PDB-6zdt: Crystal structure of eukaryotic Fibrillarin with Nop56 N-terminal...

ID or keywords:

Entry

Database: PDB / ID: 6zdt

Title

Crystal structure of eukaryotic Fibrillarin with Nop56 N-terminal domain

Components

Nucleolar protein 56
rRNA 2'-O-methyltransferase fibrillarin

Keywords

RIBOSOMAL PROTEIN / 2'-O-Methylation / Methyltransferase / Box C/D snoRNP enzyme / Ribosome biogenesis

Function / homology

Function and homology information

rRNA 2'-O-methylation / histone H2AQ104 methyltransferase activity / snoRNA guided rRNA 2'-O-methylation / rRNA modification / box C/D sno(s)RNA 3'-end processing / regulation of transcription by RNA polymerase I / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / O-methyltransferase activity / rRNA methylation ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.71 Å

Authors

Hoefler, S. / Lukat, P. / Carlomagno, T. / Blankenfeldt, W.

Citation

Journal: Rna / Year: 2021
Title: High-resolution structure of eukaryotic Fibrillarin interacting with Nop56 amino-terminal domain.
Authors: Hofler, S. / Lukat, P. / Blankenfeldt, W. / Carlomagno, T.

History

Deposition	Jun 15, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 31, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 24, 2024	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	6zdt.cif.gz	298.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6zdt.ent.gz	201.1 KB	Display	PDB format
PDBx/mmJSON format	6zdt.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6zdt_validation.pdf.gz	432.8 KB	Display	wwPDB validaton report
Full document	6zdt_full_validation.pdf.gz	434.2 KB	Display
Data in XML	6zdt_validation.xml.gz	19.9 KB	Display
Data in CIF	6zdt_validation.cif.gz	29.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zd/6zdt ftp://data.pdbj.org/pub/pdb/validation_reports/zd/6zdt	HTTPS FTP

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Related structure data

Related structure data	2ipxS S: Starting model for refinement
Similar structure data	5n9t-2 6a0j-d 5kwk-1 3hjz-d 5kx6-1 6tod-1 6vzw-4 3lx6-1 3dt1-d 2vy3-2 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
Related items in Molecule of the Month	#161 - May 2013 Ricin similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1)

Deposited unit

A: rRNA 2'-O-methyltransferase fibrillarin

B: Nucleolar protein 56

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Clear assembly formation of both proteins determined via gel filtration using S200 Increase 10/300 (Cytiva). Verified also by SDS-gelelectrophoresis

Unit cell

Length a, b, c (Å)	69.004, 118.286, 48.828
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab

Components on special symmetry positions

ID	Model	Components
1	1	A-443- HOH
2	1	A-480- HOH

#1: Protein	rRNA 2'-O-methyltransferase fibrillarin / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA- ...Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA-associated protein NOP1 Mass: 27460.850 Da / Num. of mol.: 1 / Fragment: Nop1short Source method: isolated from a genetically manipulated source Details: Cysteine 314 was found to be oxidized. Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NOP1, LOT3, YDL014W, D2870 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P15646, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein	Nucleolar protein 56 / Ribosome biosynthesis protein SIK1 / Suppressor of I kappa b protein 1 Mass: 18451.061 Da / Num. of mol.: 1 / Fragment: 56NTD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NOP56, SIK1, YLR197W, L8167.9 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12460
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.17 Å³/Da / Density % sol: 43.32 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.1 M LiCl, 0.1 M HEPES, 19 % PEG 400, Cryo: 10% 2,3-butanediol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, DESY

/ Beamline: P11 / Wavelength: 1.033198 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2019

Radiation

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

Radiation wavelength

Wavelength: 1.033198 Å / Relative weight: 1

Reflection

Resolution: 1.71→48.83 Å / Num. obs: 44280 / % possible obs: 100 % / Redundancy: 13.1 % / B_iso Wilson estimate: 22.56 Å² / CC_1/2: 1 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.021 / R_rim(I) all: 0.078 / Net I/σ(I): 22.1 / Num. measured all: 582147

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.71-1.8	13.1	1.016	83601	6368	0.896	0.29	1.057	2.6	100
5.4-48.83	12.3	0.021	19171	1558	1	0.006	0.022	80	99.8

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	3.6 Å	48.83 Å
Translation	3.6 Å	48.83 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.18rc4_3812	refinement
XDS		data reduction
Aimless	0.7.4	data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2IPX

2ipx

Resolution: 1.71→48.83 Å / SU ML: 0.1569 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2049	2184	4.94 %
R_work	0.1628	42027	-
obs	0.165	44211	99.95 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.73 Å²

Refinement step

Cycle: LAST / Resolution: 1.71→48.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3053	0	0	367	3420

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0053	3198
X-RAY DIFFRACTION	f_angle_d	0.6863	4337
X-RAY DIFFRACTION	f_chiral_restr	0.0515	490
X-RAY DIFFRACTION	f_plane_restr	0.0044	567
X-RAY DIFFRACTION	f_dihedral_angle_d	19.3995	1232

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 (%)
1.71-1.74	0.2277	132	0.2131	2587	X-RAY DIFFRACTION	99.93
1.74-1.79	0.2411	109	0.2015	2588	X-RAY DIFFRACTION	99.89
1.79-1.83	0.2335	129	0.1911	2608	X-RAY DIFFRACTION	99.96
1.83-1.88	0.2292	137	0.1846	2617	X-RAY DIFFRACTION	99.93
1.88-1.93	0.2353	119	0.1746	2588	X-RAY DIFFRACTION	99.89
1.93-2	0.2025	129	0.173	2576	X-RAY DIFFRACTION	100
2-2.07	0.2176	149	0.1681	2611	X-RAY DIFFRACTION	99.96
2.07-2.15	0.2111	139	0.1619	2581	X-RAY DIFFRACTION	99.96
2.15-2.25	0.2109	131	0.1507	2614	X-RAY DIFFRACTION	99.96
2.25-2.37	0.201	130	0.1501	2626	X-RAY DIFFRACTION	99.96
2.37-2.52	0.193	122	0.1555	2638	X-RAY DIFFRACTION	100
2.52-2.71	0.1959	151	0.1586	2625	X-RAY DIFFRACTION	100
2.71-2.98	0.1965	150	0.1675	2620	X-RAY DIFFRACTION	99.96
2.98-3.41	0.2056	167	0.1652	2625	X-RAY DIFFRACTION	100
3.41-4.3	0.1868	152	0.1444	2688	X-RAY DIFFRACTION	100
4.3-48.83	0.2156	138	0.1681	2835	X-RAY DIFFRACTION	99.83

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	1.36666646432	0.604777618162	1.13635336484	1.50160257121	-0.189156900911	1.40089113417	0.0909492760843	-0.0155125918374	-0.12226294332	-0.109721371791	0.0521248982813	-0.0688789477605	0.203396539955	0.0295019287654	0.0145234401996	0.176893680173	0.0227694454341	0.0139796450139	0.186778531878	-0.00489563569076	0.20530572798	17.6584544178	-15.1701102089	11.9827311097
2	0.208495226436	0.00651558336047	-0.366157939452	0.557668014147	0.420901249795	0.955201272413	0.0463755958155	-0.291261100163	0.185448918356	0.283159924408	-0.0696293356388	-0.0648382870524	-0.0465892300494	0.0595039183917	0.000109088636018	0.186892614715	-0.0087341875312	0.00534629971724	0.227753473274	-0.00495379482773	0.224280056834	20.8266727562	3.48630615361	23.5291557365
3	0.54246588777	-0.245921354603	0.100615342867	0.308829250538	0.270774888122	0.496377402467	-0.078904862015	-0.103088227565	0.484251340388	-0.190053280918	-0.0499222504163	0.502152177258	-0.324477974903	-0.444514843957	-0.0204072778578	0.330821491328	0.0637904786971	-0.0589936808116	0.246455838181	0.0265240773431	0.386506645711	6.79417860311	27.7995108409	6.377823715
4	0.864006448573	0.147761951104	0.261938012657	1.03996572242	-0.602860894553	0.673313493981	-0.0805593135409	-0.0914811347898	0.207502682559	0.0185113900899	0.0832263348669	0.0443676618832	-0.251803204274	-0.103432896326	-3.37839312459E-5	0.260410215265	0.0087202357041	-0.00410284868093	0.206544314282	-0.0205324818779	0.227429121814	11.7399110065	23.2405737902	10.9103199722
5	0.762465654986	-0.0826257133287	-0.0235011527278	1.3417036625	0.0103071366306	0.535554764879	-0.0440683877181	-0.0416483180186	0.11537105084	-0.00656624283789	0.0512070528594	-0.127184381755	-0.0156060534213	0.0161612676809	5.71708036775E-6	0.144927170829	-0.00361433426966	0.00798044933272	0.193273231557	-0.0066601755233	0.166616758593	20.9858536212	9.24990453214	15.10972138
6	0.204536956885	-0.0526074335174	0.301336673839	0.45133859461	0.0658139235453	0.647500838619	0.000804398979366	-0.0234153816385	0.13795950453	-0.246338847099	0.00341718535528	-0.219946159292	-0.0123593452555	0.213323015926	6.029541433E-6	0.22894153102	-0.0201460338388	0.0579865444619	0.237152357907	-0.000707506635501	0.230947855348	22.0688393856	3.18569421236	3.90751984074
7	0.0674592814991	-0.092653096229	-0.0278054625171	0.409678120904	0.422090681853	0.488273952852	-0.301740825624	0.396865015698	-0.144465089141	-0.568928223562	0.278396651662	-0.356880689408	-0.0657840006129	0.0135618511427	-0.00415596556702	0.319175209362	-0.0662711570103	0.0597672590435	0.261956491562	-0.00444312923971	0.250452441129	21.5034302227	8.50063718111	-2.20734155659
8	0.0635377518753	-0.0618874164071	0.0111887556086	0.25423571408	0.115446652971	0.0891913077104	-0.469857187756	0.0315516494698	0.000377058217817	-0.745420781544	0.305649326597	-0.498979708814	-0.0166532307253	0.130419530579	-0.0952851018453	0.51283826983	-0.0934410101103	0.143160379117	0.397887680763	-0.0192645518699	0.292482503227	25.6501064821	6.13792803677	-10.2856397523
9	0.46805678235	-0.522601467431	-0.557350010192	1.07006168773	0.156693530557	1.07159940841	-0.138284306681	0.203817068019	-0.0292042112321	-1.14640765601	0.00889274428578	-0.293450264634	0.0721016731856	0.20114402761	0.0272923378878	0.409836257267	-0.0801535663907	0.0230142626599	0.276354400109	0.0236978630295	0.205351455702	17.7629800174	10.3373374261	-5.98041311207
10	0.403135086119	-0.298064725014	0.173304488051	0.468236421441	-0.298496717534	0.372711537754	0.0475224990603	0.0482811998529	-0.165327085422	-0.0831378758345	0.00642331273941	0.0304635199964	0.123856551044	0.131756810918	9.89154573446E-5	0.221426775643	0.0148910825036	-0.00115532385335	0.177416246544	-0.0182569630826	0.201008793145	13.8371700836	-19.2221648767	10.0355242528
11	0.129964137589	-0.0597454996014	-0.0739474525568	0.844793614276	0.0039289970735	0.222378308555	-0.0348790041494	0.399679966071	-0.19792283843	-0.823826825916	0.16729788426	0.41173314906	0.266200273352	-0.0857648343694	0.0443725919359	0.356750431436	-0.0150169069183	0.000762834752015	0.330401224503	-0.0561262765777	0.273112929465	5.79192889964	-14.1002503678	0.638537937597
12	0.947741916494	0.053682422881	0.461015709489	0.219471589272	0.0605192049755	0.661627666872	0.434873620359	0.0185388341277	-0.333124154474	0.230614252924	-0.0184150681047	-0.00770363379838	0.399866052718	-0.337268152759	0.0724224094644	0.257535473793	-0.0339700730941	0.0482263669763	0.230162168655	0.00214692276389	0.196594799458	11.1487930448	-14.9065131316	22.3477988809
13	0.752531784573	-0.42990542359	0.0870934549519	0.682548551204	-0.547529447586	1.26976593403	0.0741600250807	0.0166717366422	-0.207575413807	0.241256964073	0.0778386474958	-0.117474857755	0.33916228124	0.0966641509482	0.000229741381444	0.259226902129	0.00972625495392	-0.0186517996727	0.196449528163	0.00203870577526	0.226116002723	21.9607926129	-19.2503357711	21.0490068997

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 96 through 145 )	B	B	96 - 145	102 - 152
2	2	chain 'B' and (resid 146 through 165 )	B	B	146 - 165	153 - 175
3	3	chain 'A' and (resid 86 through 109 )	A	A	86 - 109	1 - 24
4	4	chain 'A' and (resid 110 through 168 )	A	A	110 - 168	25 - 83
5	5	chain 'A' and (resid 169 through 233 )	A	A	169 - 233	84 - 158
6	6	chain 'A' and (resid 234 through 260 )	A	A	234 - 260	159 - 185
7	7	chain 'A' and (resid 261 through 281 )	A	A	261 - 281	186 - 204
8	8	chain 'A' and (resid 282 through 296 )	A	A	282 - 296	205 - 219
9	9	chain 'A' and (resid 297 through 326 )	A	A	297 - 326	220 - 253
10	10	chain 'B' and (resid -1 through 26 )	B	B	-1 - 26	1 - 28
11	11	chain 'B' and (resid 27 through 47 )	B	B	27 - 47	29 - 49
12	12	chain 'B' and (resid 48 through 58 )	B	B	48 - 58	50 - 60
13	13	chain 'B' and (resid 59 through 95 )	B	B	59 - 95	61 - 101

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