PDB-6qis: Crystal structure of CAG repeats with synthetic CMBL3a compound (...

ID or keywords:

Entry

Database: PDB / ID: 6qis

Title

Crystal structure of CAG repeats with synthetic CMBL3a compound (model II)

Components

RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

Keywords

RNA / CAG repeats / CMBL / RNA complex with ligand

Function / homology

CMBL3a / RNA

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

Authors

Kiliszek, A. / Blaszczyk, L. / Rypniewski, W. / Nakatani, K.

Funding support

Poland, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats.
Authors: Mukherjee, S. / Blaszczyk, L. / Rypniewski, W. / Falschlunger, C. / Micura, R. / Murata, A. / Dohno, C. / Nakatani, K. / Kiliszek, A.

History

Deposition	Jan 21, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 25, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2019	Group: Data collection / Database references / Category: citation Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 20, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	May 15, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6qis.cif.gz	116.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6qis.ent.gz	80.6 KB	Display	PDB format
PDBx/mmJSON format	6qis.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6qis_validation.pdf.gz	3.5 MB	Display	wwPDB validaton report
Full document	6qis_full_validation.pdf.gz	3.5 MB	Display
Data in XML	6qis_validation.xml.gz	7.2 KB	Display
Data in CIF	6qis_validation.cif.gz	9.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qi/6qis ftp://data.pdbj.org/pub/pdb/validation_reports/qi/6qis	HTTPS FTP

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Related structure data

Related structure data	6qiqC 6qirC 6qitC 6qivC C: citing same article (ref.)
Similar structure data	6qit-2 6qiv-1 6qit-1 6qir-2 6qiq-d 2jn0-d 5t8r-2 2kuh-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

B: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

C: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

D: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

E: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

F: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

G: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

H: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

hetero molecules

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

1

A: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

B: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

hetero molecules

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

2

C: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

D: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

hetero molecules

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

3

E: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

F: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

hetero molecules

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

4

G: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

H: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.810, 51.154, 118.463
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab

#1: RNA chain	RNA (5'-R(GPCPAPGPCPAPGPC)-3') Mass: 2564.617 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical	ChemComp-J48 / CMBL3a Mass: 500.529 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₆H₂₆N₇O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.38 Å³/Da / Density % sol: 63.64 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10mM MgCl2, 1M Li2SO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.917143 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.917143 Å / Relative weight: 1
Reflection	Resolution: 1.99→42.73 Å / Num. obs: 19670 / % possible obs: 99.9 % / Redundancy: 10.1 % / B_iso Wilson estimate: 42.8 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.092 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.99→2.11 Å / Redundancy: 10.4 % / R_merge(I) obs: 0.94 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3110 / CC_1/2: 0.92 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
PHENIX	1.16_3549	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→42.73 Å / SU ML: 0.2605 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.9747

	R_factor	Num. reflection	% reflection
R_free	0.2767	969	4.98 %
R_work	0.2393	-	-
obs	0.2412	19465	98.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 41.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.99→42.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	1360	301	126	1787

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	2029
X-RAY DIFFRACTION	f_angle_d	1.1865	3090
X-RAY DIFFRACTION	f_chiral_restr	0.0504	347
X-RAY DIFFRACTION	f_plane_restr	0.0064	367
X-RAY DIFFRACTION	f_dihedral_angle_d	12.0229	1161

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 (%)
1.99-2.1	0.3715	134	0.3217	2576	X-RAY DIFFRACTION	98.58
2.1-2.23	0.3193	138	0.3128	2625	X-RAY DIFFRACTION	99.42
2.23-2.4	0.369	137	0.2957	2609	X-RAY DIFFRACTION	99.38
2.4-2.64	0.3166	138	0.2902	2625	X-RAY DIFFRACTION	99.42
2.64-3.03	0.3107	138	0.2747	2650	X-RAY DIFFRACTION	99.15
3.03-3.81	0.2383	139	0.203	2641	X-RAY DIFFRACTION	98.06
3.81-42.74	0.2385	145	0.1995	2770	X-RAY DIFFRACTION	97.98

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	6.25265491757	-2.17929678601	-4.93959514994	5.72504824487	2.95344078007	6.61622313707	-0.130894285915	0.584532799763	-1.32296664434	0.255976843937	-0.437740175595	0.0585750756458	0.599152802808	0.512588973209	0.570438932474	0.320335085672	0.126664737293	0.0395259125099	0.439349501494	-0.023606671231	0.489094584783	-2.93342862831	7.14561696737	-26.4505097867
2	1.59503431133	-0.358151477175	0.282471987113	1.33652529455	0.214985181083	2.67820765641	-0.72049299586	0.0345785813976	-0.310671291894	1.64222361389	0.655597772309	0.576892788047	0.413533704006	-1.66303535593	0.0205831404234	0.728804014167	0.134202907274	0.186298590561	0.607981211491	0.0971363009798	0.543615660622	-13.2779071261	6.77942138822	-18.0441236812
3	9.48619091874	-4.229427661	1.56393541489	8.01376072714	-4.02605828773	4.10851402885	-0.916414357083	-0.268455441087	-0.646934452937	0.762265883025	1.05184253794	1.02756231961	0.383015028501	-1.34124299687	-0.205766413715	0.385414896436	0.0173234104477	0.068539222779	0.367869508001	0.0286612999972	0.411117538605	-18.0595941592	17.9992144127	-21.6962623845
4	5.19917497403	1.2959391916	0.570893617857	4.25817193448	-0.00125700168099	2.89176332495	-0.228757518851	0.570703016836	-0.0855877048496	-0.455607479924	0.139781331913	-0.348453421814	-0.0104711161495	-0.134760816559	0.0362402994685	0.266147340321	-0.0688558814155	0.0495019625058	0.451302261632	-0.0498255543607	0.356694928067	-12.6465829175	18.173552152	-29.9885372831
5	2.09889545975	-3.44440568844	0.0449582705031	6.80728822318	-0.334205948663	0.0510157097568	-0.393469047492	-0.197418197278	-0.170458830723	0.718444350065	0.437499056896	1.12049946963	0.164353389259	0.111242256754	-0.0431740870046	0.440355593287	0.011635819992	0.0111043247538	0.420404375071	0.0742811722906	0.574776948921	-4.72173373795	21.9647337965	-20.5125217249
6	4.40382742185	2.77655108655	4.89330493018	3.29972576882	1.81426584988	6.48005078874	-0.657473582704	-0.0683166357075	0.946312910657	0.503470178876	0.961236475878	-0.131912743741	-0.187731583789	0.88729333645	-0.15394796264	0.390118964016	0.131426370299	0.0470807687576	0.458365884553	0.00452572749655	0.420585385073	2.99751533868	11.5955396685	-19.2643608208
7	8.40440063568	-0.104439095493	2.45244185719	5.45349670875	-6.69433145582	8.90290515097	0.348067278155	-2.24262784571	-1.53518582841	-0.62484489863	-0.689294126428	-0.0963465661836	1.41508355245	-0.387967190535	0.343076069278	0.516535451647	-0.175500230015	0.0689891284637	0.492402548602	-0.0524970182518	0.6593621243	-21.3438524027	-17.8567805504	-2.46456398124
8	8.6145131969	-1.72212445301	0.757354907661	1.65567742489	-1.9911799314	2.64563052018	-0.0574080113479	0.53540682568	-0.045543509866	0.46190111841	0.855877820668	-0.123713567471	1.93509854936	0.981305145491	-0.677584697904	1.02473504788	-0.0373914412678	0.15083500402	0.476130807187	-0.0810264640284	0.652192234261	-12.9804210141	-17.9958870384	-11.6805525638
9	3.66660846205	-1.30421735819	-3.81036688019	5.34528341632	-0.472311902537	4.63074970764	-0.1087901355	-0.511721110043	-1.28207178828	0.130314470123	0.315835475975	-0.419414847392	0.538479958388	1.79867326317	-0.159064485071	0.341131243987	0.0323060837433	0.0767939125518	0.512984503202	-0.0499479920925	0.472309635255	-5.81638882806	-7.97392546554	-7.86401709415
10	5.70800970865	-2.47324907966	4.62893526349	5.65110540042	-1.47453458029	3.81926312219	-0.414900330708	-1.55290260557	-0.503643102339	0.713530561776	0.666587473503	-0.216102130055	-0.349890112078	-0.211835124715	-0.295687041621	0.408664822952	0.101596363025	0.0896710536713	0.534087917436	0.0356773969131	0.29345302705	-11.3404174597	-7.68611249991	0.457090458488
11	2.90225323753	2.87076587564	1.54498397071	3.35088371825	2.33912252686	2.10891249059	-0.358538670122	0.565312691783	-0.507491981495	-0.134191974266	0.442442421149	-0.429468619322	0.527683330789	-0.195722980091	0.0322025330569	0.408964432369	-0.0409781863196	0.0818028317529	0.385478887293	-0.0726660153986	0.354165977718	-18.9259487809	-3.72234367495	-9.29636634589
12	4.00274394559	-2.19077750361	3.98647902144	3.38069106459	-0.198005946102	5.83481347269	0.00428927803963	-0.250609681735	1.02846702627	-0.295364221208	0.299366236745	0.498696002388	1.02012013283	-0.725448775387	-0.328873363151	0.535995865763	-0.192617054345	0.107316860583	0.630945378083	0.0374995714725	0.548852045856	-26.9459307222	-13.8828464603	-10.2924492332
13	7.7282391821	-2.29557343405	0.110597801072	0.840193312572	-0.904750513995	5.29364929363	-0.123282269115	0.326750233571	1.34825096895	0.522412104782	-0.278130842479	-1.25855686553	-0.796557196531	0.0821651296861	0.403865403057	0.264694987385	-0.00980244351723	-0.153355309681	0.339404536841	0.0431111596493	0.735057245786	-18.7209641122	-7.23186412997	-27.1109449357
14	6.92977210356	1.72275818941	0.00508565887554	3.86435511608	4.61064093949	6.18638091072	-1.01893933453	-0.203074145235	1.01206444218	-0.991751472139	0.881246887251	3.13036271878	-0.893310956729	0.693457325846	0.0277027739147	0.529390750439	0.011174794467	-0.0963544167538	0.532679109713	0.0543878303501	0.878879089556	-9.8986882985	-5.94684406257	-19.6722099935
15	1.82972426479	1.28323889371	-0.545473713286	5.93649962301	6.01977485126	8.4296013877	-0.594489371078	-0.395368790772	0.594446962433	0.0173703821687	0.796101018898	-0.201311590786	-0.547606443108	1.34135450935	-0.2426358995	0.297152101636	-0.00481595800468	-0.000475292664388	0.330715644052	-6.59359118084E-5	0.410565283467	-4.23009428064	-17.8807601474	-22.5947620123
16	5.97049182488	0.842345481387	-3.42178916402	2.13115826771	-0.184960966165	4.14573221807	-0.402082668985	0.790014968866	0.81340570246	-0.178963318866	0.0322790559225	0.188970217398	-0.18517620573	-0.240346139429	0.436545674714	0.264227923797	-0.0568335037034	-0.0955643868438	0.450244281048	0.0984041674819	0.276826884613	-10.2359688502	-18.3514809233	-30.4993099393
17	5.53109197381	-1.94247750722	-1.17457943951	8.39628250054	3.17438865061	7.4739277397	-0.394490479588	-0.126587793132	0.794692159731	0.752578461974	0.343331745054	-0.676668193425	0.715402524864	-0.409949573962	0.0670206666497	0.394955192159	0.0303709839636	-0.0749675877737	0.348810698517	-0.0285829557882	0.364143268433	-17.7813361137	-21.7098358287	-20.4920549428
18	3.38041470338	2.14879446841	-3.20850245799	4.97895007774	-1.26087182744	3.21063310939	-0.72573290866	-1.07533430644	-0.123177502551	0.333644578577	-0.441292572544	-0.22781346236	-1.04072688997	-0.465744754208	1.32915616522	0.408666673952	0.112989674301	-0.0595979517186	0.447620317157	0.0351156744468	0.477485671047	-24.4135431865	-11.7131681628	-19.6463478529
19	2.5297004762	0.683022472176	-2.09680269773	7.61443942664	2.94751662119	7.45216255807	-0.534870802616	0.0494317407298	-0.390050639502	-0.978174416874	0.697940610626	1.02433775405	-0.873488003759	0.795683058809	-0.212271569277	0.465106567217	-0.107846210266	-0.0465500102959	0.401827736302	-0.0216525446262	0.408525553805	-4.10877036295	18.5680735345	-2.47388461796
20	5.48170181647	3.87130024351	-2.59349835791	5.89808466923	2.37205004564	6.80154523982	-0.997417944476	-0.0753354916337	-0.883564500275	0.392482303407	0.119479983196	-1.40476788878	-2.19336449954	-1.48862861859	0.951134500661	0.9930222134	-0.0075003685	-0.164350467673	0.470812047337	0.037553860062	0.582794360884	-14.3433977947	18.8229972182	-10.9176558053
21	7.25585882702	3.7420095455	4.79800592924	9.45839041382	4.97225464227	6.26297453815	-0.967637690773	-0.316300857792	0.344963056801	-0.216167955487	0.558405054607	0.287036514163	-0.340828996853	-0.371692665933	0.436436599984	0.432756994231	0.0203966394243	0.0339963816807	0.335923867803	0.00469383753337	0.267406562487	-19.5545728873	7.52260464692	-7.38476588899
22	3.89493860425	3.61199490145	0.503961397932	9.28737061583	-6.22196875822	7.72005335879	-0.417700235558	-0.472106319645	0.243278453864	0.246371094745	-0.231208519496	-0.523385078535	-0.344103531706	-0.0972286066292	0.810084967422	0.340232794231	0.0152323009108	-0.0390089002055	0.428479777501	-0.0612460234639	0.359803721678	-13.7351694971	7.16778651199	0.619405341987
23	6.11136329607	2.69516465361	2.72213183761	4.33533656117	5.98079710151	8.43908634827	-1.68578318419	0.853202639013	-0.0836662244419	-0.183421696141	1.37409456259	0.523699814465	1.38897586242	1.02708874257	0.250225280293	0.652593187024	-0.0434806292461	0.190238222608	0.59499623957	0.078102172523	0.871540731604	-5.39927579324	3.53484700212	-8.96547785586
24	6.54018570775	-3.35623620423	-4.53800531719	4.41913639853	0.65735384749	4.18763342753	-1.37183577941	-0.117676283924	-0.524579368309	-0.839284711464	0.604602201443	0.509140607988	0.103265994353	1.42524786707	0.676813619509	0.474574111584	-0.104231194732	-0.0262307444051	0.457138622301	-0.0766402534152	0.281734769193	1.39423220881	14.1997897822	-9.76326763488

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 3 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 4 through 6 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 7 through 8 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 3 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 6 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 7 through 8 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 3 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 4 through 6 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 7 through 8 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 1 through 3 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 4 through 6 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 7 through 8 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 1 through 3 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 4 through 6 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 7 through 8 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 1 through 3 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 4 through 6 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 7 through 8 )
19	X-RAY DIFFRACTION	19	chain 'G' and (resid 1 through 3 )
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 4 through 6 )
21	X-RAY DIFFRACTION	21	chain 'G' and (resid 7 through 8 )
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 1 through 3 )
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 4 through 6 )
24	X-RAY DIFFRACTION	24	chain 'H' and (resid 7 through 8 )

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