650.726983775368-0.3294087375611.408441650450.868332530465-1.06674850325-4.76696550912-2.70510844946-1.456610065421.535527357040.646295043750.1131132487551.06582063815-0.04006336801471.355535348587.6595945594767.66949750326.00049717181
32.98662710392-2.16406453652-0.02226462281876.003544399740.6711096725414.380087408050.4273880374660.7673503717610.032442976597-0.466670957188-0.103016385986-0.7628010751810.2275384262430.805899641161-0.2295573358660.3906501038830.09882668214220.05884499539310.860577352583-0.1166360497370.50893340632825.739791289839.8320696225-46.6047478563
41.56888011668-1.96254313592-1.164629220346.970189353071.211613101050.8833641344780.3019660561570.5989280072720.1185535445630.182926115406-0.132312437694-0.9878255673030.363664477930.622673220821-0.2227183651140.4032267106650.243016530528-0.1686950145320.942165249403-0.2245601237260.64463892154528.989464729227.6922810708-35.6264222714
58.660910925040.231210150592-0.6933677684469.435409248690.01242309310624.821290778870.1925641375250.447026267354-0.8347460373870.673010271310.0679320840661-1.089784624520.758422284950.916806026453-0.2624980993780.5681339268480.301428564882-0.1135169324750.654263354588-0.1381872500050.63467309905329.833635293923.3385325857-31.402691443
65.79785754015-1.427578076880.5541689304333.81193219862-1.127301986312.30394096982-0.061211647597-0.357365305696-0.6058096154840.6559096686950.4654041609120.1469656946111.039773160420.519020327013-0.4019807028620.807816266260.288848529572-0.154473130260.480203213012-0.09590574616520.42177432555718.146752658424.8938736921-23.920246649
72.96345214504-0.7108386908780.9494585232897.192497851271.067767128772.515340760110.1355765733280.100907256899-0.1997023287980.3801393898640.001336351911750.1772207290010.185334056377-0.182096901092-0.2042320832660.3535309091580.07852973878190.04005862003630.4191212124280.006955359976930.3415565985624.6857067110933.5951217614-27.6389820814
83.905691262312.870464396681.268072321423.915628888531.244419916695.387432122980.02972595628480.3006009052290.146801998972-0.314339097693-0.009404279916790.485072589545-0.258062110902-0.4317096235540.02569490408070.3297051963370.160305486217-0.01835372454960.58187281436-0.03547989016580.3737573234185.6825632055742.3665564476-42.5055695055
94.19104254421-0.1666776234125.827991555876.73462568758-2.903105922519.16054271135-0.1520970581760.253540485148-0.109823619484-1.036089725190.2901159408610.0008460459270170.640790774394-0.483442172344-0.2392831777760.4909666748230.0713463536204-0.008917379142850.726422223538-0.09442405407130.356700719312.755730634338.2058726191-49.5631245915
104.824633273432.428778891460.2178291467711.953049090291.395440641283.10847217929-0.02446732945270.5935056327350.497237981185-0.296700353417-0.179398226303-0.0179271824587-0.5401828283690.3360731157940.2284467470630.5051055397390.00211662404786-0.04770552862470.3854016507970.1627509936630.37522459629620.999015100863.6498259125-7.76530002472
117.50219420771-2.47149623835-0.2958788354053.242839386634.086147343086.55788952134-0.1943011189240.3233752993230.3328672697080.1198455632680.222301447429-0.415047724476-0.2311349540420.785527847067-0.03018157551480.415500353621-0.108514536797-0.02546350331810.4192961029330.1561120998010.38472241104833.640640593962.69222400666.28633914543
124.775003925671.734148897-0.2346440025053.69079653814-0.4656328474642.879022570980.127899923939-0.476332214471-0.3425668291980.457976102229-0.230051419042-0.2860519337640.3926347671620.3089811402420.1304062906580.490271108120.00751733815349-0.01326460182430.3428639768020.07264252632440.28338047938723.993793537952.086520014618.4363410736
132.065923761050.1086125160780.4115682738070.7630142108670.3861901482017.147762479150.1254343627720.149780972104-0.1083230467870.191824724297-0.1535570364050.04971887802170.425016623995-0.4358535735430.01055950424790.402813225507-0.04426887832560.044177479820.284251935261-0.00081453691710.3282395412959.4982420143549.68575592771.77486704964
145.99782323914-1.71966059263-0.7767679285653.758344652440.9851558098564.645118823920.3464838859320.617104503056-0.2438902892-0.191102800707-0.2252429084940.7331026893450.275300602483-0.714435782648-0.04937118195470.329195717412-0.00813320319226-0.02880573011190.4413377101340.004267482548050.548705931443-29.876310941152.7376505808-26.2610177267
153.933715541220.2408532685740.7298264746733.395496423950.2509293045952.616740778110.0251109588062-0.4965419391140.3579562461250.6290293637620.1130818470160.662411116276-0.0684604133691-0.69121887501-0.1272409658590.5076116360630.1482604576460.279510168150.646054402752-0.04010525678820.682196504169-32.576802180662.490264164-8.67584825708
163.69417328034-0.7247328609650.6646972499652.914443882780.4811169455574.458976508970.00491709084009-0.2367946045760.3473360047970.443682289133-0.02550768418230.131709308575-0.0627948823805-0.00777002879929-0.02250163427460.259365095411-0.007589326033790.05612385156990.316279204218-0.01700714721850.364491531514-11.73625814959.3432470269-16.0524410199
176.2297895794.291220881940.05980411700398.37602076897-1.09677508620.2392213764160.807885760241-0.5109111098340.685654856752-0.9605437685510.226684587474-0.762952646401-2.223792589971.48366040436-0.8523077051992.06331614264-0.1420283729340.8393314067881.515708160530.2031535263461.96086546555-17.887233088241.3265716544-14.6820389378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 186 through 194 )
2X-RAY DIFFRACTION2chain 'D' and (resid 187 through 193 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2958 through 3037 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3038 through 3082 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3083 through 3106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 3107 through 3169 )
7X-RAY DIFFRACTION7chain 'A' and (resid 3170 through 3250 )
8X-RAY DIFFRACTION8chain 'A' and (resid 3251 through 3302 )
9X-RAY DIFFRACTION9chain 'A' and (resid 3303 through 3326 )
10X-RAY DIFFRACTION10chain 'C' and (resid 2959 through 3037 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3038 through 3106 )
12X-RAY DIFFRACTION12chain 'C' and (resid 3107 through 3212 )
13X-RAY DIFFRACTION13chain 'C' and (resid 3213 through 3326 )
14X-RAY DIFFRACTION14chain 'E' and (resid 2959 through 3082 )
15X-RAY DIFFRACTION15chain 'E' and (resid 3083 through 3169 )
16X-RAY DIFFRACTION16chain 'E' and (resid 3170 through 3326 )
17X-RAY DIFFRACTION17chain 'F' and (resid 187 through 193 )

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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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