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

ID or keywords:

Entry

Database: PDB / ID: 7q45

Title

Crystal 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

Keywords

PROTEIN 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 ...
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 ...
Similarity search - Domain/homology

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09999588083 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 Myelin transcription factor 1
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	7q45.cif.gz	506.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7q45.ent.gz	368.2 KB	Display	PDB format
PDBx/mmJSON format	7q45.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7q45_validation.pdf.gz	480.5 KB	Display	wwPDB validaton report
Full document	7q45_full_validation.pdf.gz	489.3 KB	Display
Data in XML	7q45_validation.xml.gz	49.3 KB	Display
Data in CIF	7q45_validation.cif.gz	72.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q4/7q45 ftp://data.pdbj.org/pub/pdb/validation_reports/q4/7q45	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

B: Myelin transcription factor 1

D: Myelin transcription factor 1

F: Myelin transcription factor 1

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: Myelin transcription factor 1

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

2

C: E3 ubiquitin-protein ligase HERC2

D: Myelin transcription factor 1

hetero molecules

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

3

E: E3 ubiquitin-protein ligase HERC2

F: Myelin transcription factor 1

hetero molecules

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

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 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	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 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: 58.43 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999985 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 18, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999985 Å / Relative weight: 1
Reflection	Resolution: 2.1→48.473 Å / Num. obs: 84379 / % possible obs: 99.2 % / Redundancy: 26.794735657 % / B_iso Wilson estimate: 30.3915849439 Å² / CC_1/2: 0.995 / Net I/σ(I): 9.67
Reflection shell	Resolution: 2.1→2.15 Å / Num. unique obs: 6077 / CC_1/2: 0.456

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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: 2.09999588083→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

	R_factor	Num. reflection	% reflection
R_free	0.22436902922	4242	5.03089457892 %
R_work	0.184268613443	80077	-
obs	0.186274376691	84319	99.3039689083 %

Solvent computation

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

Displacement parameters

B_iso mean: 35.8498423392 Å²

Refinement step

Cycle: LAST / Resolution: 2.09999588083→48.4734816162 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8423	0	39	840	9302

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00406365384325	8628
X-RAY DIFFRACTION	f_angle_d	0.788392478161	11653
X-RAY DIFFRACTION	f_chiral_restr	0.0605568486461	1294
X-RAY DIFFRACTION	f_plane_restr	0.00389398864439	1510
X-RAY DIFFRACTION	f_dihedral_angle_d	19.378098221	3086

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 (%)
2.1-2.1239	0.31413167867	128	0.280058016658	2616	X-RAY DIFFRACTION	98.4924623116
2.1239-2.1488	0.351780375418	153	0.277165345219	2588	X-RAY DIFFRACTION	98.7391930836
2.1488-2.1751	0.307863673778	150	0.27925595638	2579	X-RAY DIFFRACTION	98.7337192475
2.1751-2.2026	0.313334297462	126	0.264724662964	2617	X-RAY DIFFRACTION	98.7045699892
2.2026-2.2316	0.302880363235	136	0.261461699333	2618	X-RAY DIFFRACTION	98.9224137931
2.2316-2.2621	0.321789334641	142	0.261200245141	2620	X-RAY DIFFRACTION	98.7839771102
2.2621-2.2945	0.340724254567	150	0.245790406171	2595	X-RAY DIFFRACTION	98.9902632528
2.2945-2.3287	0.275799920312	133	0.239026471284	2634	X-RAY DIFFRACTION	98.8567345481
2.3287-2.3651	0.270275835357	147	0.235851101145	2637	X-RAY DIFFRACTION	99.0747330961
2.3651-2.4039	0.291794841078	144	0.225873542726	2641	X-RAY DIFFRACTION	99.039829303
2.4039-2.4453	0.250998925551	169	0.225098788843	2576	X-RAY DIFFRACTION	98.9902632528
2.4453-2.4898	0.274679377899	137	0.213804981724	2635	X-RAY DIFFRACTION	99.1771019678
2.4898-2.5377	0.261460762098	154	0.217557794371	2657	X-RAY DIFFRACTION	99.2234380515
2.5377-2.5895	0.265320354159	112	0.212995653311	2656	X-RAY DIFFRACTION	99.2114695341
2.5895-2.6458	0.290941508446	156	0.215941852356	2630	X-RAY DIFFRACTION	99.2518703242
2.6458-2.7073	0.25878448422	132	0.210921709525	2658	X-RAY DIFFRACTION	99.3236027056
2.7073-2.775	0.241354348243	144	0.201451415338	2647	X-RAY DIFFRACTION	99.3592025632
2.775-2.85	0.230342857326	126	0.197271178325	2670	X-RAY DIFFRACTION	99.2193044713
2.85-2.9339	0.213078405315	134	0.187884888765	2668	X-RAY DIFFRACTION	99.5381882771
2.9339-3.0286	0.261220735191	150	0.180067089596	2672	X-RAY DIFFRACTION	99.5063469676
3.0286-3.1368	0.224363002818	146	0.185525208228	2650	X-RAY DIFFRACTION	99.679144385
3.1368-3.2623	0.219726764676	126	0.177089075744	2731	X-RAY DIFFRACTION	99.6164574616
3.2623-3.4108	0.242408229386	138	0.180321735708	2683	X-RAY DIFFRACTION	99.5764207554
3.4108-3.5906	0.174721860055	134	0.156103666207	2676	X-RAY DIFFRACTION	99.7161107168
3.5906-3.8154	0.172871044807	151	0.14283155283	2708	X-RAY DIFFRACTION	99.8254189944
3.8154-4.1099	0.154849234291	134	0.131681829269	2730	X-RAY DIFFRACTION	99.8257232485
4.1099-4.5232	0.19291265776	150	0.135349263803	2744	X-RAY DIFFRACTION	99.9654576857
4.5232-5.1771	0.164521573811	132	0.145489031164	2777	X-RAY DIFFRACTION	100
5.1771-6.5201	0.18850691933	148	0.164513968923	2799	X-RAY DIFFRACTION	99.9321804001
6.5201-48.4734816162	0.207701254869	160	0.18902098329	2965	X-RAY DIFFRACTION	99.7446536866

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	2.01442787263	-2.3138012781	0.0800457431046	5.08468381792	0.427846550013	1.74615077723	0.155906306681	0.305785822609	-0.0751507925524	-0.391593670016	-0.0688694865565	0.49906537437	-0.0667420192432	-0.471568240001	-0.0883046702876	0.217999868149	0.0371519236292	-0.00761069081999	0.486852848008	0.0716026127456	0.253122862693	-25.9006606821	-36.0564343024	-44.9562308829
2	3.63112617411	-0.647033162244	0.17277578265	3.04281299521	0.631496255393	3.19994228903	-0.0817865641027	-0.0560027770524	0.338018173845	0.144281415186	0.234210527261	0.280846700497	-0.596560671499	-0.629971455194	-0.160823681326	0.385349206761	0.201932986374	0.0846163839187	0.438082859074	0.072837506457	0.287225581409	-25.8037117615	-24.218268052	-27.0813767565
3	3.3193467645	-1.09788939857	-0.526539018087	3.2506748696	0.280709579029	2.92086160871	-0.0235142206286	-0.183593491675	0.318157943477	0.254904397261	0.143320861958	-0.0889136361406	-0.391244148815	0.0622973172545	-0.120387813587	0.23084725046	0.0380673248555	-0.00196131591271	0.211511089939	0.00959007494035	0.173805013775	-6.43538445455	-31.1053305273	-27.2517482301
4	3.2965855325	1.83651639079	-1.25586952797	5.58304035844	-1.35340295702	4.75542717769	0.116467474834	0.292735573079	0.0470331330402	-0.229263530116	0.00297269334146	-0.200723105195	-0.0281280609502	0.204956130698	-0.121781739385	0.183704934287	0.0728501750852	0.0181365321903	0.272438217366	0.0218738051387	0.161264024164	-7.6267137657	-40.4356847957	-44.7683401325
5	3.21465689355	1.02507451991	-1.61734917601	2.7255179707	-1.31196938657	2.7252413787	-0.134889560368	0.459209984013	-0.114588352864	-0.55600976891	-0.0453512177217	0.0398233254622	0.268662087371	-0.24823801142	0.191036301811	0.277141738456	-0.00603097032812	-0.0125455727544	0.299744167248	-0.0534276598281	0.159177136288	-21.1023750461	-63.3806057646	-7.87514353523
6	5.18936850041	-0.471129855031	-0.0577384216589	2.09396647447	-1.36744056525	5.50082233218	-0.00614027272692	0.124206189807	0.0736220918533	-0.0426465894417	0.045445085873	0.449622245773	0.165833902345	-0.483868436739	-0.023360184682	0.186001003547	-0.0484365566869	-0.00409290652539	0.232907522038	-0.0572531311168	0.264332847613	-33.6594387461	-62.3204624523	6.19901104552
7	3.52544421717	-1.2094187157	0.978440381877	8.24038674313	-2.68033216795	3.51280680077	0.0465121737862	-0.238475319452	-0.0635707442355	0.274081973408	-0.0209724846622	0.529358699339	-0.119052256161	-0.2743291744	-0.0119105816261	0.18226123708	-0.0357652912251	0.00664252603409	0.217234492336	-0.0428604522181	0.150428129576	-27.8374009477	-54.9441426278	18.0128803894
8	4.42325712537	-0.887716326743	-1.09345677553	2.41830386993	0.648517162577	2.17309023198	0.112300760169	-0.191265695675	0.225503027721	0.170948813262	-0.0998190058164	-0.0770482996441	-0.174910825623	0.109670289806	-0.00771209492997	0.214262352311	-0.0408211759146	-0.0316551262391	0.16203177029	-0.00332793548599	0.15956072998	-13.3465438094	-47.8084914367	15.1206602484
9	2.47224731174	-0.425038876427	-0.755510399184	6.25723414125	-1.13378002632	3.98777029382	0.111493853176	0.25987166147	0.237391292658	0.0194474612367	-0.177571505817	-0.219662266712	-0.244043113829	0.166387241193	0.0566080073093	0.155119333588	0.00974375496139	-0.0113185995411	0.245916828871	0.0571943855562	0.169669762041	-9.97667326011	-49.9605080371	-3.36599353969
10	5.26770317619	-1.39859031314	1.3326920711	1.99040939272	-0.229271052515	2.88531571673	0.0954448014574	0.639011583487	0.34076045139	-0.274428584919	-0.0822760464702	-0.371092718524	-0.144771719176	0.25873586416	-0.000299650437572	0.205806588851	-0.0178336680456	0.0388883646625	0.268809542231	0.0499732906905	0.265315707469	28.323513474	-51.4648312295	-28.4770181765
11	3.92371797246	1.01844308652	-0.426616870725	2.73024581644	-0.960547658889	3.42040488774	0.0484345047325	-0.184077705765	-0.370040564113	0.0264909610972	-0.0187035129084	-0.530497145525	0.171730499618	0.253841200804	-0.0404520379344	0.202286336988	0.0315211819391	-0.0885573394237	0.213515340435	0.0158990436559	0.351722687355	33.6783086054	-61.5796062317	-10.0477438252
12	2.75785050763	-0.122208949765	0.575315061872	2.01374625128	-0.450853624485	3.01343376322	0.0745229773102	-0.0775827828714	-0.241278173223	0.0543917335705	0.0646641421857	0.0194560886247	0.11326344295	-0.229093637461	-0.144819299701	0.131512596006	-0.0118369960519	-0.0113803315717	0.189881401537	0.0111098865939	0.198509683717	11.7712555118	-59.1623900435	-16.2699087883
13	2.03751328476	5.32751508665	5.0852418549	8.73698222674	4.57404261662	2.0220094516	0.645708989229	-0.914242043122	-0.843109753836	1.3005558373	-0.181338532427	0.340443483519	1.93537366053	-1.85962371367	-0.412322807735	0.633185351792	-0.166129884271	0.0356144870604	0.821483343514	0.195588686709	0.662626429214	-20.7250914453	-50.4205264788	-33.0631757068
14	4.06226947591	-1.54736492981	-2.46953559343	6.10161510094	3.84731406481	8.53679642828	0.090971697836	-0.381232810375	-0.265643874394	1.25289948865	0.510326591488	-1.38864084379	3.12199780342	1.39942980102	-0.675517421433	0.886195344682	0.209608708076	-0.0457837977631	0.569493876564	0.0180229975415	0.721459710025	-7.67604518874	-68.487305114	4.48662722087
15	6.27310460316	-7.24595161707	6.10477488811	9.37942166172	-7.76270164429	2.00177628056	-0.0707750795299	-0.618765470649	0.430347520297	1.26255367728	0.51061323554	0.519271873597	-3.96418427465	0.954255070099	-0.453304925036	1.19235058192	-0.00580411000604	-0.126105424812	0.645018551499	-0.148759816291	0.863551717762	18.0793010153	-41.1598092541	-14.6393799973

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2958 through 3063 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 3064 through 3144 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 3145 through 3250 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 3251 through 3326 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 2959 through 3037 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 3038 through 3106 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 3107 through 3169 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 3170 through 3250 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 3251 through 3326 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 2959 through 3063 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 3064 through 3169 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 3170 through 3326 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 249 through 257 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 248 through 257 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 249 through 255 )

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