PDB-5h3t: m7G cap bound to GEMIN5-WD

ID or keywords:

Entry

Database: PDB / ID: 5h3t

Title

m7G cap bound to GEMIN5-WD

Components

Gem-associated protein 5

Keywords

RNA BINDING PROTEIN / GEMIN5 / SMN complex / WD40 domain

Function / homology

Function and homology information

SMN-Gemin2 complex / Gemini of coiled bodies / SMN complex / U4atac snRNA binding / snRNA binding / RNA 7-methylguanosine cap binding / U4 snRNA binding / SMN-Sm protein complex / spliceosomal snRNP assembly / U1 snRNA binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.571 Å

Authors

Bharath, S.R. / Tang, X. / Song, H.

Citation

Journal: Cell Res. / Year: 2016
Title: Structural basis for specific recognition of pre-snRNA by Gemin5
Authors: Tang, X. / Bharath, S.R. / Piao, S. / Tan, V.Q. / Bowler, M.W. / Song, H.

History

Deposition	Oct 27, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2	Nov 8, 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	5h3t.cif.gz	1018.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5h3t.ent.gz	852.2 KB	Display	PDB format
PDBx/mmJSON format	5h3t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5h3t_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	5h3t_full_validation.pdf.gz	1.8 MB	Display
Data in XML	5h3t_validation.xml.gz	91.2 KB	Display
Data in CIF	5h3t_validation.cif.gz	122.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h3/5h3t ftp://data.pdbj.org/pub/pdb/validation_reports/h3/5h3t	HTTPS FTP

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Related structure data

Related structure data	5h3sC 5h3uC 2ymuS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5tha-d 1kpi-2 5h3s-2 6xn0-d 5x93-d 5gxh-d 5h1m-d 3iiv-d 5gxi-d 5h3s-1 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

Related structure data

5h3sC

5h3uC

2ymuS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (1) #177 - Sep 2014 Apoptosomes similarity (2) #245 - May 2020 Spliceosomes similarity (2)

Deposited unit

A: Gem-associated protein 5

B: Gem-associated protein 5

C: Gem-associated protein 5

D: Gem-associated protein 5

hetero molecules

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

1

A: Gem-associated protein 5

hetero molecules

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

2

B: Gem-associated protein 5

hetero molecules

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

3

C: Gem-associated protein 5

hetero molecules

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

4

D: Gem-associated protein 5

hetero molecules

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

Unit cell

Length a, b, c (Å)	113.159, 91.007, 153.717
Angle α, β, γ (deg.)	90.00, 100.59, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Gem-associated protein 5 / Gemin5 Mass: 82295.203 Da / Num. of mol.: 4 / Fragment: UNP residues 1-740 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GEMIN5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEQ6
#2: Chemical	ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE Mass: 539.223 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₂₀N₅O₁₄P₃
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.36 Å³/Da / Density % sol: 47.96 %
Crystal grow	Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris propane, 0.2 M Na/K phosphate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.57→49.33 Å / Num. obs: 96204 / % possible obs: 97.9 % / Redundancy: 7 % / B_iso Wilson estimate: 55 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.07 / Net I/σ(I): 16.4
Reflection shell	Resolution: 2.57→2.61 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.734 / Mean I/σ(I) obs: 2 / CC_1/2: 0.722 / % possible all: 71.1

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2386: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2YMU

2ymu

Resolution: 2.571→49.326 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2281	4803	5 %
R_work	0.1709	-	-
obs	0.1738	96106	98.11 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.571→49.326 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20190	0	144	114	20448

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	21128
X-RAY DIFFRACTION	f_angle_d	1.109	28882
X-RAY DIFFRACTION	f_dihedral_angle_d	16.212	12182
X-RAY DIFFRACTION	f_chiral_restr	0.062	3206
X-RAY DIFFRACTION	f_plane_restr	0.007	3641

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 (%)
2.5705-2.5997	0.3684	123	0.3035	2075	X-RAY DIFFRACTION	67
2.5997-2.6303	0.3238	169	0.249	3057	X-RAY DIFFRACTION	100
2.6303-2.6624	0.316	160	0.238	3018	X-RAY DIFFRACTION	99
2.6624-2.6961	0.3001	154	0.2308	3127	X-RAY DIFFRACTION	100
2.6961-2.7315	0.2916	163	0.2191	3057	X-RAY DIFFRACTION	99
2.7315-2.769	0.2801	171	0.2303	3074	X-RAY DIFFRACTION	100
2.769-2.8085	0.3223	159	0.224	3051	X-RAY DIFFRACTION	100
2.8085-2.8504	0.2807	160	0.2171	3112	X-RAY DIFFRACTION	100
2.8504-2.895	0.2619	139	0.2047	3097	X-RAY DIFFRACTION	100
2.895-2.9424	0.2978	156	0.2052	3072	X-RAY DIFFRACTION	100
2.9424-2.9932	0.2837	169	0.2062	3054	X-RAY DIFFRACTION	100
2.9932-3.0476	0.2577	146	0.2045	3129	X-RAY DIFFRACTION	100
3.0476-3.1062	0.279	173	0.1912	3062	X-RAY DIFFRACTION	100
3.1062-3.1696	0.2436	179	0.1907	3047	X-RAY DIFFRACTION	100
3.1696-3.2385	0.281	172	0.1983	3106	X-RAY DIFFRACTION	100
3.2385-3.3138	0.2579	169	0.1944	3049	X-RAY DIFFRACTION	100
3.3138-3.3967	0.2519	163	0.1853	3092	X-RAY DIFFRACTION	100
3.3967-3.4885	0.2241	171	0.1754	3060	X-RAY DIFFRACTION	99
3.4885-3.5911	0.2391	174	0.1633	2986	X-RAY DIFFRACTION	98
3.5911-3.707	0.2169	166	0.1588	2971	X-RAY DIFFRACTION	96
3.707-3.8394	0.2109	146	0.1599	3067	X-RAY DIFFRACTION	97
3.8394-3.9931	0.2207	160	0.1593	3081	X-RAY DIFFRACTION	100
3.9931-4.1747	0.2098	158	0.1521	3111	X-RAY DIFFRACTION	100
4.1747-4.3947	0.203	138	0.1415	3104	X-RAY DIFFRACTION	99
4.3947-4.6698	0.1679	159	0.1241	3101	X-RAY DIFFRACTION	99
4.6698-5.0301	0.1912	180	0.1239	3081	X-RAY DIFFRACTION	99
5.0301-5.5356	0.2083	143	0.1488	3119	X-RAY DIFFRACTION	99
5.5356-6.3352	0.2022	158	0.1777	3124	X-RAY DIFFRACTION	99
6.3352-7.9763	0.2214	161	0.1849	3008	X-RAY DIFFRACTION	95
7.9763-49.3351	0.2125	164	0.1762	3211	X-RAY DIFFRACTION	99

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	2.1829	-0.0528	0.5881	3.0156	0.6964	2.6767	-0.0351	0.3036	0.0007	-0.2898	-0.0258	0.2692	-0.0981	-0.0091	0.0507	0.6715	0.0013	0.0204	0.6389	0.0569	0.6958	11.3067	-20.7236	150.8661
2	1.3355	-0.0167	0.9877	1.0442	-0.4456	2.9446	-0.3595	-0.0053	0.3782	-0.0057	0.0683	-0.2576	-0.4013	0.0614	0.2842	0.5819	0.0177	-0.1754	0.4471	0.0093	0.8474	25.9777	-4.525	188.1481
3	2.3936	0.1006	0.0223	2.2891	-0.8095	2.1721	0.0038	-0.1096	0.0003	0.0406	-0.0192	-0.0565	0.0309	0.1861	0.0163	0.3946	0.0146	-0.0162	0.2975	-0.0351	0.3298	31.2456	24.4369	230.582
4	1.4909	0.4987	0.3813	1.4209	0.2039	3.2092	-0.0409	0.2506	-0.0133	-0.1351	0.1776	0.3067	-0.0029	-0.1953	-0.1292	0.3403	0.0122	-0.0859	0.3421	0.0367	0.5166	15.8522	40.9397	193.4768
5	2.9411	0.4915	0.6843	2.8804	0.8146	2.3882	0.0584	-0.0024	0.1997	-0.0033	-0.3091	0.7522	-0.1537	-0.4248	0.2386	0.2946	0.0307	0.0434	0.3287	-0.1058	0.4321	47.137	-22.9491	222.9445
6	3.4976	-0.6916	-0.1149	1.9085	0.0982	2.595	-0.1691	-0.5973	0.8051	0.5898	-0.2854	0.9081	-0.3235	-0.3877	0.0646	0.5055	0.0091	0.1705	0.4619	-0.2815	0.7126	50.5034	-8.4478	236.3508
7	3.3738	0.5688	0.5882	3.7349	0.7553	2.5095	0.1654	-0.5162	0.0277	0.7228	-0.2546	0.1514	0.0876	0.0195	0.0288	0.4444	-0.0857	0.059	0.3916	-0.0249	0.2919	63.57	-18.9238	237.1847
8	0.8608	-0.2786	-0.5804	1.4479	1.2557	3.745	-0.0365	-0.1297	-0.0259	0.2128	0.1172	-0.0295	0.1612	0.4232	0.0124	0.2849	0.0091	-0.0219	0.2957	-0.0276	0.2819	69.2286	-33.4955	216.5332
9	2.0419	-0.0536	-0.1699	1.3297	-0.4379	2.6501	0.0435	0.3528	-0.0989	-0.2937	-0.1591	-0.1294	0.2581	0.3519	0.0855	0.355	0.0985	-0.012	0.3756	0.0095	0.2615	70.0073	-40.1565	190.6172
10	1.9026	0.0519	0.2254	2.3196	-0.8241	2.3462	-0.1384	0.1976	0.1106	0.0067	0.0103	-0.4189	-0.1978	0.3356	0.1252	0.3515	-0.0178	0.016	0.5187	-0.0748	0.3371	-6.5819	26.8288	152.3051
11	4.5015	-0.2453	-0.4446	3.5144	0.6524	3.7179	-0.1157	0.5698	-0.0447	-0.2675	0.053	0.1076	0.2146	-0.1907	0.1203	0.3647	-0.0441	-0.0008	0.6873	-0.0737	0.2692	-20.8009	21.2351	143.2263
12	1.265	0.4729	-1.367	1.1297	-1.4556	3.1545	-0.1446	0.4008	-0.0875	-0.0892	0.2688	-0.0314	0.4484	-0.5827	-0.1525	0.4668	-0.0071	0.0017	0.6001	-0.0756	0.3355	-28.4083	9.9638	164.4026
13	2.398	-0.2517	-0.1621	2.2835	0.7052	1.7023	-0.1713	-0.2508	-0.358	0.8188	0.0452	0.1589	0.3417	-0.0911	0.1361	0.7533	0.0696	0.0678	0.4784	-0.0308	0.3433	-28.8117	4.5468	187.5435

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 376 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 377 through 722 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 3 through 375 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 376 through 722 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 3 through 171 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 172 through 246 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 247 through 349 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 350 through 428 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 429 through 722 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 3 through 302 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 303 through 356 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 357 through 440 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 441 through 722 )

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