PDB-7q44: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2...

ID or keywords:

Entry

Database: PDB / ID: 7q44

Title

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35

Components

Deubiquitinase USP35 peptide
E3 ubiquitin-protein ligase HERC2

Keywords

PROTEIN BINDING / 7-bladed beta-propeller HERC2 RCC1-like Domain 2 RLD2 ubiquitin ligase USP35 deubiquitinase DXDKDED motif

Function / homology

Function and homology information

SUMO binding / HECT-type E3 ubiquitin transferase / protein deubiquitination / 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 ...
Similarity search - Function

: / Ubiquitin carboxyl-terminal hydrolase 38-like, N-terminal domain / 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 ...
Similarity search - Domain/homology

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.20007772782 Å

Authors

Demenge, A. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / McEwen, A.G. / Trave, G.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of deubiquitinase USP35
Authors: Demenge, A. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / McEwen, A.G. / Trave, G.

History

Deposition	Oct 29, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7q44.cif.gz	501.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7q44.ent.gz	364.3 KB	Display	PDB format
PDBx/mmJSON format	7q44.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q4/7q44 ftp://data.pdbj.org/pub/pdb/validation_reports/q4/7q44	HTTPS FTP

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Related structure data

Related structure data	3kciS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (6) #142 - Oct 2011 PDB Pioneers similarity (5) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #55 - Jul 2004 DNA Ligase similarity (2) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: E3 ubiquitin-protein ligase HERC2

C: E3 ubiquitin-protein ligase HERC2

E: E3 ubiquitin-protein ligase HERC2

D: Deubiquitinase USP35 peptide

B: Deubiquitinase USP35 peptide

F: Deubiquitinase USP35 peptide

hetero molecules

134 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: E3 ubiquitin-protein ligase HERC2

B: Deubiquitinase USP35 peptide

defined by author
44.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: E3 ubiquitin-protein ligase HERC2

D: Deubiquitinase USP35 peptide

hetero molecules

defined by author
44.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: E3 ubiquitin-protein ligase HERC2

F: Deubiquitinase USP35 peptide

hetero molecules

defined by author
44.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	108.460, 108.460, 242.850
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2
Space group name Hall	P4nw2abw
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

#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	Deubiquitinase USP35 peptide / Deubiquitinating enzyme 35 / Ubiquitin thioesterase 35 / Ubiquitin-specific-processing protease 35 ...Deubiquitinating enzyme 35 / Ubiquitin thioesterase 35 / Ubiquitin-specific-processing protease 35 / Ubiquitin carboxyl-terminal hydrolase 35 Mass: 1554.461 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: Q9P2H5, ubiquitinyl hydrolase 1
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.49 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG 3350 0.18M tris amonium citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000029 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 10, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.000029 Å / Relative weight: 1
Reflection	Resolution: 2.2→49.516 Å / Num. obs: 74354 / % possible obs: 99.9 % / Redundancy: 26.7427710681 % / B_iso Wilson estimate: 32.0006866889 Å² / CC_1/2: 0.994 / Net I/σ(I): 8.65
Reflection shell	Resolution: 2.2→2.26 Å / Num. unique obs: 5417 / CC_1/2: 0.444

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
PHENIX	1.12_2829	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KCI

3kci

Resolution: 2.20007772782→49.5160649028 Å / SU ML: 0.272364994255 / Cross valid method: FREE R-VALUE / σ(F): 1.34635839883 / Phase error: 22.4754614035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.231046732051	3709	4.99474804062 %
R_work	0.182249275454	70549	-
obs	0.184693201749	74258	99.928678123 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 37.187308999 Å²

Refinement step

Cycle: LAST / Resolution: 2.20007772782→49.5160649028 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8436	0	39	644	9119

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00336706399674	8641
X-RAY DIFFRACTION	f_angle_d	0.633893708813	11668
X-RAY DIFFRACTION	f_chiral_restr	0.0495003936953	1293
X-RAY DIFFRACTION	f_plane_restr	0.00342762737229	1513
X-RAY DIFFRACTION	f_dihedral_angle_d	20.9804520664	3093

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2001-2.229	0.353539197518	140	0.283374409626	2668	X-RAY DIFFRACTION	99.6805111821
2.229-2.2596	0.335321688547	143	0.286332259063	2705	X-RAY DIFFRACTION	99.8597475456
2.2596-2.2918	0.326994828444	138	0.269236406619	2637	X-RAY DIFFRACTION	99.8560633321
2.2918-2.3261	0.296633934909	140	0.256834144341	2656	X-RAY DIFFRACTION	100
2.3261-2.3624	0.298330727045	140	0.240228170727	2663	X-RAY DIFFRACTION	99.7508896797
2.3624-2.4011	0.283854807802	143	0.230742109664	2703	X-RAY DIFFRACTION	99.9297752809
2.4011-2.4425	0.294481197304	139	0.238188058847	2637	X-RAY DIFFRACTION	99.8561151079
2.4425-2.4869	0.284137888991	141	0.219512557856	2686	X-RAY DIFFRACTION	99.9646393211
2.4869-2.5348	0.262321657485	141	0.217455391096	2669	X-RAY DIFFRACTION	99.9644254714
2.5348-2.5865	0.281812732171	142	0.21471685738	2706	X-RAY DIFFRACTION	99.9648999649
2.5865-2.6427	0.264626694399	141	0.223396401069	2679	X-RAY DIFFRACTION	99.9645515775
2.6427-2.7042	0.26461056464	141	0.212761102045	2682	X-RAY DIFFRACTION	100
2.7042-2.7718	0.270230799705	141	0.209900259869	2671	X-RAY DIFFRACTION	99.9644507643
2.7718-2.8468	0.235608565391	142	0.203926453516	2699	X-RAY DIFFRACTION	99.9648135116
2.8468-2.9305	0.246533504059	143	0.192538756269	2715	X-RAY DIFFRACTION	99.9650227352
2.9305-3.0251	0.241668151437	141	0.190447458945	2680	X-RAY DIFFRACTION	100
3.0251-3.1332	0.255457607625	142	0.192512886226	2712	X-RAY DIFFRACTION	100
3.1332-3.2586	0.24475375499	141	0.183525867393	2704	X-RAY DIFFRACTION	100
3.2586-3.4069	0.234853295609	143	0.187001578157	2722	X-RAY DIFFRACTION	100
3.4069-3.5865	0.205284866062	144	0.163573136036	2729	X-RAY DIFFRACTION	100
3.5865-3.8111	0.20224819419	143	0.150047310089	2717	X-RAY DIFFRACTION	99.9650471863
3.8111-4.1052	0.194409892303	144	0.134437243031	2755	X-RAY DIFFRACTION	100
4.1052-4.5181	0.164442414036	144	0.13522941296	2792	X-RAY DIFFRACTION	100
4.5181-5.1713	0.187176065032	146	0.137641480716	2764	X-RAY DIFFRACTION	100
5.1713-6.513	0.182556627204	148	0.157166395667	2810	X-RAY DIFFRACTION	100
6.513-49.5160649028	0.228244017018	158	0.180605217539	2988	X-RAY DIFFRACTION	99.6515679443

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.96253451908	-1.45619674579	0.199557728199	2.52508825628	0.280289864772	1.84765370784	0.100187980918	0.300937974379	-0.0777033131878	-0.183626371675	0.0776340456689	0.42415783193	-0.0916892642756	-0.706958581339	-0.160754994962	0.215801736952	0.0812272864834	0.0257661736974	0.565469632445	0.153726143469	0.335811336634	-26.5610036303	-34.7464509033	-42.9028540077
2	3.00504385417	-1.27803502778	-0.0774266148499	1.68591824802	-0.466894779439	2.80787961423	-0.0353681741371	-0.12887845389	0.309116474365	0.288055603768	0.237430296993	0.0258107244518	-0.566376740011	-0.30074921794	-0.17284300629	0.312762229504	0.108836935075	0.0740968132	0.278670849041	0.0470225695077	0.22227580296	-13.3831002224	-28.5913116641	-26.8333126715
3	2.10884176432	0.715393778931	0.0300386022984	2.42533889115	0.0512347356066	3.00481619097	0.109462966046	0.247249429599	0.0433630333031	-0.202567052518	-0.0223412787943	-0.0600847807004	0.0137375607493	0.179111498975	-0.077537204279	0.229045566797	0.0786923640986	0.0180631931238	0.303873920318	0.0445094466098	0.223487798054	-7.60991467266	-40.6430737034	-44.8514355664
4	2.58144553095	0.995446135226	-1.09878217918	2.0158001921	-0.456945100525	2.96373212376	-0.0863264014161	0.528663830364	-0.103199110678	-0.445654852805	-0.103101687501	-0.0645857662037	0.257278332246	-0.0934954500882	0.162156719816	0.28659820272	0.0109080512619	0.0289169789715	0.303783993343	-0.0125365398826	0.191940809914	-17.4372290468	-60.1915646334	-10.7838090658
5	2.27148476707	0.191722737635	-0.781431820796	2.15801711769	-0.460805679359	2.34578942055	-0.0433643063513	0.358596354603	-0.131713429305	-0.212952101906	-0.0550751703111	0.265291605427	0.137015602496	-0.193490192834	0.0630478964304	0.188677963487	-0.0197052822014	-0.0249962952778	0.24122212043	-0.0531053305223	0.207637478241	-29.6236858432	-64.566708404	0.431853411122
6	3.71191431298	0.432226672227	-0.438000391778	1.63492233251	0.29805834399	3.52591157356	-0.13238653862	0.0387126612911	-0.0150219219453	-0.122398411119	0.0585183945976	0.426296929944	0.1920524925	-0.459747461154	0.046596072662	0.197425171167	-0.0394074347933	0.00350692150443	0.266853926061	-0.0268909587385	0.30860797186	-36.1697802799	-62.3703510831	9.25755011607
7	2.83774698711	0.237487428862	-0.173093336635	1.49572785345	-0.0111010235233	1.5687278652	0.0429685293748	-0.163518334873	0.128468139852	0.175106564841	-0.110552276084	0.035266639642	-0.134827298114	0.0288510581976	0.0642048662807	0.267080814792	-0.0191131085482	-0.0239446552042	0.196710942216	-0.00691525085759	0.193484836938	-19.7768912125	-51.0559944081	16.382732255
8	1.68622137789	0.209720136394	-0.716202349121	2.21033033709	0.0141244730553	2.37914024809	0.046042337903	0.265207559283	0.140206681835	-0.0150718074147	-0.15513373441	-0.173802511717	-0.16986748528	0.139422271385	0.0723336230847	0.218085660062	0.0357896787889	-0.0250745242603	0.270055684863	0.073140882947	0.246651353179	-10.1024356243	-50.1373822695	-3.40767328862
9	3.38761126113	0.0369148671302	0.195268414795	2.37564343556	0.0595604366549	2.74727129964	0.0691595590908	0.742766897416	0.137020989757	-0.437904980826	0.0125691045878	-0.173383922568	-0.171882220515	-0.0292199860921	-0.0916559827665	0.20358636341	-0.0102485086005	0.0286294883756	0.383547824339	0.0418891197202	0.193444704783	20.9541916057	-49.7431293417	-32.7664937626
10	2.99465756513	-0.00487917592176	0.938107514704	1.52509903709	-0.180441286024	2.74710837887	0.112528393365	0.293382451227	0.108414368662	-0.171454235196	-0.0325223778186	-0.41175582447	0.00342491599188	0.331000255919	-0.0785586366928	0.158385691949	0.00100337928737	0.0345387695851	0.218410545959	-0.00196083478715	0.295593739202	34.4962870669	-53.9577617937	-23.0287077752
11	2.17891553067	-0.271741973026	-0.548106256216	2.39621008514	-0.398832806841	2.85283050373	0.156278736376	0.114294380233	-0.405611709178	-0.0629092640077	0.039429685957	-0.707000750161	0.203966310313	0.516668351891	-0.142239280364	0.236431477656	0.0581283374458	-0.0577300474692	0.337535893426	-0.0291511629693	0.491739421597	39.5874382317	-60.5269812207	-15.5771726557
12	2.49261762629	0.812680593616	0.00882079498491	1.75587778505	-0.253556865333	1.77543850793	0.148334500348	-0.326463393514	-0.466057654509	0.123781454396	-0.0197056221306	-0.391471579626	0.200938792884	0.063404052084	-0.119962380846	0.233898657449	0.0104245673432	-0.100337718612	0.236430834261	0.0322033014871	0.357188484718	29.479746552	-63.4908251369	-6.12119569229
13	2.44275857488	-0.100287146538	0.0533028380196	2.06851108473	-0.0856377880797	1.71011433542	0.124206301957	-0.365749549832	-0.297322968889	0.196711247713	-0.0356674552696	-0.0554442305279	0.134994218733	-0.182237410064	-0.0808744265001	0.205645864372	-0.0200069558152	-0.0510858137098	0.2584704137	0.0455551695903	0.230869657022	13.208801061	-62.2083760004	-7.69746000608
14	1.9071322332	-0.533208235711	-0.132327235164	3.06384863533	0.074412238145	1.27085877852	0.00291714184836	0.155221077302	-0.0498547085733	-0.111584579885	0.0818082904655	0.238275657346	-0.0659940548035	-0.308671128091	-0.0844137354905	0.161503969779	0.0146799130377	-0.0152190648007	0.245156110936	0.0289000588185	0.167136898978	7.9388963009	-55.6557250706	-22.842319299
15	3.559571445	1.11420584219	2.34915190419	1.67453874236	0.446778743138	3.36628730544	0.0859763683917	0.472118121144	-0.412894333487	-0.283713636246	0.0741630985186	-0.182956587628	0.0496204850308	-0.0776604158711	-0.134202021595	0.176998841926	0.0211569366792	0.0159269334515	0.288956255933	-0.0409458674773	0.212973506951	14.4824068033	-57.087506729	-30.9932789792
16	4.16818227165	-1.06551759881	-2.41755679667	2.29360316103	-0.161565484522	3.25073993617	-0.329456552023	-0.232555461799	-0.197672730685	0.86346262642	0.0986103173423	-0.402954308196	0.818287605281	0.204418904344	0.172671013346	0.696182096035	0.143620061514	-0.0704629794266	0.473973031094	0.0360081497344	0.731526539921	-8.20617624767	-68.1208553708	5.43202812621
17	2.46114587345	0.350043778785	-2.28727665479	5.98652342359	2.78252219678	4.42963224696	0.134028719983	-0.622610462096	-0.651057969852	1.14165153152	-0.38781543427	0.04687973352	0.551816574215	-0.637695495771	0.223217952517	0.647454139515	-0.122514133374	0.0461156751379	0.502722724351	0.174409815075	0.628538779074	-20.4471009451	-50.7465787362	-32.5014656566
18	3.93688425693	-0.287992344456	-0.0599200794719	2.37047396421	1.25134265919	0.651539118103	0.168107591795	-0.485226219841	-0.33160183124	0.190842964106	-0.431099985882	-0.195677949626	-0.588441303537	0.0205359642283	0.149702477294	0.986568496472	-0.0439129781451	0.143216418094	0.61302461192	0.107113822044	1.05329329864	17.7241653176	-41.9382633662	-14.4723147558

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2958 through 3082 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 3083 through 3250 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 3251 through 3326 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 2958 through 3000 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 3001 through 3082 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 3083 through 3106 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 3107 through 3250 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 3251 through 3326 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 2958 through 3000 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 3001 through 3082 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 3083 through 3106 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 3107 through 3169 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 3170 through 3250 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 3251 through 3302 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 3303 through 3326 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 989 through 997 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 989 through 998 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 990 through 996 )

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