PDB-6dcb: Structure of methylphosphate capping enzyme methyltransferase dom...

ID or keywords:

Entry

Database: PDB / ID: 6dcb

Title

Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7SK RNA

Components

7SK snRNA methylphosphate capping enzyme
human 7SK RNA stem-loop 1 proximal

Keywords

Transferase/RNA / RNA methyl transferase / MePCE /

7SK RNA / Transferase-RNA complex

Function / homology

Function and homology information

RNA 5'-gamma-phosphate methyltransferase activity / snRNA metabolic process / snRNA modification / 7SK snRNP / positive regulation of snRNA transcription by RNA polymerase II / 7SK snRNA binding /

snRNA binding / positive regulation of protein localization to Cajal body / RNA methyltransferase activity /

RNA methylation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.998 Å

Model details

methyltransferase domain in complex with RNA

Authors

Yang, Y. / Eichhorn, C. / Cascio, D. / Feigon, J.

Funding support

United States, 1items

Citation

Journal: Nat. Chem. Biol. / Year: 2019
Title: Structural basis of 7SK RNA 5'-gamma-phosphate methylation and retention by MePCE.
Authors: Yang, Y. / Eichhorn, C.D. / Wang, Y. / Cascio, D. / Feigon, J.

History

Deposition	May 4, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 26, 2018	Group: Data collection / Derived calculations Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2	Jan 2, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3	Jan 30, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Oct 11, 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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PDBx/mmCIF format	6dcb.cif.gz	161.5 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	6dccC 5unaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2raj-d 3k51-d 3dyt-d 4ac9-1 2rak-d 3l0m-2 4xcm-d 3tf4-1 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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Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #10 - Oct 2000 Ribosome similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #161 - May 2013 Ricin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #227 - Nov 2018 Telomerase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

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Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
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#181 - Jan 2015
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#260 - Aug 2021
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#249 - Sep 2020
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#146 - Feb 2012
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#87 - Mar 2007
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#10 - Oct 2000
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#245 - May 2020
Spliceosomes
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#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
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#161 - May 2013
Ricin
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#143 - Nov 2011
Toll-like Receptors
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
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#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#227 - Nov 2018
Telomerase
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#241 - Jan 2020
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similarity (1)

Deposited unit

B: human 7SK RNA stem-loop 1 proximal

A: 7SK snRNA methylphosphate capping enzyme

hetero molecules

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

1

A: 7SK snRNA methylphosphate capping enzyme

hetero molecules

B: human 7SK RNA stem-loop 1 proximal

defined by author&software
Evidence: native gel electrophoresis
47.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	118.280, 118.280, 78.630
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃

#1: RNA chain	human 7SK RNA stem-loop 1 proximal Mass: 11709.824 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: in vitro T7 polymerase transciption from synthetic DNA template Source: (synth.) Homo sapiens (human)
#2: Protein	7SK snRNA methylphosphate capping enzyme / MePCE / Bicoid-interacting protein 3 homolog / Bin3 homolog Mass: 35122.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MEPCE, BCDIN3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7L2J0, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.54 Å³/Da / Density % sol: 65.3 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: crystallization solution 0.214 M lithium sulfate, 0.1 M phosphate/citrate, pH 4.2, 17.25% w/v PEG 1,000 mixed 1:2 volume ratio to 10 mg/mL protein:RNA complex solution

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.9792 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 1.998→62.373 Å / Num. obs: 42441 / % possible obs: 99.9 % / Redundancy: 12.885 % / B_iso Wilson estimate: 38.1 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.069 / R_rim(I) all: 0.072 / Χ²: 1.061 / Net I/σ(I): 20.94 / Num. measured all: 546849

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.998-2.05	12.448	0.752	3.33	38278	3119	3075	0.887	0.784	98.6
2.05-2.11	13.029	0.596	4.45	39529	3034	3034	0.941	0.62	100
2.11-2.17	13.095	0.444	6.06	38985	2977	2977	0.969	0.462	100
2.17-2.23	12.938	0.39	6.89	37211	2876	2876	0.97	0.406	100
2.23-2.31	12.22	0.291	8.58	34229	2801	2801	0.983	0.304	100
2.31-2.39	13.107	0.247	10.54	35323	2694	2695	0.989	0.257	100
2.39-2.48	13.377	0.21	12.47	34807	2602	2602	0.992	0.218	100
2.48-2.58	13.186	0.177	14.65	33375	2531	2531	0.993	0.184	100
2.58-2.69	12.955	0.144	17.49	31287	2415	2415	0.996	0.15	100
2.69-2.83	12.038	0.118	19.98	27506	2285	2285	0.996	0.123	100
2.83-2.98	13.304	0.098	25.41	29309	2203	2203	0.997	0.101	100
2.98-3.16	13.399	0.076	31.4	27924	2084	2084	0.998	0.08	100
3.16-3.38	13.101	0.061	37.35	25638	1957	1957	0.999	0.063	100
3.38-3.65	12.296	0.053	41.47	22281	1812	1812	0.999	0.055	100
3.65-4	13	0.047	45.94	21840	1680	1680	0.999	0.049	100
4-4.47	13.289	0.045	49.91	20252	1524	1524	0.999	0.047	100
4.47-5.16	12.757	0.043	49.83	17184	1347	1347	0.999	0.045	100
5.16-6.32	12.429	0.045	47.1	14107	1135	1135	0.999	0.047	100
6.32-8.94	12.978	0.043	51.51	11719	903	903	0.999	0.044	100
8.94-62.373	12.01	0.039	54.14	6065	506	505	0.999	0.041	99.8

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	6.59 Å	62.37 Å
Translation	6.59 Å	62.37 Å

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Processing

Software

Name	Version	Classification
PHENIX		refinement
XSCALE		data scaling
PHASER	2.7.17	phasing
PDB_EXTRACT	3.24	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5UNA

5una

Resolution: 1.998→62.373 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1782	4243	10 %
R_work	0.16	38194	-
obs	0.1619	42437	99.88 %

Solvent computation

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

Displacement parameters

B_iso max: 166.27 Å² / B_iso mean: 47.6433 Å² / B_iso min: 22.99 Å²

Refinement step

Cycle: final / Resolution: 1.998→62.373 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1827	775	41	149	2792
B_iso mean	-	-	36.69	47.04	-
Num. residues	-	-	-	-	261

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2792
X-RAY DIFFRACTION	f_angle_d	0.956	3966
X-RAY DIFFRACTION	f_chiral_restr	0.051	454
X-RAY DIFFRACTION	f_plane_restr	0.005	364
X-RAY DIFFRACTION	f_dihedral_angle_d	15.854	1558

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9982-2.0209	0.2602	134	0.2339	1215	1349	97
2.0209-2.0446	0.2253	141	0.1974	1269	1410	100
2.0446-2.0696	0.221	143	0.1891	1282	1425	100
2.0696-2.0958	0.1913	139	0.1682	1256	1395	100
2.0958-2.1234	0.1512	142	0.1563	1275	1417	100
2.1234-2.1524	0.2112	141	0.1657	1274	1415	100
2.1524-2.1832	0.218	141	0.1683	1273	1414	100
2.1832-2.2158	0.1906	139	0.1712	1246	1385	100
2.2158-2.2504	0.1896	139	0.1661	1256	1395	100
2.2504-2.2873	0.1873	146	0.1673	1307	1453	100
2.2873-2.3267	0.2203	138	0.1689	1250	1388	100
2.3267-2.3691	0.2066	143	0.1746	1288	1431	100
2.3691-2.4146	0.19	139	0.1619	1248	1387	100
2.4146-2.4639	0.1974	145	0.1666	1300	1445	100
2.4639-2.5175	0.1796	138	0.1718	1246	1384	100
2.5175-2.5761	0.216	141	0.1749	1267	1408	100
2.5761-2.6405	0.2121	140	0.1804	1261	1401	100
2.6405-2.7119	0.205	143	0.1856	1283	1426	100
2.7119-2.7917	0.1907	139	0.183	1258	1397	100
2.7917-2.8818	0.1778	144	0.1775	1288	1432	100
2.8818-2.9848	0.1985	139	0.1862	1260	1399	100
2.9848-3.1043	0.2041	144	0.1862	1289	1433	100
3.1043-3.2455	0.2025	140	0.1735	1266	1406	100
3.2455-3.4166	0.1772	143	0.1617	1280	1423	100
3.4166-3.6307	0.1803	142	0.1519	1279	1421	100
3.6307-3.911	0.1635	142	0.1474	1278	1420	100
3.911-4.3045	0.1514	144	0.1349	1296	1440	100
4.3045-4.9271	0.1351	143	0.1282	1290	1433	100
4.9271-6.2068	0.1579	143	0.154	1288	1431	100
6.2068-62.4029	0.1659	148	0.1534	1326	1474	100

Refinement TLS params.

Method: refined / Origin x: 46.3253 Å / Origin y: 52.634 Å / Origin z: 43.4787 Å

	11	12	13	21	22	23	31	32	33
T	0.2246 Å²	0.0325 Å²	-0.0096 Å²	-	0.2234 Å²	-0.0212 Å²	-	-	0.2257 Å²
L	2.218 °²	0.0671 °²	0.5492 °²	-	1.0619 °²	-0.1655 °²	-	-	0.7925 °²
S	-0.0568 Å °	-0.0231 Å °	0.2688 Å °	0.0574 Å °	-0.0534 Å °	0.0397 Å °	-0.1325 Å °	-0.036 Å °	0.0064 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	all	B	1 - 116
2	X-RAY DIFFRACTION	1	all	A	411 - 688
3	X-RAY DIFFRACTION	1	all	C	1
4	X-RAY DIFFRACTION	1	all	D	1
5	X-RAY DIFFRACTION	1	all	D	2
6	X-RAY DIFFRACTION	1	all	D	3
7	X-RAY DIFFRACTION	1	all	E	1 - 149

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