PDB-5w5i: Human IFIT1 dimer with PPP-AAAA

ID or keywords:

Entry

Database: PDB / ID: 5w5i

Title

Human IFIT1 dimer with PPP-AAAA

Components

Interferon-induced protein with tetratricopeptide repeats 1
RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

Keywords

RNA binding protein/RNA / triphosphate RNA / tetratricopeptide repeat / RNA binding protein / RNA binding protein-RNA complex

Function / homology

Function and homology information

RNA sequestering activity / intracellular transport of viral protein in host cell / cellular response to type I interferon / negative regulation of viral translation / negative regulation of viral genome replication / cellular response to exogenous dsRNA / positive regulation of viral genome replication / enzyme inhibitor activity / antiviral innate immune response / ISG15 antiviral mechanism ...
Similarity search - Function

Biological species

Homo sapiens (human)
unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Abbas, Y.M. / Martinez-Montero, S. / Damha, M.J. / Nagar, B.

Citation

Journal: To Be Published
Title: Structural insights into IFIT1 dimerization and conformational changes associated with mRNA binding
Authors: Abbas, Y.M. / Martinez-Montero, S. / Cencic, R. / Pelletier, J. / Damha, M.J. / Pawelek, P.D. / Nagar, B.

History

Deposition	Jun 15, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 28, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5w5i.cif.gz	527.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5w5i.ent.gz	445.8 KB	Display	PDB format
PDBx/mmJSON format	5w5i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w5/5w5i ftp://data.pdbj.org/pub/pdb/validation_reports/w5/5w5i	HTTPS FTP

-
Related structure data

Related structure data	5w5hC C: citing same article (ref.)
Similar structure data	5w5h-d 3fyi-d 3of6-d 3oma-d 1nu9-d 3om3-d 6ci0-d 6pa3-1 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	#230 - Feb 2019 Initiation Factor eIF4E similarity (7) #141 - Sep 2011 O-GlcNAc Transferase similarity (6) #166 - Oct 2013 Proteasome similarity (3)

Deposited unit

A: Interferon-induced protein with tetratricopeptide repeats 1

B: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

C: Interferon-induced protein with tetratricopeptide repeats 1

D: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, IFIT1 migrates as a dimer on gel filtration, light scattering, Calculated MW corresponds to IFIT1 homodimer, equilibrium centrifugation, Analytical ultracentrifugation shows ...Evidence: gel filtration, IFIT1 migrates as a dimer on gel filtration, light scattering, Calculated MW corresponds to IFIT1 homodimer, equilibrium centrifugation, Analytical ultracentrifugation shows reversible monomer-dimer interaction

2

A: Interferon-induced protein with tetratricopeptide repeats 1

B: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

C: Interferon-induced protein with tetratricopeptide repeats 1

D: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

A: Interferon-induced protein with tetratricopeptide repeats 1

B: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

C: Interferon-induced protein with tetratricopeptide repeats 1

D: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

A: Interferon-induced protein with tetratricopeptide repeats 1

B: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

C: Interferon-induced protein with tetratricopeptide repeats 1

D: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

A: Interferon-induced protein with tetratricopeptide repeats 1

B: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

C: Interferon-induced protein with tetratricopeptide repeats 1

D: RNA (5'-D(*(ATP))-R(P*AP*AP*A)-3')

defined by software
456 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	184.789, 184.789, 88.864
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

#1: Protein	Interferon-induced protein with tetratricopeptide repeats 1 / IFIT-1 / Interferon-induced 56 kDa protein / P56 Mass: 55532.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFIT1, G10P1, IFI56, IFNAI1, ISG56 / Production host: Escherichia coli (E. coli) / References: UniProt: P09914
#2: RNA chain	RNA (5'-D((ATP))-R(PAPAPA)-3') Mass: 1431.826 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.46 Å³/Da / Density % sol: 64.5 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 27 - 32 % PEG 200, 0.1 M Tris pH 8.1, 200 mM CaCl2

-
Data collection

Diffraction	Mean temperature: 94 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.65→50 Å / Num. obs: 43686 / % possible obs: 99.8 % / Redundancy: 6.4 % / R_pim(I) all: 0.025 / R_sym value: 0.058 / Net I/σ(I): 29.6
Reflection shell	Resolution: 2.65→2.7 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2 / CC_1/2: 0.85 / R_pim(I) all: 0.383 / R_sym value: 0.899 / % possible all: 99.2

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10_2142: ???)	refinement
HKL-2000		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→44.397 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 2.65 / Phase error: 26.32

	R_factor	Num. reflection	% reflection
R_free	0.2416	1922	4.97 %
R_work	0.2189	-	-
obs	0.22	38680	88.59 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.65→44.397 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7072	194	0	35	7301

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7416
X-RAY DIFFRACTION	f_angle_d	0.477	10002
X-RAY DIFFRACTION	f_dihedral_angle_d	12.903	4520
X-RAY DIFFRACTION	f_chiral_restr	0.033	1083
X-RAY DIFFRACTION	f_plane_restr	0.002	1243

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 (%)
2.6499-2.7162	0.2748	52	0.29	1111	X-RAY DIFFRACTION	37
2.7162-2.7896	0.2909	68	0.291	1416	X-RAY DIFFRACTION	48
2.7896-2.8717	0.3169	99	0.3045	1956	X-RAY DIFFRACTION	66
2.8717-2.9643	0.328	140	0.2977	2655	X-RAY DIFFRACTION	91
2.9643-3.0702	0.3198	156	0.2895	2919	X-RAY DIFFRACTION	99
3.0702-3.1931	0.3227	157	0.2896	2923	X-RAY DIFFRACTION	100
3.1931-3.3384	0.303	157	0.2682	2943	X-RAY DIFFRACTION	100
3.3384-3.5144	0.2927	153	0.2495	2962	X-RAY DIFFRACTION	100
3.5144-3.7344	0.2598	149	0.2185	2969	X-RAY DIFFRACTION	100
3.7344-4.0226	0.1951	161	0.1905	2938	X-RAY DIFFRACTION	100
4.0226-4.4271	0.1763	156	0.1734	2962	X-RAY DIFFRACTION	100
4.4271-5.0669	0.1848	156	0.1672	2964	X-RAY DIFFRACTION	100
5.0669-6.3808	0.2261	155	0.2022	2998	X-RAY DIFFRACTION	100
6.3808-44.4029	0.2158	163	0.1847	3042	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	1.3167	1.1368	-1.624	1.7425	-0.5701	3.8837	0.1245	0.0042	0.5405	-0.1062	0.174	0.0874	-0.325	-0.0636	-0.2415	0.303	-0.0226	-0.0563	0.6824	-0.1825	0.4568	12.1732	247.9767	-4.8103
2	0.2411	-0.134	0.0672	0.3566	0.2445	1.4611	0.3521	-1.2002	0.5983	-0.1226	-0.4332	-0.4378	-0.4531	1.2176	0.0103	0.2639	-0.364	-0.1191	1.145	-0.2953	0.4634	17.5318	247.2537	3.4336
3	1.9553	0.4999	0.2657	0.8784	-0.5506	1.4517	-0.1694	0.075	-0.7149	-0.2301	-0.1576	-0.2099	0.363	0.4124	0.1349	-0.4946	0.3124	-0.0777	1.0549	0.0178	0.5058	8.7202	228.4969	3.4434
4	3.6097	-2.5114	0.1436	2.6541	-0.7191	0.4353	-0.2517	-0.3954	-0.8641	0.2378	0.0273	-0.2105	0.5658	0.7413	0.1124	0.591	0.2723	0.0156	0.9946	0.1905	0.7684	5.9276	220.3097	15.6729
5	1.5057	0.9876	1.6015	3.1829	0.5817	2.2077	0.0663	-0.6477	-0.3993	0.4359	0.2243	-0.4357	0.1696	0.4628	-0.2973	0.4803	0.0263	-0.0614	1.6613	0.0395	0.495	3.5145	231.5649	27.4321
6	1.706	-0.1505	0.5022	0.7441	0.3403	1.1741	0.0864	-1.0383	-0.3256	0.7117	0.048	0.1611	-0.148	0.2462	-0.0827	-0.0786	-0.287	-0.6112	1.3009	-0.4576	-0.2095	-10.7408	238.5332	25.8141
7	2.0399	-0.1382	0.3613	0.9412	-0.9544	1.0574	0.079	-0.4037	-0.0717	0.1129	0.0296	0.2038	-0.1564	0.4284	-0.1004	0.2102	-0.0139	0.0235	0.4652	-0.1622	0.2966	-22.259	236.9301	12.1229
8	5.636	1.4934	2.8705	2.0067	-0.8518	3.0821	0.0385	-0.3629	0.0206	0.6154	-0.1078	0.6505	0.24	-0.5436	0.0222	0.3168	-0.0526	0.1301	0.4789	-0.1013	0.5998	-30.9461	224.9253	10.8043
9	2.8729	0.5875	1.1862	0.9402	0.3736	2.83	0.2538	-0.4566	-0.4918	-0.0541	-0.2469	0.7053	0.3607	-0.4418	-0.1192	0.3268	-0.0732	-0.0744	0.4885	-0.2558	0.9342	-37.8327	222.2408	-0.5561
10	2.1896	-0.9525	0.5132	2.1551	-0.2309	2.7472	-0.0646	-0.3414	-0.6582	0.1447	0.0676	-0.0015	0.1712	0.1108	0.0181	0.2937	-0.0345	0.0257	0.9837	0.028	0.3324	-6.9447	231.0031	16.4098
11	0.814	-0.436	0.2931	1.7868	-0.7534	1.4691	-0.2033	-0.0023	-0.2913	-0.3978	0.3161	1.0671	0.7303	-0.7833	-0.0057	0.599	-0.349	-0.1452	0.3371	0.0439	0.6431	-67.1467	172.148	-13.3995
12	0.3565	0.248	-0.4638	1.3138	-0.9715	1.2804	-0.2074	-0.1316	-0.1418	-0.0698	-0.0424	-0.2749	0.4468	0.1	0.1841	0.4944	0.0254	0.0243	0.1349	-0.0301	0.3052	-49.6177	175.0035	-13.8467
13	2.6552	-2.2449	-0.5997	3.3494	-0.0527	0.3463	0.022	0.3699	-0.194	-0.6613	-0.08	-0.7849	0.4273	0.3554	-0.1256	0.8104	0.1434	0.1752	0.4076	-0.0533	0.4648	-39.8314	180.7251	-30.5117
14	4.4091	-0.5167	0.3877	1.9599	0.9004	2.213	0.0767	0.6054	0.0259	-1.2585	-0.137	0.0748	0.4801	-0.0881	0.064	0.9655	-0.0434	-0.1282	0.3572	-0.0515	0.2467	-55.1627	191.8348	-41.2448
15	1.0439	-0.0323	-0.7596	2.7907	-0.1048	0.6392	0.0598	0.2214	0.1029	-0.2486	-0.0396	0.0817	0.2286	-0.1391	-0.0178	0.3178	-0.024	-0.1028	0.1639	0.0143	0.2704	-54.5611	207.9751	-25.9558
16	0.8679	1.0792	0.7166	2.0003	1.6113	2.6743	-0.2652	0.1319	0.5925	-0.3678	0.1486	-0.2977	-0.5543	0.5242	0.0142	0.3527	-0.1276	-0.1449	0.3269	-0.0356	0.7842	-38.0655	222.0821	-17.5418
17	2.4097	-1.6713	-0.0508	1.8288	1.6184	3.7397	0.136	0.1189	0.1989	-0.314	-0.1002	-0.3772	-0.1146	0.3366	-0.0513	0.4992	-0.073	0.0186	0.2105	0.0777	0.2933	-49.5689	194.2588	-29.5267
18	4.5999	0.1854	-0.6952	1.8599	-2.0477	2.3058	-0.2272	0.42	-0.3782	-0.2827	-0.0953	0.0434	0.3753	-0.198	0.2431	0.4379	-0.0591	-0.0322	0.3274	-0.0664	0.2334	-54.9015	185.887	-25.06
19	1.7021	0.0291	-1.5601	5.3658	-0.6526	1.5016	-0.0833	-0.1574	0.1139	0.4219	-0.0423	-0.6027	-0.2115	0.3802	0.1133	0.2083	-0.0632	-0.0608	0.9728	-0.1045	0.375	1.9113	236.4256	12.8946

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 153 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 154 through 192 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 193 through 245 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 246 through 284 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 285 through 352 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 353 through 412 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 413 through 432 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 433 through 469 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 4 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 9 through 127 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 128 through 192 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 193 through 245 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 246 through 335 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 336 through 412 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 413 through 469 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 4 )
18	X-RAY DIFFRACTION	18	chain 'D' and resid ' 1 '
19	X-RAY DIFFRACTION	19	chain 'B' and resid ' 1 '

-
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