PDB-3eud: Structure of the CS domain of the essential H/ACA RNP assembly pr...

ID or keywords:

Entry

Database: PDB / ID: 3eud

Title

Structure of the CS domain of the essential H/ACA RNP assembly protein Shq1p

Components

Protein SHQ1

Keywords

NUCLEAR PROTEIN / CS domain HSP20-like domain Shq1 H/ACA snoRNP Ribosome biogenesis / Nucleus

Function / homology

Function and homology information

Telomere Extension By Telomerase / box H/ACA snoRNP assembly / unfolded protein binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.4 Å

Authors

Singh, M. / Cascio, D. / Gonzales, F.A. / Heckmann, N. / Chanfreau, G. / Feigon, J.

Citation

Journal: J.Biol.Chem. / Year: 2009
Title: Structure and Functional Studies of the CS Domain of the Essential H/ACA Ribonucleoparticle Assembly Protein SHQ1.
Authors: Singh, M. / Gonzales, F.A. / Cascio, D. / Heckmann, N. / Chanfreau, G. / Feigon, J.

History

Deposition	Oct 9, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 18, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3eud.cif.gz	254.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3eud.ent.gz	207.4 KB	Display	PDB format
PDBx/mmJSON format	3eud.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3eud_validation.pdf.gz	466.2 KB	Display	wwPDB validaton report
Full document	3eud_full_validation.pdf.gz	479.1 KB	Display
Data in XML	3eud_validation.xml.gz	23.1 KB	Display
Data in CIF	3eud_validation.cif.gz	32.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eu/3eud ftp://data.pdbj.org/pub/pdb/validation_reports/eu/3eud	HTTPS FTP

-
Related structure data

Similar structure data	3cmy-d 3jqw-2 1d7h-1 3wzt-5 1uy1-d 4e3b-1 2mwy-d 3iux-1 4s1z-1 4jp7-2 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) 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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#108 - Dec 2008 Hsp90 similarity (3) #127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: Protein SHQ1

B: Protein SHQ1

C: Protein SHQ1

D: Protein SHQ1

E: Protein SHQ1

F: Protein SHQ1

82.8 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein SHQ1

defined by software
13.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Protein SHQ1

defined by software
13.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Protein SHQ1

defined by software
13.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Protein SHQ1

defined by software
13.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Protein SHQ1

defined by software
13.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Protein SHQ1

defined by software
13.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	141.938, 146.293, 48.511
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Protein SHQ1 / Small nucleolar RNAs of the box H/ACA family quantitative accumulation protein 1 Mass: 13799.377 Da / Num. of mol.: 6 / Fragment: CS domain, UNP residues 1-98 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SHQ1, YIL104C / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40486
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.04 Å³/Da / Density % sol: 65.22 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 6 Details: 0.1 M Bis-Tris HCl,0.2 M Ammonium Sulfate 25% w/v PEG 3350, pH 6.0, VAPOR DIFFUSION, temperature 298K

-
Data collection

Diffraction

Mean temperature: 298 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.97949 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2007 / Details: mirrors

Radiation

Monochromator: Cryo-Cooled Si(111) double crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 2.4→90 Å / Num. obs: 39269 / % possible obs: 95.2 % / Redundancy: 6.9 % / B_iso Wilson estimate: 37.9 Å² / R_merge(I) obs: 0.067 / Χ²: 1.024 / Net I/σ(I): 24.621

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.4-2.49	2.4	0.398	4701	1.052	61.5
2.49-2.59	4	0.335	7022	1.072	91
2.59-2.7	6.4	0.279	7664	1.056	99.8
2.7-2.85	7.6	0.193	7638	1.037	100
2.85-3.02	7.8	0.131	7688	0.993	100
3.02-3.26	7.8	0.084	7639	0.997	100
3.26-3.59	7.8	0.064	7667	0.952	100
3.59-4.1	7.7	0.06	7660	1.108	100
4.1-5.17	7.6	0.066	7662	1.06	100
5.17-90	7.6	0.046	7653	0.975	99.5

-
Phasing

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 40976

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
10.96-100	27.1	0.584	508
8.27-10.96	27.8	0.836	613
6.92-8.27	25.7	0.891	743
6.07-6.92	31.3	0.877	853
5.47-6.07	23.2	0.913	952
5.02-5.47	25.9	0.911	1039
4.66-5.02	25.2	0.9	1125
4.37-4.66	22.1	0.915	1179
4.13-4.37	23.1	0.902	1268
3.93-4.13	26.7	0.876	1322
3.75-3.93	25.5	0.891	1348
3.59-3.75	26.6	0.856	1469
3.46-3.59	26.7	0.878	1479
3.33-3.46	26.6	0.856	1563
3.22-3.33	29.3	0.846	1579
3.12-3.22	28.3	0.847	1679
3.03-3.12	32.1	0.835	1679
2.95-3.03	33.3	0.817	1784
2.87-2.95	35.4	0.796	1761
2.8-2.87	34.7	0.796	1870
2.73-2.8	36.6	0.782	1885
2.67-2.73	36.1	0.782	1925
2.61-2.67	38.8	0.757	1983
2.56-2.61	39.5	0.76	1973
2.51-2.56	38.5	0.738	2061
2.46-2.51	38.4	0.707	1830
2.41-2.46	43.1	0.652	1513
2.37-2.41	40.8	0.64	1157
2.33-2.37	41.9	0.606	836

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
DM	6	phasing
PHENIX		refinement
PDB_EXTRACT	3.006	data extraction
HKL2Map		phasing

Refinement

Resolution: 2.4→35.416 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.774 / Cross valid method: THROUGHOUT / Stereochemistry target values: mlhl

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.248	1959	5.01 %	RANDOM
R_work	0.228	-	-	-
obs	-	39133	96.74 %	-

Solvent computation

B_sol: 41.701 Å² / k_sol: 0.346 e/Å³

Displacement parameters

B_iso max: 142.96 Å² / B_iso mean: 52.794 Å² / B_iso min: 19.27 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.174 Å²	-0 Å²	0 Å²
2-	-	-1.327 Å²	-0 Å²
3-	-	-	1.502 Å²

Refine analyze

Luzzati coordinate error obs: 0.3 Å

Refinement step

Cycle: LAST / Resolution: 2.4→35.416 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4848	0	0	103	4951

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	1.286	1
X-RAY DIFFRACTION	f_bond_d	0.01	1
X-RAY DIFFRACTION	f_chiral_restr	0.08	1
X-RAY DIFFRACTION	f_dihedral_angle_d	18.164	1
X-RAY DIFFRACTION	f_plane_restr	0.005	1
X-RAY DIFFRACTION	f_nbd_refined	4.129	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.4-2.411	0.349	293	X-RAY DIFFRACTION	74	56
2.411-2.422	0.311	329	X-RAY DIFFRACTION	74	59
2.422-2.434	0.315	331	X-RAY DIFFRACTION	74	62
2.434-2.445	0.292	377	X-RAY DIFFRACTION	74	71
2.445-2.457	0.331	398	X-RAY DIFFRACTION	74	74
2.457-2.469	0.283	385	X-RAY DIFFRACTION	74	76
2.469-2.481	0.312	441	X-RAY DIFFRACTION	74	81
2.481-2.493	0.296	461	X-RAY DIFFRACTION	74	85
2.493-2.506	0.315	479	X-RAY DIFFRACTION	74	87
2.506-2.519	0.292	458	X-RAY DIFFRACTION	74	88
2.519-2.532	0.307	491	X-RAY DIFFRACTION	74	88
2.532-2.546	0.289	479	X-RAY DIFFRACTION	74	90
2.546-2.56	0.32	515	X-RAY DIFFRACTION	74	94
2.56-2.574	0.302	491	X-RAY DIFFRACTION	74	93
2.574-2.588	0.307	497	X-RAY DIFFRACTION	74	95
2.588-2.603	0.285	512	X-RAY DIFFRACTION	74	96
2.603-2.618	0.293	517	X-RAY DIFFRACTION	74	94
2.618-2.634	0.32	497	X-RAY DIFFRACTION	74	96
2.634-2.65	0.316	526	X-RAY DIFFRACTION	74	94
2.65-2.666	0.312	500	X-RAY DIFFRACTION	74	93
2.666-2.683	0.308	525	X-RAY DIFFRACTION	74	95
2.683-2.7	0.301	504	X-RAY DIFFRACTION	74	94
2.7-2.717	0.31	517	X-RAY DIFFRACTION	74	96
2.717-2.735	0.291	505	X-RAY DIFFRACTION	74	96
2.735-2.754	0.288	514	X-RAY DIFFRACTION	74	94
2.754-2.773	0.303	473	X-RAY DIFFRACTION	74	93
2.773-2.792	0.284	529	X-RAY DIFFRACTION	74	95
2.792-2.812	0.266	507	X-RAY DIFFRACTION	74	93
2.812-2.833	0.27	543	X-RAY DIFFRACTION	74	95
2.833-2.854	0.289	511	X-RAY DIFFRACTION	74	96
2.854-2.876	0.299	516	X-RAY DIFFRACTION	74	96
2.876-2.899	0.306	498	X-RAY DIFFRACTION	74	94
2.899-2.922	0.302	501	X-RAY DIFFRACTION	74	95
2.922-2.946	0.282	513	X-RAY DIFFRACTION	74	94
2.946-2.971	0.297	511	X-RAY DIFFRACTION	74	95
2.971-2.997	0.273	528	X-RAY DIFFRACTION	74	95
2.997-3.024	0.261	533	X-RAY DIFFRACTION	74	96
3.024-3.052	0.263	516	X-RAY DIFFRACTION	74	96
3.052-3.08	0.265	514	X-RAY DIFFRACTION	74	94
3.08-3.11	0.261	501	X-RAY DIFFRACTION	74	97
3.11-3.141	0.243	524	X-RAY DIFFRACTION	74	96
3.141-3.174	0.245	519	X-RAY DIFFRACTION	74	95
3.174-3.207	0.243	520	X-RAY DIFFRACTION	74	95
3.207-3.243	0.254	532	X-RAY DIFFRACTION	74	95
3.243-3.279	0.251	502	X-RAY DIFFRACTION	74	96
3.279-3.318	0.247	512	X-RAY DIFFRACTION	74	95
3.318-3.358	0.254	515	X-RAY DIFFRACTION	74	96
3.358-3.401	0.243	517	X-RAY DIFFRACTION	74	95
3.401-3.446	0.23	536	X-RAY DIFFRACTION	74	96
3.446-3.493	0.215	526	X-RAY DIFFRACTION	74	95
3.493-3.543	0.206	510	X-RAY DIFFRACTION	74	96
3.543-3.595	0.195	510	X-RAY DIFFRACTION	74	95
3.595-3.651	0.212	533	X-RAY DIFFRACTION	74	95
3.651-3.711	0.187	524	X-RAY DIFFRACTION	74	95
3.711-3.775	0.215	523	X-RAY DIFFRACTION	74	95
3.775-3.844	0.18	515	X-RAY DIFFRACTION	74	94
3.844-3.918	0.191	507	X-RAY DIFFRACTION	74	94
3.918-3.997	0.185	534	X-RAY DIFFRACTION	74	96
3.997-4.084	0.181	525	X-RAY DIFFRACTION	74	93
4.084-4.179	0.176	518	X-RAY DIFFRACTION	74	95
4.179-4.284	0.171	519	X-RAY DIFFRACTION	74	95
4.284-4.399	0.161	542	X-RAY DIFFRACTION	74	95
4.399-4.528	0.153	508	X-RAY DIFFRACTION	74	95
4.528-4.674	0.156	514	X-RAY DIFFRACTION	74	94
4.674-4.841	0.153	551	X-RAY DIFFRACTION	74	95
4.841-5.034	0.159	511	X-RAY DIFFRACTION	74	94
5.034-5.263	0.162	533	X-RAY DIFFRACTION	74	95
5.263-5.539	0.184	529	X-RAY DIFFRACTION	74	94
5.539-5.885	0.184	531	X-RAY DIFFRACTION	74	96
5.885-6.337	0.21	544	X-RAY DIFFRACTION	74	95
6.337-6.97	0.227	561	X-RAY DIFFRACTION	74	95
6.97-7.968	0.194	546	X-RAY DIFFRACTION	74	96
7.968-10.002	0.194	563	X-RAY DIFFRACTION	74	95
10.002-35.42	0.236	584	X-RAY DIFFRACTION	74	92

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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