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- PDB-7q40: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 -

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Basic information

Entry
Database: PDB / ID: 7q40
TitleCrystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2
ComponentsE3 ubiquitin-protein ligase HERC2
KeywordsPROTEIN BINDING / 7-bladed beta-propeller HERC2 RCC1-like Domain 2 RLD2 ubiquitin ligase 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 / DNA damage response / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
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: 2.35002226075 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,04112
Polymers128,3123
Non-polymers1,7299
Water4,270237
1
A: E3 ubiquitin-protein ligase HERC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1553
Polymers42,7711
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E3 ubiquitin-protein ligase HERC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3474
Polymers42,7711
Non-polymers5763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: E3 ubiquitin-protein ligase HERC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5395
Polymers42,7711
Non-polymers7684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.540, 108.540, 243.090
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: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.35→54.27 Å / Num. obs: 60722 / % possible obs: 98.8 % / Redundancy: 26.6657389414 % / Biso Wilson estimate: 48.3943368623 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.21
Reflection shellResolution: 2.35→2.41 Å / Num. unique obs: 4062 / CC1/2: 0.473

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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: 2.35002226075→54.27 Å / SU ML: 0.328804329183 / Cross valid method: FREE R-VALUE / σ(F): 1.35165496232 / Phase error: 25.8528569351
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.230322144529 3033 5.00387705608 %
Rwork0.178924037543 57580 -
obs0.181466050477 60613 98.8003064435 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.9293356942 Å2
Refinement stepCycle: LAST / Resolution: 2.35002226075→54.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8249 0 117 237 8603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006859265367268529
X-RAY DIFFRACTIONf_angle_d0.85350909916911527
X-RAY DIFFRACTIONf_chiral_restr0.05374117659041270
X-RAY DIFFRACTIONf_plane_restr0.00403929788251492
X-RAY DIFFRACTIONf_dihedral_angle_d20.96840302943054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35002226075-2.38670.382307067281210.3189925555492288X-RAY DIFFRACTION88.3064516129
2.3867-2.42590.3707752503351310.2991148802382488X-RAY DIFFRACTION95.5490696826
2.4259-2.46770.3455765018751340.2813633024722540X-RAY DIFFRACTION96.5342960289
2.4677-2.51260.2795186378461330.2500896864782539X-RAY DIFFRACTION98.2714233174
2.5126-2.56090.2931991930651370.2303551154772596X-RAY DIFFRACTION99.0217391304
2.5609-2.61320.2876966616691360.2304535437152573X-RAY DIFFRACTION99.3399339934
2.6132-2.670.2784290643841370.2335603295752596X-RAY DIFFRACTION99.5628415301
2.67-2.73210.2695665432931370.2284081786182595X-RAY DIFFRACTION99.5626822157
2.7321-2.80040.330185301451380.2188570436942625X-RAY DIFFRACTION99.6393797331
2.8004-2.87610.2611873298711370.2165314017392605X-RAY DIFFRACTION99.7090909091
2.8761-2.96080.2581948317511390.2175877844322643X-RAY DIFFRACTION99.4637111191
2.9608-3.05630.3109775711891360.2150088599932580X-RAY DIFFRACTION99.5966263293
3.0563-3.16550.3306649872691390.2174834117612630X-RAY DIFFRACTION99.7837837838
3.1655-3.29230.241956425471390.2040586556092648X-RAY DIFFRACTION99.8566821928
3.2923-3.44210.2678328374981380.2002708633462618X-RAY DIFFRACTION99.8189061934
3.4421-3.62350.2386447524451400.1740287420452663X-RAY DIFFRACTION99.8574991094
3.6235-3.85050.2016230560631390.1566867818632650X-RAY DIFFRACTION99.9641577061
3.8505-4.14770.2025199937661400.1418604942822664X-RAY DIFFRACTION99.9643493761
4.1477-4.56490.1746727198271420.1306082708332679X-RAY DIFFRACTION100
4.5649-5.2250.1724653714281410.1301124562012716X-RAY DIFFRACTION99.9650104969
5.225-6.58110.2063056229051450.1495280416332745X-RAY DIFFRACTION100
6.5811-54.270.1844583274631540.1715405568912899X-RAY DIFFRACTION99.4786575432
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)
13.19650467201-2.62090704281-0.1899307095415.34372653291.380394762572.853454638640.2460302743460.537458127274-0.0885234741837-0.370949734557-0.166522221230.688712906199-0.242605851187-0.921547896494-0.0675939588280.3698650087650.1066840914870.002011148338940.8255962657370.116775066690.450623268475-26.6435732801-34.7849690363-42.8303747054
26.54351950479-0.6981100029690.5647684392328.180401810721.033989453915.343079800980.07865222034380.3956435544360.5348207955650.3200477744050.03067135504160.768064314114-0.817506387479-1.16785915491-0.1476249759140.5813386549470.2975358019210.09898989138560.8495607676120.1784777684680.438468852987-29.6962045854-22.8519065785-31.4673636756
35.64989915688-1.94670559916-0.8325243794432.445783819850.902148290544.3262680334-0.0466884693311-0.3945395040690.5738768960.6208231022430.4647387014720.143958371609-1.08724161468-0.784479834473-0.4327159371060.6789659625050.2342464784550.08849440528510.5023134280670.07436961761740.393595700422-18.0608016176-24.6768655103-23.9129402751
43.2313506103-0.369453420671-0.3482293281674.290390877730.2440029994893.459927466950.03412688486420.007789997140520.3339163534870.3145511939610.143071948507-0.105443423598-0.2424109167250.182451982837-0.1841461349040.3431373337940.0580245094861-0.01247416665190.3615522550310.02639495596720.309271982592-4.66275636145-33.3521410648-27.5424057025
55.859799992731.66051921228-1.069001617947.47627544976-0.3590574339184.437889842790.0625216654840.409520725708-0.0268667329019-0.189878744081-0.0806230576893-0.6576085917040.1384903753550.407039913025-0.0348094414750.326368817150.102393824505-0.01445357262690.450072792120.0500061018130.287792106956-5.52418592529-41.9871768006-42.5339572826
66.649586412681.05952785351-6.275415107347.610731782590.3328879090969.325563527250.198945587580.5990718193930.260530643094-0.9532022347590.2264845347630.443548819662-0.389594553485-0.527704566033-0.4348726815340.4424122394840.081234273875-0.06476525762170.6465227613310.09242845147610.355293605124-12.4261156382-37.7783986871-49.6517671073
76.13589327934-0.224962660926-0.01372099365164.11485633739-1.486249145514.198221511380.1865543711130.919692857777-0.113396991949-0.695175123634-0.3286490949490.009417165816070.3154413380460.05107684430220.15434260630.4777389668270.01507195332490.008934649465580.44138718199-0.0311517337940.245385158159-17.6834575812-59.8254605873-10.8315004754
83.38660752498-0.0954800759925-0.7497831986843.96217291754-0.7434051300772.690209459860.02315961061350.393046530665-0.309045829784-0.704775023976-0.1527499359240.2632769164770.516382352105-0.491988271270.08830282581670.449857586615-0.0255631032748-0.01704805322860.487485298992-0.1084629843250.311637282778-26.1013177544-66.9682071932-4.61615785664
97.91864039739-1.663513225680.1151323703532.63755152208-2.087561170097.24492798483-0.02111892286530.259366083497-0.210099964518-0.146334342762-0.01345933692420.4261321775710.472919745478-0.5811742890220.03446509885490.433392613501-0.0732541271868-0.02819983726450.371051157113-0.09084786097220.387908574103-33.686162242-62.50048989326.37399523351
102.383593146451.038950170020.2354549437862.53834995776-0.5301795620531.601509022010.0399459230722-0.3028695067970.2022452762240.235599489792-0.1389506754640.105727597957-0.315398359851-0.1890479233950.08832866309860.4410918344310.00814359205577-0.008109071184850.373468411021-0.06667683258440.313758855104-23.864223874-51.995215160918.4669401964
112.03196392729-0.0543668296022-0.4955469978881.893367272420.3777472332425.42567380685-0.02441254239420.08822758878120.25196924254-0.0526450384459-0.0881322847159-0.263125313855-0.2868955097580.419448734640.1074792511170.320162127462-0.0167761721317-0.03143089891080.3452448004270.05485792687570.32458365055-7.98510474844-49.22245703294.33227566346
122.448328345184.61403483176-4.900963393799.98008147587-8.355301312382.13350313774-0.02666260552260.3951852492250.1040080671740.1436749512320.07658274123590.0451201030847-0.117551352584-0.2572628762310.03222132126530.4670255864340.0498292161731-0.0869807410280.447921044138-0.03035270848830.242663306159-15.337692904-51.1456946897-8.32716903768
137.37313684948-0.4536118550541.052260181315.445988823441.686834924616.625163755920.2267790157690.7405142019140.026849644037-0.707488676735-0.0250177309434-0.322622571749-0.2884700998750.251091551393-0.2006580890510.312784315850.0210118737770.04404551073360.4153287782150.05279481105440.3096955471821.1059341872-50.0982739201-32.8295457991
144.63340983964-0.9385989212921.475187190873.00913313017-0.4707234151915.373669588220.1877968073950.1687577906440.0232008942304-0.0632283228461-0.0924644470426-0.643013405135-0.01097905255310.731247689188-0.1129573892080.30074035291-0.0213964922676-0.01003052222050.4273654792420.01954727316390.52091279258934.5334919722-53.9791199689-22.9540084963
150.6291184238112.08141182443-0.7260879921279.634519668160.2639160037634.426302624830.01865401487870.00876076787759-0.433254796201-0.08937514074850.0725507582489-1.062982352550.3883652890.72873282327-0.124367276870.3232633607360.0823833862206-0.08309419705260.5405817026260.05281489399280.59847067533939.5936447555-60.5693677147-15.5412460015
164.24120892494-0.1293230822270.5564971749161.52276494799-0.2275836043292.10660500270.114659992211-0.594965225297-0.5245405270370.427620516065-0.0350010614441-0.42289247440.180908809934-0.0293994252459-0.0779326018680.452897126521-0.0271558531146-0.125447523710.3895812019640.09633144885260.44572111134920.2376773827-62.6830925417-6.94644032458
173.20339002926-0.899443256571-0.4133982107523.81812835773-0.04363076262742.962068655790.04485896213180.236774765407-0.1138269717470.02165837898360.006248875298390.142931836691-0.0174789390881-0.41388206011-0.07015880536940.2973344544350.0169757414908-0.05097126854560.411395631023-0.0009413068679660.2901691350127.96342905599-55.6337385885-22.7931361713
185.538138706161.827211511274.820795741567.781067711381.585520698115.210656230040.2653486712250.671857720318-0.330822618514-0.2892076743390.0124405918075-0.5936210340040.2508125488250.0314302662599-0.3179109969170.328284765821-0.02917728146690.0674157607870.414922550041-0.02332334765970.29701245784914.4864683019-57.0831107504-30.8982884112
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 3169 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3170 through 3250 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3251 through 3302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 3303 through 3326 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2957 through 3000 )
8X-RAY DIFFRACTION8chain 'C' and (resid 3001 through 3037 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3038 through 3106 )
10X-RAY DIFFRACTION10chain 'C' and (resid 3107 through 3212 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3213 through 3302 )
12X-RAY DIFFRACTION12chain 'C' and (resid 3303 through 3326 )
13X-RAY DIFFRACTION13chain 'E' and (resid 2958 through 3000 )
14X-RAY DIFFRACTION14chain 'E' and (resid 3001 through 3082 )
15X-RAY DIFFRACTION15chain 'E' and (resid 3083 through 3106 )
16X-RAY DIFFRACTION16chain 'E' and (resid 3107 through 3250 )
17X-RAY DIFFRACTION17chain 'E' and (resid 3251 through 3302 )
18X-RAY DIFFRACTION18chain 'E' and (resid 3303 through 3326 )

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  • 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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