PDB-9i9f: Crystal structure of apoform human eIF4A1 C-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 9i9f

Title

Crystal structure of apoform human eIF4A1 C-terminal domain

Components

Eukaryotic initiation factor 4A-I

Keywords

TRANSLATION / INITIATION FACTOR / DEAD-BOX / HELICASE / ATPASE

Function / homology

Function and homology information

Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / RNA cap binding / eukaryotic translation initiation factor 4F complex / nuclear stress granule / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / cytoplasmic translational initiation / translation factor activity, RNA binding / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Ribosomal scanning and start codon recognition ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.731 Å

Authors

Turnbull, A.P. / Schmidt, T. / Bushell, M.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: The mechanism of selective eIF4A1-dependent translation
Authors: Schmidt, T. / Turnbull, A.P. / Bushell, M.

History

Deposition	Feb 6, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 18, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9i9f.cif.gz	260.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9i9f.ent.gz	162 KB	Display	PDB format
PDBx/mmJSON format	9i9f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i9/9i9f ftp://data.pdbj.org/pub/pdb/validation_reports/i9/9i9f	HTTPS FTP

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Related structure data

Related structure data	9i9gC C: citing same article (ref.)
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	#230 - Feb 2019 Initiation Factor eIF4E similarity (7) #60 - Dec 2004 Ubiquitin similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (3) #86 - Feb 2007 Exosomes similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (2)

Deposited unit

A: Eukaryotic initiation factor 4A-I

B: Eukaryotic initiation factor 4A-I

C: Eukaryotic initiation factor 4A-I

59.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Eukaryotic initiation factor 4A-I

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

2

B: Eukaryotic initiation factor 4A-I

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

3

C: Eukaryotic initiation factor 4A-I

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

Unit cell

Length a, b, c (Å)	84.970, 84.970, 66.420
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	240 - 403	4 - 167
2	1	1	ALA	ALA	240 - 403	4 - 167
3	2	2	LEU	LEU	240 - 400	4 - 164
4	2	2	LEU	LEU	240 - 400	4 - 164
5	3	3	LEU	LEU	240 - 400	4 - 164
6	3	3	LEU	LEU	240 - 400	4 - 164

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	Eukaryotic initiation factor 4A-I / eIF-4A-I / eIF4A-I / ATP-dependent RNA helicase eIF4A-1 Mass: 19858.535 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A1, DDX2A, EIF4A / Production host: Escherichia coli (E. coli) / References: UniProt: P60842, RNA helicase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H₂O
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: 2.43 Å³/Da / Density % sol: 49.4 % / Description: needle-like
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 18.5% (w/v) PEG 8000, 0.2M sodium acetate trihydrate, 0.1M MES, pH 6.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 14, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.73→42.49 Å / Num. obs: 14242 / % possible obs: 100 % / Redundancy: 6.4 % / CC_1/2: 0.994 / R_rim(I) all: 0.189 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.73→2.78 Å / Num. unique obs: 730 / CC_1/2: 0.507 / R_rim(I) all: 1.375

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.731→40.003 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.881 / SU B: 50.716 / SU ML: 0.445 / Cross valid method: FREE R-VALUE / ESU R Free: 0.431
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2937	674	4.738 %
R_work	0.2287	13550	-
all	0.232	-	-
obs	-	14224	99.86 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 62.688 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.372 Å²	0.686 Å²	-0 Å²
2-	-	1.372 Å²	-0 Å²
3-	-	-	-4.45 Å²

Refinement step

Cycle: LAST / Resolution: 2.731→40.003 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3732	0	0	43	3775

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	3782
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3542
X-RAY DIFFRACTION	r_angle_refined_deg	1.438	1.826	5132
X-RAY DIFFRACTION	r_angle_other_deg	0.523	1.763	8065
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.72	5	482
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.35	5	28
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.199	10	608
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.34	10	164
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	621
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4485
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	859
X-RAY DIFFRACTION	r_nbd_refined	0.241	0.2	812
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.213	0.2	3380
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	1925
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	2152
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	92
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.306	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.202	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.291	0.2	6
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.062	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.966	4.03	1940
X-RAY DIFFRACTION	r_mcbond_other	2.966	4.03	1940
X-RAY DIFFRACTION	r_mcangle_it	4.833	7.238	2418
X-RAY DIFFRACTION	r_mcangle_other	4.832	7.238	2419
X-RAY DIFFRACTION	r_scbond_it	2.91	4.08	1842
X-RAY DIFFRACTION	r_scbond_other	2.909	4.081	1843
X-RAY DIFFRACTION	r_scangle_it	4.783	7.457	2714
X-RAY DIFFRACTION	r_scangle_other	4.782	7.457	2715
X-RAY DIFFRACTION	r_lrange_it	7.015	37.822	4175
X-RAY DIFFRACTION	r_lrange_other	7.014	37.825	4173
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.137	0.05	4741
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.109	0.05	4389
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.09	0.05	4477

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.13658	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.13658	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.10889	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.10889	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09005	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09005	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.731-2.801	0.407	68	0.422	963	0.421	1032	0.915	0.909	99.9031	0.42
2.801-2.878	0.405	44	0.416	1010	0.416	1054	0.931	0.913	100	0.41
2.878-2.961	0.375	44	0.393	943	0.392	987	0.92	0.919	100	0.39
2.961-3.051	0.406	38	0.354	927	0.356	967	0.913	0.929	99.7932	0.342
3.051-3.151	0.381	58	0.287	884	0.293	945	0.924	0.953	99.6825	0.263
3.151-3.261	0.307	34	0.242	880	0.244	916	0.938	0.964	99.7817	0.221
3.261-3.383	0.321	40	0.221	807	0.225	852	0.929	0.97	99.4131	0.2
3.383-3.52	0.259	68	0.225	773	0.228	841	0.955	0.972	100	0.212
3.52-3.675	0.347	26	0.216	784	0.22	811	0.951	0.978	99.8767	0.205
3.675-3.853	0.193	14	0.197	770	0.197	784	0.977	0.981	100	0.189
3.853-4.059	0.223	24	0.207	692	0.208	716	0.974	0.982	100	0.2
4.059-4.303	0.279	45	0.191	651	0.196	696	0.959	0.983	100	0.181
4.303-4.596	0.247	32	0.179	622	0.183	654	0.96	0.981	100	0.17
4.596-4.959	0.248	43	0.163	568	0.169	611	0.966	0.983	100	0.163
4.959-5.424	0.289	16	0.202	544	0.205	560	0.936	0.977	100	0.193
5.424-6.05	0.209	16	0.238	504	0.237	520	0.974	0.971	100	0.223
6.05-6.96	0.363	26	0.227	409	0.234	435	0.938	0.975	100	0.221
6.96-8.46	0.241	16	0.232	370	0.233	386	0.975	0.973	100	0.231
8.46-11.705	0.343	15	0.173	279	0.18	295	0.972	0.981	99.661	0.188
11.705-40.003	0.306	7	0.24	170	0.243	178	0.903	0.961	99.4382	0.261

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	3.9426	-0.8219	-0.9426	4.4877	-1.3557	4.5382	-0.0671	0.0333	-0.0845	0.2202	0.0684	0.6673	0.0063	-0.4754	-0.0013	0.0144	-0.0056	0.0285	0.0538	-0.0106	0.1372	113.9665	-21.6119	-7.0429
2	5.8919	0.6698	0.4808	3.7439	-1.7372	3.1702	-0.1909	-0.1008	-0.4028	-0.1959	0.1085	0.3367	0.43	-0.2387	0.0824	0.1278	-0.0396	-0.0059	0.0453	0.0043	0.1905	117.2023	14.6685	-4.7902
3	7.0196	-0.5789	2.5148	0.9771	1.2759	5.3528	-0.0214	0.1698	-0.3036	0.0058	-0.0163	-0.3269	0.4378	0.5603	0.0377	0.3486	0.0281	0.1263	0.2761	0.1385	0.3974	97.0899	-6.2637	23.8073

Refinement TLS group

Selection: ALL

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