PDB-1n9s: Crystal structure of yeast SmF in spacegroup P43212

ID or keywords:

Entry

Database: PDB / ID: 1n9s

Title

Crystal structure of yeast SmF in spacegroup P43212

Components

Small nuclear ribonucleoprotein F

Keywords

TRANSLATION / snrnp / Sm protein / heptamer

Function / homology

Function and homology information

U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / splicing factor binding / commitment complex / U2-type prespliceosome assembly / U2 snRNP / U1 snRNP / U4 snRNP / poly(U) RNA binding ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Collins, B.M. / Cubeddu, L. / Naidoo, N. / Harrop, S.J. / Kornfeld, G.D. / Dawes, I.W. / Curmi, P.M.G. / Mabbutt, B.C.

Citation

Journal: J.Biol.Chem. / Year: 2003
Title: Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA: Crystal structure of an oligomeric complex of yeast SmF
Authors: Collins, B.M. / Cubeddu, L. / Naidoo, N. / Harrop, S.J. / Kornfeld, G.D. / Dawes, I.W. / Curmi, P.M.G. / Mabbutt, B.C.

History

Deposition	Nov 26, 2002	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 13, 2002	Provider: repository / Type: Initial release
Revision 1.1	Apr 28, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 27, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4	Aug 16, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	1n9s.cif.gz	202.2 KB	Display	PDBx/mmCIF format
PDB format	pdb1n9s.ent.gz	165.5 KB	Display	PDB format
PDBx/mmJSON format	1n9s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	1n9s_validation.pdf.gz	557.3 KB	Display	wwPDB validaton report
Full document	1n9s_full_validation.pdf.gz	616.8 KB	Display
Data in XML	1n9s_validation.xml.gz	41.6 KB	Display
Data in CIF	1n9s_validation.cif.gz	57.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n9/1n9s ftp://data.pdbj.org/pub/pdb/validation_reports/n9/1n9s	HTTPS FTP

-
Related structure data

Related structure data	1n9rSC 1i4k 1i5l 1i81 1i8f 1jr1 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1n9r-d 1i5l-1 1jri-1 1i4k-3 1jri-2 1h64-3 5mki-2 1h64-2 5mkn-3 4rhs-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#245 - May 2020 Spliceosomes similarity (7) #107 - Nov 2008 Mechanosensitive Channels similarity (1)

Deposited unit

A: Small nuclear ribonucleoprotein F

B: Small nuclear ribonucleoprotein F

C: Small nuclear ribonucleoprotein F

D: Small nuclear ribonucleoprotein F

E: Small nuclear ribonucleoprotein F

F: Small nuclear ribonucleoprotein F

G: Small nuclear ribonucleoprotein F

H: Small nuclear ribonucleoprotein F

I: Small nuclear ribonucleoprotein F

J: Small nuclear ribonucleoprotein F

K: Small nuclear ribonucleoprotein F

L: Small nuclear ribonucleoprotein F

M: Small nuclear ribonucleoprotein F

N: Small nuclear ribonucleoprotein F

149 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Small nuclear ribonucleoprotein F

B: Small nuclear ribonucleoprotein F

C: Small nuclear ribonucleoprotein F

D: Small nuclear ribonucleoprotein F

E: Small nuclear ribonucleoprotein F

F: Small nuclear ribonucleoprotein F

G: Small nuclear ribonucleoprotein F

defined by author&software
74.3 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: Small nuclear ribonucleoprotein F

I: Small nuclear ribonucleoprotein F

J: Small nuclear ribonucleoprotein F

K: Small nuclear ribonucleoprotein F

L: Small nuclear ribonucleoprotein F

M: Small nuclear ribonucleoprotein F

N: Small nuclear ribonucleoprotein F

defined by author&software
74.3 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	105.635, 105.635, 235.563
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Cell setting	tetragonal
Space group name H-M	P4₃2₁2

Details

The assymetric unit contains two heptameric rings stacked face to face. This dimer of rings is observed in solution.

#1: Protein	Small nuclear ribonucleoprotein F / SmF / Sm-like snRNP protein / snRNP-F / Sm protein F / Sm-F Mass: 10613.957 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P54999

-
Experiment

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

-
Sample preparation

Crystal

Density Matthews: 2.21 Å³/Da / Density % sol: 44.35 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris, PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K

Crystal grow

*PLUS

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details
2	20 mg/ml	protein	1	drop
3	24 %	PEG3350	1	reservoir
4	0.1 M	Tris	1	reservoir	pH8.5
5	0.1 M	sodium acetate	1	reservoir
1		Tris-NaCl	1	drop

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
Detector	Detector: AREA DETECTOR
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.5→95 Å / Num. obs: 16292 / % possible obs: 99.3 % / Redundancy: 6.7 % / B_iso Wilson estimate: 88.9 Å² / R_merge(I) obs: 0.064 / Net I/σ(I): 23.5
Reflection shell	Resolution: 3.5→3.69 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.381 / Mean I/σ(I) obs: 6 / % possible all: 99.3
Reflection	PLUS Highest resolution: 3.5 Å / Lowest resolution*: 95 Å
Reflection shell	PLUS % possible obs: 99.3 % / R_merge(I) obs*: 0.353

-
Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
AMoRE		phasing
REFMAC	5	refinement
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ID: 1N9R

1n9r

Resolution: 3.5→20 Å / Cor.coef. F_o:F_c: 0.886 / Cor.coef. F_o:F_c free: 0.896 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement used / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29683	876	5.1 %	RANDOM
R_work	0.29167	-	-	-
all	0.29193	-	-	-
obs	0.29193	16292	98.41 %	-

Solvent computation

Shrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 44.801 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.05 Å²	0 Å²	0 Å²
2-	-	8.05 Å²	0 Å²
3-	-	-	-16.09 Å²

Refinement step

Cycle: LAST / Resolution: 3.5→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7887	0	0	0	7887

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.021	8036
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	7274
X-RAY DIFFRACTION	r_angle_refined_deg	2.282	1.95	10858
X-RAY DIFFRACTION	r_angle_other_deg	1.332	3	16833
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.003	3	969
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.23	15	1400
X-RAY DIFFRACTION	r_chiral_restr	0.13	0.2	1223
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	9009
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1731
X-RAY DIFFRACTION	r_nbd_refined	0.295	0.2	2112
X-RAY DIFFRACTION	r_nbd_other	0.278	0.2	8393
X-RAY DIFFRACTION	r_nbtor_other	0.108	0.2	5822
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.258	0.2	322
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.166	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.445	0.2	32
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.42	0.2	36
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.659	0.2	4
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	0.851	1.5	4856
X-RAY DIFFRACTION	r_mcangle_it	1.636	2	7812
X-RAY DIFFRACTION	r_scbond_it	1.879	3	3180
X-RAY DIFFRACTION	r_scangle_it	3.383	4.5	3046
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.5→3.588 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.37	55
R_work	0.383	1183

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	8.7142	0.0348	1.1703	14.1065	3.8113	10.3521	0.4893	-1.5586	-0.1741	0.8457	-0.8268	0.187	0.9708	-0.5335	0.3375	0.621	-0.3296	0.0233	1.4015	0.4166	0.822	27.847	7.377	77.545
2	6.2107	-1.5753	-1.0288	14.9034	6.18	17.7391	0.1112	-1.2865	0.02	0.3813	-0.3812	0.5342	0.5842	-1.4364	0.27	0.3725	-0.3679	0.1169	1.7745	-0.1012	0.8049	10.094	12.204	74.796
3	0.8386	0.1941	-2.342	7.299	-0.423	17.8621	0.4628	-0.8286	0.8294	1.0237	-0.1137	0.471	-0.3817	-1.1545	-0.3492	0.4344	-0.0389	0.1877	1.9666	-0.3401	1.22	3.048	29.768	72.765
4	4.8759	2.8807	-3.903	10.5429	0.9592	14.5051	0.1999	-1.4483	0.6011	0.6269	-0.8162	0.5451	-0.3707	-0.5351	0.6164	0.4156	0.3343	-0.0415	1.56	-0.5188	1.0694	12.116	45.525	71.567
5	12.2809	-1.2964	0.7215	9.6338	-0.3679	15.6796	-0.3537	-2.1706	0.773	0.1913	-0.261	-0.1196	-0.4577	-0.4565	0.6147	0.3421	0.1942	-0.1461	1.1151	-0.4533	0.8645	30.015	48.727	72.535
6	8.2753	1.2869	-0.1154	5.403	-1.1628	16.1578	-0.0854	-0.9158	-0.2642	0.4391	-0.3889	-0.4453	0.1111	-0.1776	0.4742	0.2184	0.0482	-0.1156	1.1483	-0.0442	0.8898	43.532	36.525	76.175
7	6.371	1.4389	-2.3949	9.1423	5.3384	16.3537	0.4943	-1.0336	-0.8232	0.9629	-0.6274	-0.7051	0.9492	-0.6864	0.1331	0.3054	-0.0717	-0.106	1.077	0.3778	1.0915	42.413	18.196	78.517
8	7.7001	-1.5479	-1.0991	8.6624	-1.6776	14.4059	-0.4037	0.4242	0.1506	-0.7868	0.347	1.0054	0.228	0.0189	0.0567	0.4775	0.0718	-0.3996	0.6413	-0.179	0.9996	11.855	37.227	37.711
9	11.9521	0.891	3.9303	9.0855	-0.9901	18.5232	-0.0918	0.0191	-0.1214	-1.4648	0.2567	0.4036	1.3516	-0.2006	-0.1649	0.6436	-0.1314	-0.1621	0.4592	-0.069	1.0009	7.617	19.526	39.659
10	12.2501	-1.5271	-0.2299	7.512	2.0957	15.1926	0.1358	-0.1545	-0.4589	-1.2122	0.1402	-0.2492	0.4959	0.0665	-0.2759	0.9279	-0.0752	0.0594	0.2852	0.014	0.897	19	5.355	42.354
11	9.7547	3.114	1.9979	10.4732	2.3964	15.4029	-0.001	0.4378	-1.0326	-1.2298	-0.3058	-1.5988	0.9915	0.3906	0.3068	0.8228	0.2488	0.5211	0.2942	0.1412	1.1695	36.988	5	45.297
12	9.1737	-1.8161	0.2485	8.3934	1.5552	14.3264	-0.1809	0.2125	-0.3569	-1.0356	0.3542	-0.3939	-0.204	0.2292	-0.1733	0.4961	0.0254	0.4225	0.5877	0.1328	1.0828	48.305	19.402	43.511
13	10.2518	-2.9605	-1.3823	8.0805	0.0391	15.9021	0.1178	-0.2787	0.2751	-1.2028	-0.1572	-0.5366	-0.4641	-0.0847	0.0394	0.5481	0.0077	0.1442	0.4291	-0.0051	0.8234	44.607	37.219	41.875
14	11.7306	2.0111	-0.5981	9.329	-0.3198	16.0849	-0.1278	0.5081	0.5534	-1.4519	0.0645	0.6538	0.2792	0.094	0.0633	0.6247	0.0742	-0.282	0.2602	-0.0922	0.9672	28.609	45.09	39.166

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	19 - 86	26 - 93
2	X-RAY DIFFRACTION	2	B	B	19 - 86	26 - 93
3	X-RAY DIFFRACTION	3	C	C	15 - 86	22 - 93
4	X-RAY DIFFRACTION	4	D	D	16 - 86	23 - 93
5	X-RAY DIFFRACTION	5	E	E	19 - 86	26 - 93
6	X-RAY DIFFRACTION	6	F	F	17 - 86	24 - 93
7	X-RAY DIFFRACTION	7	G	G	17 - 86	24 - 93
8	X-RAY DIFFRACTION	8	H	H	16 - 86	23 - 93
9	X-RAY DIFFRACTION	9	I	I	17 - 86	24 - 93
10	X-RAY DIFFRACTION	10	J	J	15 - 86	22 - 93
11	X-RAY DIFFRACTION	11	K	K	18 - 86	25 - 93
12	X-RAY DIFFRACTION	12	L	L	13 - 86	20 - 93
13	X-RAY DIFFRACTION	13	M	M	17 - 86	24 - 93
14	X-RAY DIFFRACTION	14	N	N	18 - 85	25 - 92

Refinement

*PLUS

Highest resolution: 3.5 Å / Lowest resolution: 20 Å / R_factor R_free: 0.297 / R_factor R_work: 0.292

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.023
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	2.3

LS refinement shell

*PLUS

R_factor R_free: 0.37

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi