PDB-9gek: Structure of the FAST1-FAST2-RAP module from human FASTKD4 by car...

ID or keywords:

Entry

Database: PDB / ID: 9gek

Title

Structure of the FAST1-FAST2-RAP module from human FASTKD4 by carrier-driven crystallisation with maltose binding protein from E. coli.

Components

Maltose/maltodextrin-binding periplasmic protein,FAST kinase domain-containing protein 4,FAST kinase domain-containing protein 4

Keywords

RNA BINDING PROTEIN / mitochondrial RNA splicing / RNA stability / RNA binding / mitochondrial disease

Function / homology

Function and homology information

FASTK family proteins regulate processing and stability of mitochondrial RNAs / regulation of mitochondrial mRNA stability / mitochondrial mRNA processing / mRNA metabolic process / ribonucleoprotein granule / mitochondrial RNA processing / regulation of cell cycle / mitochondrial matrix / positive regulation of cell population proliferation / mitochondrion / RNA binding
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Hothorn, M. / Lau, K. / Yang, X.

Funding support

1items

Citation

Journal: Nucleic Acids Res. / Year: 2025
Title: The Vsr-like protein FASTKD4 regulates the stability and polyadenylation of the MT-ND3 mRNA.
Authors: Yang, X. / Stentenbach, M. / Hughes, L.A. / Siira, S.J. / Lau, K. / Hothorn, M. / Martinou, J.C. / Rackham, O. / Filipovska, A.

History

Deposition	Aug 7, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release
Revision 1.1	Mar 19, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9gek.cif.gz	406.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9gek_validation.pdf.gz	656.6 KB	Display	wwPDB validaton report
Full document	9gek_full_validation.pdf.gz	659.4 KB	Display
Data in XML	9gek_validation.xml.gz	31.5 KB	Display
Data in CIF	9gek_validation.cif.gz	42.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ge/9gek ftp://data.pdbj.org/pub/pdb/validation_reports/ge/9gek	HTTPS FTP

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Related structure data

Similar structure data	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	#186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (2) #254 - Feb 2021 Cellulose Synthase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Maltose/maltodextrin-binding periplasmic protein,FAST kinase domain-containing protein 4,FAST kinase domain-containing protein 4

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	80.058, 88.315, 114.809
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-701- P33

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Protein , 1 types, 1 molecules A

#1: Protein	Maltose/maltodextrin-binding periplasmic protein,FAST kinase domain-containing protein 4,FAST kinase domain-containing protein 4 / Cell cycle progression restoration protein 2 / Cell cycle progression protein 2 / Protein TBRG4 / ...Cell cycle progression restoration protein 2 / Cell cycle progression protein 2 / Protein TBRG4 / Transforming growth factor beta regulator 4 Mass: 80110.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: malE, Z5632, ECs5017, TBRG4, CPR2, FASTKD4, KIAA0948 / Production host: Escherichia coli (E. coli) / References: UniProt: Q969Z0

#1: Protein

Maltose/maltodextrin-binding periplasmic protein,FAST kinase domain-containing protein 4,FAST kinase domain-containing protein 4 / Cell cycle progression restoration protein 2 / Cell cycle progression protein 2 / Protein TBRG4 / ...

Mass: 80110.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: malE, Z5632, ECs5017, TBRG4, CPR2, FASTKD4, KIAA0948 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q969Z0

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Sugars , 2 types, 4 molecules

#4: Sugar

ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂O₆

#5: Sugar

ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂O₆

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Non-polymers , 3 types, 263 molecules

#2: Chemical	ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₃₀O₈ / Comment: precipitant*YM
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	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: 2.55 Å³/Da / Density % sol: 51.83 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 15% (v/v) PEG 8.000, 60 mM potassium phosphate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000027 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 2, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.000027 Å / Relative weight: 1
Reflection	Resolution: 2.15→48.13 Å / Num. obs: 85063 / % possible obs: 0.993 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / B_iso Wilson estimate: 28.9 Å² / CC_1/2: 1 / R_rim(I) all: 0.19 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.15→2.28 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 14074 / CC_1/2: 0.36 / R_rim(I) all: 2.15 / % possible all: 0.982

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.1_5286: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→48.13 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2407	4240	4.98 %
R_work	0.2025	-	-
obs	0.2044	85062	99.26 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.15→48.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5343	0	73	261	5677

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5566
X-RAY DIFFRACTION	f_angle_d	0.552	7562
X-RAY DIFFRACTION	f_dihedral_angle_d	13.774	2094
X-RAY DIFFRACTION	f_chiral_restr	0.037	840
X-RAY DIFFRACTION	f_plane_restr	0.004	968

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 (%)
2.15-2.17	0.4229	126	0.3493	2493	X-RAY DIFFRACTION	92
2.17-2.2	0.3633	142	0.3424	2661	X-RAY DIFFRACTION	98
2.2-2.23	0.3451	142	0.3259	2703	X-RAY DIFFRACTION	99
2.23-2.25	0.36	144	0.3307	2668	X-RAY DIFFRACTION	99
2.25-2.28	0.3454	139	0.3152	2675	X-RAY DIFFRACTION	99
2.28-2.31	0.3498	142	0.3055	2675	X-RAY DIFFRACTION	99
2.31-2.35	0.3321	141	0.3068	2724	X-RAY DIFFRACTION	99
2.35-2.38	0.3397	139	0.2884	2681	X-RAY DIFFRACTION	99
2.38-2.42	0.2869	143	0.268	2692	X-RAY DIFFRACTION	99
2.42-2.46	0.3024	143	0.2615	2697	X-RAY DIFFRACTION	99
2.46-2.5	0.2875	143	0.2522	2682	X-RAY DIFFRACTION	99
2.5-2.55	0.2597	141	0.2413	2682	X-RAY DIFFRACTION	99
2.55-2.6	0.2722	141	0.2443	2736	X-RAY DIFFRACTION	99
2.6-2.65	0.3086	139	0.2348	2673	X-RAY DIFFRACTION	100
2.65-2.71	0.2846	143	0.2338	2686	X-RAY DIFFRACTION	100
2.71-2.77	0.249	146	0.2353	2745	X-RAY DIFFRACTION	100
2.77-2.84	0.2666	139	0.2382	2701	X-RAY DIFFRACTION	100
2.84-2.92	0.3052	142	0.2197	2707	X-RAY DIFFRACTION	100
2.92-3	0.2539	141	0.2164	2701	X-RAY DIFFRACTION	100
3-3.1	0.2472	145	0.2058	2690	X-RAY DIFFRACTION	100
3.1-3.21	0.2906	140	0.2021	2728	X-RAY DIFFRACTION	100
3.21-3.34	0.2195	143	0.192	2711	X-RAY DIFFRACTION	100
3.34-3.49	0.2485	144	0.1912	2712	X-RAY DIFFRACTION	100
3.49-3.67	0.2056	142	0.1725	2713	X-RAY DIFFRACTION	100
3.67-3.9	0.2066	143	0.1609	2702	X-RAY DIFFRACTION	100
3.9-4.2	0.1811	139	0.1479	2724	X-RAY DIFFRACTION	100
4.2-4.63	0.1941	145	0.1393	2704	X-RAY DIFFRACTION	100
4.63-5.3	0.1723	140	0.1445	2710	X-RAY DIFFRACTION	100
5.3-6.67	0.2126	143	0.1835	2734	X-RAY DIFFRACTION	100
6.67-48.13	0.193	140	0.1745	2712	X-RAY DIFFRACTION	100

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	3.9702	1.0285	-0.6346	1.4572	0.2553	3.8113	-0.2235	0.9224	-0.0878	-0.3961	0.1983	-0.1272	0.3719	-0.3173	0.0236	0.5044	-0.062	0.1013	0.4709	-0.0128	0.3188	4.7736	19.3403	-1.6581
2	1.6129	-0.263	0.06	1.5417	0.0227	0.8069	0.0336	-0.0567	-0.0684	0.0427	0.0384	-0.0305	-0.0198	0.0352	-0.0725	0.22	0.0021	0.0287	0.2249	-0.062	0.2569	6.378	4.3494	24.5062
3	1.2852	0.085	0.2304	1.3999	-0.5444	2.683	0.0101	0.242	0.1818	-0.2134	0.0542	0.0035	-0.1221	-0.1001	-0.0586	0.3129	-0.0055	0.0722	0.2793	-0.001	0.3504	3.2743	20.0782	12.3551
4	1.6371	-0.8153	-1.2131	0.3919	0.591	0.8874	0.0279	0.009	0.2679	0.0014	0.0012	-0.0572	0.0175	0.063	-0.0171	0.3181	-0.012	0.002	0.2876	-0.0014	0.3578	27.4166	-4.2738	10.8177
5	2.3638	-0.7607	0.5027	4.0354	-2.4039	3.231	-0.0022	0.0642	-0.0809	-0.0042	-0.265	-0.4606	0.0487	0.4407	0.2688	0.2729	-0.0054	0.0387	0.2603	0.055	0.3583	47.8355	-20.8143	10.7822
6	3.5552	0.1777	-1.5066	2.9425	-1.005	2.488	-0.0619	-0.2952	-0.2871	0.0357	-0.0996	-0.0323	0.2144	0.1916	0.1341	0.2504	-0.0214	-0.0044	0.2532	0.0158	0.2702	30.2542	-32.0405	28.2804

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -58 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 185 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 186 through 273 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 274 through 341 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 342 through 490 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 491 through 633 )

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Protein , 1 types, 1 molecules A

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