PDB-6we9: YTH domain of human YTHDC1 with 11mer ssDNA Containing N6mA

ID or keywords:

Entry

Database: PDB / ID: 6we9

Title

YTH domain of human YTHDC1 with 11mer ssDNA Containing N6mA

Components

DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*CP*TP*G)-3')
YTH domain-containing protein 1

Keywords

DNA BINDING PROTEIN/DNA / N6-methyladenine binding protein domain / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

primary follicle stage / mRNA alternative polyadenylation / mRNA splice site recognition / Nuclear RNA decay / N6-methyladenosine-containing RNA reader activity / dosage compensation by inactivation of X chromosome / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / regulation of alternative mRNA splicing, via spliceosome / molecular sequestering activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.59 Å

Authors

Horton, J.R. / Cheng, X.

Funding support

United States, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2020
Title: Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA.
Authors: Woodcock, C.B. / Horton, J.R. / Zhou, J. / Bedford, M.T. / Blumenthal, R.M. / Zhang, X. / Cheng, X.

History

Deposition	Apr 1, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 15, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Database references / Category: citation Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Oct 21, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6we9.cif.gz	179.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/we/6we9 ftp://data.pdbj.org/pub/pdb/validation_reports/we/6we9	HTTPS FTP

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Related structure data

Related structure data	6we8C 6weaC 4r3hS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5n8q-1 5cwf-4 2k1q-d 2j0v-1 4kmx-d 3su2-d 6fvj-7 5cqy-d 6wea-3 4x3t-3 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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

C: YTH domain-containing protein 1

A: YTH domain-containing protein 1

B: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*CP*TP*G)-3')

F: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*CP*TP*G)-3')

hetero molecules

45.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: YTH domain-containing protein 1

F: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*CP*TP*G)-3')

defined by author
Evidence: isothermal titration calorimetry
22.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: YTH domain-containing protein 1

B: DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*CP*TP*G)-3')

hetero molecules

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

Unit cell

Length a, b, c (Å)	119.966, 42.535, 90.019
Angle α, β, γ (deg.)	90.000, 103.461, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-606- EDO
2	1	A-808- HOH

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Protein / DNA chain , 2 types, 4 molecules CABF

#1: Protein	YTH domain-containing protein 1 / Splicing factor YT521 / YT521-B Mass: 18823.826 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96MU7
#2: DNA chain	DNA (5'-D(CPGPCPGPGP(6MA)PCPTPCPTPG)-3') Mass: 3364.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens* (human)

#1: Protein

YTH domain-containing protein 1 / Splicing factor YT521 / YT521-B

Mass: 18823.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: YTHDC1, KIAA1966, YT521 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96MU7

#2: DNA chain

DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*CP*TP*G)-3')

Mass: 3364.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.)

Homo sapiens (human)

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Non-polymers , 4 types, 192 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.52 Å³/Da / Density % sol: 51.13 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M Bis-Tris pH 6.0, 0.2 M ammonium sulfate, 29% (w/v) polyethylene glycol (PEG) 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.59→35.31 Å / Num. obs: 54367 / % possible obs: 91.6 % / Redundancy: 4.7 % / B_iso Wilson estimate: 15.29 Å² / R_merge(I) obs: 0.204 / R_pim(I) all: 0.094 / Net I/σ(I): 10.4
Reflection shell	Resolution: 1.59→1.65 Å / Redundancy: 1.7 % / R_merge(I) obs: 0.693 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3725 / CC_1/2: 0.468 / CC star: 0.799 / R_pim(I) all: 0.543

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Processing

Software

Name	Version	Classification
SERGUI	1.17.1_3660	data collection
PHENIX	1.17.1_3660	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4r3h

4r3h

Resolution: 1.59→35.31 Å / SU ML: 0.1898 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.6923

	R_factor	Num. reflection	% reflection
R_free	0.2456	1998	3.68 %
R_work	0.2222	-	-
obs	0.2231	54296	91.27 %

Solvent computation

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

Displacement parameters

B_iso mean: 64.68 Å²

Refinement step

Cycle: LAST / Resolution: 1.59→35.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2503	390	45	182	3120

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0026	3060
X-RAY DIFFRACTION	f_angle_d	0.5555	4212
X-RAY DIFFRACTION	f_chiral_restr	0.0397	460
X-RAY DIFFRACTION	f_plane_restr	0.0029	465
X-RAY DIFFRACTION	f_dihedral_angle_d	19.4348	1151

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 (%)
1.59-1.63	0.3783	92	0.3237	2431	X-RAY DIFFRACTION	59.28
1.63-1.68	0.2847	105	0.2969	2726	X-RAY DIFFRACTION	68.17
1.68-1.73	0.3174	124	0.2929	3242	X-RAY DIFFRACTION	79.74
1.73-1.78	0.3443	140	0.2879	3666	X-RAY DIFFRACTION	90.06
1.78-1.85	0.286	149	0.2734	3903	X-RAY DIFFRACTION	95.7
1.85-1.92	0.3067	153	0.26	3983	X-RAY DIFFRACTION	98.15
1.92-2.01	0.2303	153	0.2305	4011	X-RAY DIFFRACTION	98.72
2.01-2.11	0.2381	154	0.2084	4028	X-RAY DIFFRACTION	98.61
2.11-2.24	0.2224	153	0.2061	4002	X-RAY DIFFRACTION	97.9
2.25-2.42	0.205	150	0.2065	3931	X-RAY DIFFRACTION	96.45
2.42-2.66	0.2365	156	0.2107	4112	X-RAY DIFFRACTION	99.7
2.66-3.05	0.2445	156	0.2221	4084	X-RAY DIFFRACTION	99.32
3.05-3.84	0.2352	157	0.2017	4072	X-RAY DIFFRACTION	98.74
3.84-35.31	0.2295	156	0.2079	4107	X-RAY DIFFRACTION	96.54

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	2.02610463168	-6.18471310768	-0.369384592329	4.5033009911	2.30685422492	4.83478932868	-0.111020514621	-0.657993153168	-1.19200028678	0.460262157016	0.179655585038	0.43870406125	0.277151917068	-0.280399413652	0.0447161556217	0.195251962141	0.00188448446087	0.0117196734263	0.185739630236	0.0785900269197	0.280179435996	-16.0824496435	-22.9846809341	11.5263505735
2	8.87754339385	6.69572239506	5.22398134919	7.30775516731	8.05115212866	2.06844141655	0.279556581304	-0.612948183233	0.423507945522	1.14287415009	0.002897617649	-1.18900982135	0.309628216801	0.515991044034	-0.27667409012	0.334797564672	-0.0779617299864	-0.143083320858	0.408964182507	0.0327651356343	0.501632076289	-1.49719496735	-18.1329114678	11.8642890044
3	1.57918416853	-3.17472440944	0.443213677477	6.34621998939	-0.888375702873	0.128590656284	-0.444297644156	-0.706199734909	0.702564749395	-0.088357756964	0.324937638311	0.553076779905	-1.16817181363	0.052764410865	0.262139423783	0.630852580157	0.0354908278187	-0.267638726335	0.670494805144	-0.0667213731666	0.404943311637	-6.37461481689	-9.26470856212	21.5982773135
4	6.14769638502	1.01643823615	0.621688400581	2.36423370033	-3.10346689561	2.69017912282	-0.281559222093	0.611236913454	-0.0105576411603	-0.295746590281	0.536911036595	1.08516426636	0.165275899493	-0.0753130373874	-0.212059921478	0.182291990436	-0.096947174698	-0.0719725179547	0.308084282249	0.0523324634497	0.385350717429	-21.6073598141	-7.25586088237	-9.6233535002
5	1.92492219506	1.18747790017	-0.649637497984	0.510638804582	-0.248348791931	0.0788988155144	0.718138024589	1.49624697638	0.265069145446	-1.34011465245	0.508846746928	-0.973603690196	-1.08612264483	0.788600009785	-0.827533104541	0.790591969724	-0.218655665186	0.616367554431	1.44470327409	-0.199254706366	1.19767655278	-17.5510378332	10.9138498578	-24.2038742996
6	9.1104619338	0.00892811731529	-3.87519544352	3.66461412234	-5.59249773452	1.9981314651	0.941596385093	0.566891365038	0.517042467881	-0.596845594526	1.57038054243	1.35591022081	-1.05092833708	-3.72756700206	-2.31306218698	0.91574590246	0.10000143105	-0.0587640572829	1.18396914677	0.411238948794	1.44384450975	2.04761674363	38.2357954868	-41.4165371779
7	5.45184119352	2.19573456331	1.52520258392	2.01386907461	0.824282927732	1.7074247353	0.106596111732	1.79360724098	1.70273654901	-0.575535063524	-0.0937460116463	0.811283806997	-0.0596963491436	-1.97750911264	0.458741692755	0.623873337015	-0.154895748133	-0.195102233227	2.38327650418	0.297579778838	0.53822670503	-10.6755789266	26.0036722206	-33.2925115383
8	5.01019702673	4.22054167434	-4.64667768597	9.0103368809	-1.16865481821	5.69169034399	0.273704041277	1.17899199898	-0.135375531545	0.133972440521	0.154583858608	1.78548007647	0.297338651149	-1.97142936584	-0.365028888313	0.682527317731	-0.371661687362	-0.0846803694667	2.06213254364	-0.111826483137	1.34038049265	-23.2798809007	21.9136920465	-29.5950484915
9	3.12353765583	1.55052493877	-2.6041132126	0.765425562345	-1.29788065725	2.21410495816	-0.624229389835	1.64236426988	1.17840884712	-1.07103713917	0.370289562933	0.258650001417	0.202998544685	-0.635930478844	0.429216461439	0.684491441232	0.189335062972	-0.243758654711	2.63143169356	0.379944677595	1.07872125377	-7.08277014894	25.1747641928	-41.9493259486
10	1.28376662944	0.494005271046	-2.55689936915	2.24141066513	-0.187834954978	5.40719139277	-0.319290292807	0.498132739139	-0.404061405083	-0.545279526355	-0.169765513966	-0.12198723685	0.891842184123	-0.0908399199778	0.5158147489	0.962242914754	0.0450436251119	0.179251228823	1.37401902262	-0.110817920353	0.512957017824	4.1026265267	18.0110868528	-32.3400808377
11	0.407746771818	0.0565458294078	-0.0559667876221	1.40246747797	-1.22578059715	1.06769433293	-0.451774175585	0.556025878787	0.100857822868	-1.06157050917	-0.109078679979	-0.546602561112	0.542548907581	0.159796053518	0.359746448041	1.000421895	-0.276920055139	0.288089031889	2.34311347357	0.443967371412	-0.678507952497	3.51713898764	26.3617077966	-36.1209472703
12	3.31589950211	-1.64582123512	3.9607395565	3.93741983984	-5.22014922271	8.10657498969	0.526798253172	1.87685907193	1.1003955314	-1.00589322573	-0.325443095714	0.423837213882	-0.171538141271	0.179927777254	-0.247793070728	0.829562552176	0.138187234725	-0.142450591136	2.15198021964	0.732936262411	1.47699664831	-6.09511088241	35.656038581	-45.9206855893
13	6.66605652516	2.37615339177	5.04131026273	8.76284887573	-1.0768196419	4.90736832996	-0.126736385662	-1.85756756428	-0.315801867465	1.72603060587	0.198347615975	0.164694820236	0.432290407967	-0.0102452061582	-0.120902411354	0.590291904682	0.001117730147	0.0520136672082	0.55086774357	0.0793404213529	0.181209259033	-11.017044374	-18.5423126734	20.492562861
14	4.84446535243	0.38462878909	-0.937634666178	2.71895412031	-0.163034137514	2.65248887187	-0.00944007730089	0.0707193153629	0.275197378196	0.0173444577076	0.0503183838679	0.00462404692164	-0.00576132393529	-0.123177040997	-0.0231607712726	0.106290976748	0.0153380908548	-0.00626478030145	0.0523509930602	-0.013922869916	0.0529986782472	-10.9216207591	-7.7251268174	1.80641660619
15	7.82465429767	-2.65013270485	5.07493002088	6.08009249723	-3.80065934608	2.10446021053	-0.382838333182	-0.257327013462	0.585308706554	0.566859293845	-0.202805396134	0.547284875596	-0.625575372093	-0.759662838637	0.477329075126	0.209335755153	0.0542700793107	0.047336425239	0.219173654927	-0.075381231884	0.321171608186	-21.8594182036	-2.18409904967	9.27958945282
16	4.92508678137	0.0911855055672	-2.69449244337	4.97845537913	1.86950047202	9.38423815985	-0.0141654397799	-0.583834932035	-0.0437663471879	0.497563321173	0.0551375833668	0.0102961482939	0.0827432668262	0.0155876205788	-0.0982030484342	0.149303707748	0.0155654098413	-0.0123728814004	0.148452075494	-0.0281374278874	0.0410379327743	-14.4290059273	-11.8436927564	9.40506916912
17	3.67401751647	-0.67998917543	-0.149690417321	6.34423174731	1.53923104057	4.6405588394	-0.0407718666947	-0.0767044127263	0.248358077359	0.175287466193	-0.0255392437745	-0.0451747042116	-0.0438020706365	-0.222809583716	0.05274482379	0.023704784914	-0.00866214170668	-0.0137751203281	0.0981717784647	-0.000396848843382	0.0675838845651	-11.7727836924	-10.1729675913	4.5780171951
18	5.49828218873	0.557093081592	-1.46017858286	2.16083457088	6.81469671108	8.16378839352	0.39437208301	-0.167722625464	1.20239657887	-0.950834803844	0.246677999092	-0.303470912981	-1.32253978589	-0.165024731509	-0.328816812171	0.378282336464	-0.0280075676727	-0.00703530681494	0.126508941321	0.0137328199724	0.424698528044	-8.00603234428	4.20681696944	-0.614358925255
19	3.71492208582	0.267104498019	0.0766866135424	3.38358246876	0.813317674294	1.38588016222	-0.0660255024613	0.158883748409	-0.162526272019	-0.0493998392472	0.0696327157704	0.175103456928	-0.0196737870112	-0.102049935842	-0.0114026300524	0.114562378266	0.0101928830211	0.00225875144198	0.103388472383	0.0106686879882	0.10559714109	-15.9267996016	-14.6727893816	2.52219312656

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 482 through 491 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 492 through 499 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 500 through 507 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 11 )
5	X-RAY DIFFRACTION	5	chain 'F' and (resid 1 through 9 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 344 through 354 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 355 through 420 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 421 through 442 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 443 through 457 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 458 through 477 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 478 through 491 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 492 through 507 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 344 through 354 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 355 through 380 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 381 through 393 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 394 through 403 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 404 through 420 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 421 through 430 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 431 through 481 )

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