PDB-8w6b: crystal structure of TAX1BP1 SKICH domain in complex with RB1CC1 ...

ID or keywords:

Entry

Database: PDB / ID: 8w6b

Title

crystal structure of TAX1BP1 SKICH domain in complex with RB1CC1 coiled-coil domain

Components

RB1-inducible coiled-coil protein 1
Tax1-binding protein 1

Keywords

PROTEIN BINDING / T6BP / Coiled coil / FIP200

Function / homology

Function and homology information

protein localization to phagocytic vesicle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of protein lipidation / ribophagy / glycophagy / Atg1/ULK1 kinase complex / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.39 Å

Authors

Zhang, M.F. / Pan, L.F.

Funding support

China, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins.
Authors: Zhang, M. / Wang, Y. / Gong, X. / Wang, Y. / Zhang, Y. / Tang, Y. / Zhou, X. / Liu, H. / Huang, Y. / Zhang, J. / Pan, L.

History

Deposition	Aug 28, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8w6b.cif.gz	341.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8w6b.ent.gz	234.4 KB	Display	PDB format
PDBx/mmJSON format	8w6b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8w6b_validation.pdf.gz	480.8 KB	Display	wwPDB validaton report
Full document	8w6b_full_validation.pdf.gz	487.8 KB	Display
Data in XML	8w6b_validation.xml.gz	25.6 KB	Display
Data in CIF	8w6b_validation.cif.gz	36.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/8w6b ftp://data.pdbj.org/pub/pdb/validation_reports/w6/8w6b	HTTPS FTP

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Related structure data

Related structure data	8w6aC C: citing same article (ref.)
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	#60 - Dec 2004 Ubiquitin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: Tax1-binding protein 1

B: Tax1-binding protein 1

C: RB1-inducible coiled-coil protein 1

D: RB1-inducible coiled-coil protein 1

E: Tax1-binding protein 1

F: Tax1-binding protein 1

G: RB1-inducible coiled-coil protein 1

H: RB1-inducible coiled-coil protein 1

83.4 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: isothermal titration calorimetry

Unit cell

Length a, b, c (Å)	40.239, 86.815, 147.860
Angle α, β, γ (deg.)	90.000, 95.737, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

#1: Protein	Tax1-binding protein 1 / TRAF6-binding protein Mass: 14137.850 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAX1BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86VP1
#2: Protein	RB1-inducible coiled-coil protein 1 Mass: 6707.487 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RB1CC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDY2
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.08 Å³/Da / Density % sol: 60.09 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 5% (w/v) PEG 4000, 50 mM Magnesium chloride, 100 mM MES at pH 6.5, 10% 2-propanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9789 Å / Relative weight: 1
Reflection	Resolution: 2.39→75.36 Å / Num. obs: 39479 / % possible obs: 97.7 % / Redundancy: 6.7 % / B_iso Wilson estimate: 44.27 Å² / CC_1/2: 0.998 / Net I/σ(I): 13.8
Reflection shell	Resolution: 2.39→2.52 Å / Num. unique obs: 5914 / CC_1/2: 0.767

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
autoPROC		data reduction
autoPROC		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.39→42.7 Å / SU ML: 0.3248 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2342	1966	4.98 %
R_work	0.1931	37483	-
obs	0.1952	39449	97.63 %

Solvent computation

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

Displacement parameters

B_iso mean: 60.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.39→42.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5339	0	0	160	5499

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0091	5490
X-RAY DIFFRACTION	f_angle_d	0.9949	7434
X-RAY DIFFRACTION	f_chiral_restr	0.0551	766
X-RAY DIFFRACTION	f_plane_restr	0.0063	963
X-RAY DIFFRACTION	f_dihedral_angle_d	20.4312	711

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 (%)
2.39-2.45	0.3274	133	0.2613	2698	X-RAY DIFFRACTION	100
2.45-2.51	0.3129	153	0.258	2783	X-RAY DIFFRACTION	100
2.51-2.59	0.2963	145	0.2408	2672	X-RAY DIFFRACTION	99.93
2.59-2.66	0.2898	122	0.232	2334	X-RAY DIFFRACTION	97.5
2.68-2.76	0.2819	120	0.2292	2222	X-RAY DIFFRACTION	99.87
2.76-2.88	0.2801	141	0.2311	2793	X-RAY DIFFRACTION	100
2.88-3.01	0.3422	132	0.231	2693	X-RAY DIFFRACTION	100
3.01-3.16	0.2858	151	0.2206	2735	X-RAY DIFFRACTION	99.93
3.16-3.36	0.2366	148	0.2033	2760	X-RAY DIFFRACTION	100
3.36-3.62	0.2368	142	0.1917	2712	X-RAY DIFFRACTION	99.93
3.62-3.99	0.2356	146	0.177	2765	X-RAY DIFFRACTION	99.93
3.99-4.56	0.1786	140	0.1573	2760	X-RAY DIFFRACTION	99.97
4.56-5.75	0.1823	149	0.1602	2765	X-RAY DIFFRACTION	99.86
5.75-42.7	0.2078	144	0.1855	2791	X-RAY DIFFRACTION	99.69

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	2.75999571054	-1.24626384803	0.677553011282	3.97898173106	0.131511152771	3.28213199083	-0.282194161819	-0.019389233992	-0.197059915973	-0.245004429793	0.198566998518	0.695102703721	0.471497751126	-0.292429169788	0.0576756047468	0.356173597834	-0.0441525023002	-0.071766630722	0.340411121004	-0.0473883043376	0.496603664951	-12.3070812795	-36.9345993919	62.1088809383
2	2.77906025415	0.969712906633	0.211949482002	5.38565343337	0.330043556286	3.68508893789	-0.0529625348092	0.274302112724	-0.205723046056	-0.0933297039587	-4.37896598825E-5	0.246902140208	0.0998534929585	-0.240071612345	0.0671894181346	0.267274599235	-0.0121833658863	0.00511844324286	0.285345919135	-0.0250319502768	0.278474738864	-10.7293800755	-31.2676515024	64.9290500151
3	4.69199501664	3.06651429819	-2.80835901997	5.35696413647	-0.898812416033	1.93882614993	-0.147862423288	0.282583101539	0.72013671656	0.296302534966	0.127239955196	-0.453773736548	-0.953490597897	0.409921329763	-0.0185849924068	0.571766805073	-0.208003774301	0.0369838337735	0.21989300736	0.0308259571945	1.42882025993	3.43032231253	8.48845642808	60.1785029607
4	2.39370117572	-0.269816835866	-2.22945692367	0.513431799983	0.228708467493	6.32309418196	-0.19363315625	0.618568317546	0.973895576175	-0.856558504428	-0.286904624564	0.167837513584	-0.253341044959	-0.295586177287	0.148724512995	0.465740523911	-0.0784737538862	-0.0714295772506	0.417963024278	0.187249558614	0.789250358496	-8.14237181494	3.13240032308	55.7764004186
5	6.38874326265	-3.7156547318	-1.1902688396	2.86841205854	-1.27413589937	5.63121732906	-0.32962958656	-0.374519485331	0.560975870527	0.439616746453	0.114359219152	-1.46463838154	-0.572669602612	0.912629514054	0.175784336967	0.357698898084	-0.116954469717	0.0307734021142	0.672663199608	0.00787288138364	1.05184778681	12.2614195143	2.04242250185	58.417572354
6	6.59768211465	-4.37787277472	-0.529114635777	3.33511516566	1.55198247024	3.8898329238	-0.137796704263	-0.30746357071	0.955910151543	0.879349055593	0.414134470853	-0.745213289735	-0.138684270771	0.0997684004915	-0.170118149304	0.475912957749	-0.0513202745018	-0.0973608251385	0.265863423002	-0.0664973646628	0.467839382391	-2.00632695541	-1.80297127684	68.5950153313
7	6.33290125841	2.30954197696	2.93931760708	5.52693904197	0.198106968288	2.12637702316	0.0208625789201	-0.209261760906	0.359460369937	0.309154234342	-0.0475555781821	-0.174321104809	-0.158282117873	-0.70376969164	0.0422496620464	0.28709247586	0.0330137893465	0.0231919350984	0.350067426949	-0.0873381057111	0.292736369151	-1.10577166658	-7.8957554904	64.9706003159
8	5.99611396122	2.56158113772	0.928185599955	5.59222045464	-0.149171194313	1.8386779841	-0.755090154832	1.14644899246	0.68319020531	-1.22482162405	0.600380005878	-0.568657167405	-0.137008138187	0.609898639562	0.175321677205	0.606910834698	-0.139959767212	0.0573722111314	0.667416255576	0.0930406111747	0.509600794181	4.66241577517	-0.136811517884	51.9079107957
9	0.454922164291	-1.07412839978	-0.1193541262	3.91308725038	0.0674356343126	2.96385161094	0.00727463650606	-0.588513144749	0.300769558074	0.246324827984	-0.28557623866	0.119088240969	-0.012242577008	-0.159916027401	0.293194721258	0.340155042014	0.010014831765	0.00462277430409	0.401370686465	-0.0501189783042	0.528634989238	-8.87564868985	-0.618116131267	65.4053768672
10	5.91409014388	-4.50305409679	4.86473134303	8.09858189784	-4.6606126025	4.19339815505	-0.373248227454	0.145850430314	0.995863624144	0.206997467993	-0.634723358942	-1.52857419107	-0.835015302447	0.601360958179	1.1704066008	0.473846127307	-0.07339487728	-0.0853958168548	0.61447382753	-0.105381288984	0.721851442804	9.22975859008	0.328317562944	65.8039713507
11	2.5794733912	3.15841796325	4.65204177219	4.521970976	6.42422066814	9.26017710127	-0.455449896207	0.569635209384	1.31423434982	-0.374568316703	0.53349601239	1.06631968968	-0.19642259847	0.156908069956	0.14050671036	0.362125910024	0.0426332291053	-0.0808665226448	0.377102437907	-0.00467148061278	0.603043081383	-12.334052222	4.38038412497	63.7257486501
12	2.07269736542	0.173275989685	0.283893184562	2.19097854175	-0.214621291355	2.57847967677	0.160708020188	0.0379662844993	-0.000860763009142	0.139307562233	0.133128904746	0.00470641440014	-0.556408363279	0.368883903381	-0.105705549857	0.451670459663	-0.00604026238972	-0.0074360749437	0.267036190386	0.00737586311991	0.437066263608	-4.30433346524	-16.2525923587	59.8448812139
13	1.86255426576	-0.239875117139	0.322883780196	4.24333333337	2.33398398565	6.53702667396	-0.138650972117	-0.0396275968988	0.0320325447128	0.251412697937	-0.157156008675	0.25609576245	0.0751710502715	-0.136313511182	0.19960681347	0.404329513629	-0.0195440765073	-0.0195222404573	0.339177743926	-3.71148477446E-5	0.375722608332	-8.58483004495	-16.3026002866	62.7181796966
14	7.2989615457	0.773361999666	-0.531481296808	2.74174801072	-0.994102637982	2.96893498703	-0.190610410205	-0.20631266333	0.246878529153	0.61210046247	0.233851309692	0.292789447073	-0.450893507551	-0.1196312217	-0.0169085712844	0.427905864757	0.0723918959057	0.0513972537967	0.360161303532	-0.019931855806	0.394253629402	-24.4375610542	-1.31048991003	12.1975921745
15	2.42938427413	-0.343341852959	0.773130944092	6.39527172615	-0.348859066525	1.69869435499	-0.222384464889	-0.25849998629	0.0897478039334	0.417680752201	0.210494006787	0.559617821699	-0.0467331191514	-0.330684419918	0.0268345598071	0.309232735318	0.0235222792016	0.0219507525483	0.389483227512	-0.0214070397524	0.32518594007	-25.9499016583	-7.73978172403	11.5732145948
16	0.850039588075	1.52598478949	-1.15975042198	4.52306664737	-0.538971437771	5.42701238733	0.284102549652	0.48751796957	-0.119526690543	-0.312400757407	-0.143516452151	0.243295769948	-0.0221875529984	-0.269500345298	-0.0783685467689	0.324990663523	-0.00361773673885	-0.0191375816926	0.235468859046	-0.0284972697873	0.313960130078	-21.8384185414	-6.95346236649	4.79415923452
17	5.3518854144	-6.88501922282	5.70680009608	8.89708352171	-7.42652795518	6.15669844428	-0.320630296354	-0.197869328342	0.428335248621	-0.102074669146	-0.0860666765301	-1.00758512213	0.125131029156	0.188957283326	0.336526136981	0.298869502463	-0.0444109371557	-0.0456714072209	0.46491651182	-0.00356032287643	0.509066663925	-12.0855541464	-2.01086442945	5.65397106373
18	3.53530873812	-1.07268582604	3.48658677171	5.03904434935	1.07746974247	4.62130161332	-0.467009584487	-0.347122882402	-0.49756187207	0.0361775408859	0.354044475434	-0.324507730935	2.14744627579	1.17808233161	-0.100981991314	0.787573679686	0.185274503814	0.0639588253465	0.490694517387	0.155319737642	1.37353185659	-9.3071884255	-46.8626651743	12.8928062673
19	6.08115825854	-4.14055467989	0.05836334971	7.89502527497	2.20732834407	6.11207167117	-0.137857083475	-0.157134006813	-1.03396740579	0.700508670686	-0.213435165668	-1.04500094389	0.134192113668	-0.305247003393	0.430061424614	0.38630970283	-0.0222294760536	0.184734296131	0.483205973157	0.263706773733	1.03930836089	-25.5618867284	-40.7015311883	16.3228488653
20	8.50213147825	-4.64493922886	3.10199974376	5.29497351099	0.0563546040939	2.73297114965	-0.7159710178	-1.22380665125	-1.30386614255	0.978193951177	-0.125401188091	-0.134590835981	0.576773753536	0.54106252099	0.280630406131	0.537496032413	0.106756377224	0.0143081474253	0.514711155591	0.28232902876	0.743546943469	-13.6729900173	-42.0649687806	19.1432896032
21	4.57239413451	-2.40488226233	1.2100213574	5.43620394413	-1.21506408841	4.36540288376	-0.561568863833	-0.195704927902	-1.38825333666	0.036466378193	0.301753912035	-1.35720681112	0.0611961162828	0.58988803226	0.41682087895	0.305695141309	0.0451872534995	0.00502135599996	0.484088693159	0.0496614220862	0.843718606315	-5.72444599009	-38.4967593543	12.2321426184
22	7.78949478763	3.11652049558	2.75258299334	4.22040462541	2.74247974995	1.86530190716	-0.0580346740842	0.481255380609	-0.964327260589	-0.565651865009	0.116824195307	-0.292853634399	-0.217111623143	0.173085786096	-0.310113780996	0.43705247355	0.03063422869	-0.0185268384578	0.373970322856	-0.0323302285061	0.416406022225	-13.9719289317	-32.5695339837	5.71306286767
23	4.04658626853	-1.89663730878	0.738612701788	3.8496379939	-1.13667233823	0.831849897041	-0.755883546205	-1.14147019696	-0.765320639248	0.899052120858	0.479142496777	-0.626901265148	-0.0361300605217	0.414411664591	0.317381174884	0.617282361741	0.152216454055	-0.0852498992174	0.727223746307	0.205096926627	0.671351146068	-7.80871776208	-38.2107871989	21.2209514886
24	3.00559673674	0.341603472446	0.52169092439	1.52741500907	0.124979131172	4.28345087746	-0.219702207626	0.141323564821	-0.0917491492748	-0.0562271314937	-0.0539269279778	0.146795163089	0.309546638222	-0.157928306671	0.43772284369	0.336837881402	0.00219084730697	0.0088798403671	0.358575069905	-0.0508046105518	0.595105842038	-21.4850600742	-37.4388860115	7.89850334564
25	5.23538064072	6.37706415887	-3.38056390414	7.76818497496	-4.07601057747	2.25258782975	-0.548473370374	0.206346993106	-1.82116619048	-0.573926374187	0.263527875108	-1.55347137715	0.721184261076	0.498871983624	0.371494759715	0.385100005576	0.104792621773	0.0718638364861	0.566217208301	-0.0866748316987	0.673573706055	-3.47085348625	-38.6040396734	7.06970366733
26	3.48925115381	-3.03220344887	2.32689852855	4.88615371734	-0.143452016879	4.43850521297	0.263854101632	-0.134999984131	-1.79355143847	-0.206563522221	-0.289807818671	1.00326669412	0.837925773903	-0.388954344114	0.240648957033	0.447042578124	-0.135233686656	0.0678643909056	0.491875889023	-0.115281618673	0.829065325697	-24.9755090774	-42.3956605494	9.54118675627
27	2.5470850263	0.219063280948	0.133817129183	3.53662765128	-1.36309631188	4.94887770114	0.0380526469052	0.156377433898	0.0223996362401	-0.0798709410697	0.0630102783902	-0.274454794767	-0.0998837929206	0.292298478991	0.0555684759217	0.357279148682	0.00310714437687	-0.011269913745	0.249612873013	0.0249870516909	0.433374754087	-16.2476368764	-21.5672620875	10.2796657084
28	2.08731476686	-0.17553612623	0.213857041887	3.52141339734	0.891036186258	2.57624039855	-0.126953175913	-0.00599037738274	-0.0703258200614	-0.0902652894396	0.0496638380905	0.0926336566708	0.00329671671619	-0.420044456437	0.0699029673146	0.421155583163	0.0436226520874	0.0323516623325	0.328752476474	0.0317552208811	0.434073443967	-20.2301913414	-20.9155445946	13.5659778299

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 121 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 15 through 20 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 21 through 38 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 39 through 48 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 49 through 59 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 60 through 68 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 69 through 91 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 92 through 105 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 106 through 114 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 115 through 121 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1339 through 1395 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 1345 through 1393 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 15 through 48 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 49 through 91 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 92 through 114 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 115 through 121 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 15 through 20 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 21 through 31 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 32 through 38 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 39 through 54 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 55 through 68 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 69 through 91 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 92 through 105 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 106 through 114 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 115 through 121 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 1344 through 1395 )
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 1339 through 1395 )

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