PDB-5w5h: Human IFIT1 dimer with m7Gppp-AAAA

ID or keywords:

Entry

Database: PDB / ID: 5w5h

Title

Human IFIT1 dimer with m7Gppp-AAAA

Components

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

Keywords

RNA binding protein/RNA / mRNA cap / N7-Methylguanosine-triphosphate RNA /

tetratricopeptide repeat /

RNA binding protein / RNA binding protein-RNA complex

Function / homology

Function and homology information

intracellular transport of viral protein in host cell / cellular response to type I interferon /

host cell / negative regulation of helicase activity / negative regulation of viral genome replication / cellular response to exogenous dsRNA / antiviral innate immune response / positive regulation of viral genome replication / negative regulation of protein binding / response to virus ...
Similarity search - Function

Biological species

Homo sapiens (human)
unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.79 Å

Authors

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

Funding support

Canada, 1items

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	Jul 19, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	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

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PDBx/mmCIF format	5w5h.cif.gz	551 KB	Display	PDBx/mmCIF format
PDB format	pdb5w5h.ent.gz	469 KB	Display	PDB format
PDBx/mmJSON format	5w5h.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w5/5w5h ftp://data.pdbj.org/pub/pdb/validation_reports/w5/5w5h	HTTPS FTP

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Related structure data

Related structure data	5w5iC C: citing same article (ref.)
Similar structure data	5w5i-d 1pn2-d 3of6-d 2o39-d 11891 1nu9-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

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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) #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(*(GTA))-R(P*AP*AP*A)-3')

C: Interferon-induced protein with tetratricopeptide repeats 1

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

C: Interferon-induced protein with tetratricopeptide repeats 1

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

A: Interferon-induced protein with tetratricopeptide repeats 1

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

C: Interferon-induced protein with tetratricopeptide repeats 1

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

A: Interferon-induced protein with tetratricopeptide repeats 1

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

C: Interferon-induced protein with tetratricopeptide repeats 1

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

A: Interferon-induced protein with tetratricopeptide repeats 1

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

C: Interferon-induced protein with tetratricopeptide repeats 1

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

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

Unit cell

Length a, b, c (Å)	184.355, 184.355, 88.762
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((GTA))-R(PAPAPA)-3') Mass: 1712.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 23 / 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: 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

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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: Jan 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.79→50 Å / Num. obs: 37109 / % possible obs: 100 % / Redundancy: 5.1 % / R_pim(I) all: 0.028 / Net I/σ(I): 26.1
Reflection shell	Resolution: 2.79→2.84 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.72 / Num. measured obs: 1854 / CC_1/2: 0.79 / R_pim(I) all: 0.512 / % possible all: 99.9

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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: 2.79→42.01 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 2.79 / Phase error: 25.72

	R_factor	Num. reflection	% reflection
R_free	0.241	1637	5.05 %
R_work	0.219	-	-
obs	0.22	32445	87.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.79→42.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7327	234	0	23	7584

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7838
X-RAY DIFFRACTION	f_angle_d	0.702	10613
X-RAY DIFFRACTION	f_dihedral_angle_d	13.128	4760
X-RAY DIFFRACTION	f_chiral_restr	0.035	1140
X-RAY DIFFRACTION	f_plane_restr	0.002	1300

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 (%)
2.7926-2.8748	0.3445	58	0.3049	1074	X-RAY DIFFRACTION	37
2.8748-2.9675	0.3362	88	0.3057	1452	X-RAY DIFFRACTION	50
2.9675-3.0736	0.2877	100	0.281	2087	X-RAY DIFFRACTION	71
3.0736-3.1966	0.2873	154	0.2891	2652	X-RAY DIFFRACTION	92
3.1966-3.342	0.2906	152	0.2623	2903	X-RAY DIFFRACTION	99
3.342-3.5181	0.2516	154	0.2487	2922	X-RAY DIFFRACTION	100
3.5181-3.7384	0.2458	150	0.232	2929	X-RAY DIFFRACTION	100
3.7384-4.0269	0.2258	158	0.2038	2926	X-RAY DIFFRACTION	100
4.0269-4.4317	0.2091	155	0.186	2958	X-RAY DIFFRACTION	100
4.4317-5.072	0.2178	154	0.1802	2926	X-RAY DIFFRACTION	100
5.072-6.3866	0.2296	155	0.2122	2972	X-RAY DIFFRACTION	100
6.3866-42.0177	0.2201	159	0.1924	3007	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	1.5541	-0.2502	-0.7477	1.0791	-0.0569	2.1413	0.3315	-0.7061	0.7251	-0.1807	-0.3434	-0.3394	-0.7083	1.061	0.0034	0.0706	-0.1777	-0.0442	0.7386	-0.119	0.5665	11.9339	244.7993	1.1987
2	2.3064	-1.7566	-0.4128	2.2302	-0.5828	0.8707	-0.1581	-0.8386	-0.4703	0.3242	0.025	-0.2708	0.4626	0.6282	0.0156	0.3604	0.265	-0.106	0.9947	0.1403	0.395	3.908	226.9158	19.8539
3	1.5154	-0.2837	0.297	2.3918	0.5252	0.4239	-0.0596	-1.1037	0.1994	0.6556	0.1804	0.193	-0.1377	0.3167	0.0106	0.3758	-0.001	-0.0021	0.8038	-0.2061	0.2899	-13.76	242.1613	25.0422
4	1.3005	0.9783	1.0835	1.7783	0.5988	1.8124	0.0478	-0.2335	-0.6935	-0.0541	-0.0704	0.805	0.1996	-0.2349	0.0049	0.196	-0.0174	-0.0373	0.365	-0.1345	0.6122	-32.9359	227.0037	7.5203
5	0.824	0.0339	-0.1157	0.9966	-0.6551	1.7503	-0.7091	-0.2586	-0.581	-0.9847	0.4232	0.7858	1.3629	-0.4627	0.2021	1.1099	-0.3927	-0.2348	0.0952	-0.2243	0.4825	-61.6986	166.9407	-15.3271
6	1.6374	0.8245	-0.5381	2.9376	0.244	2.1062	-0.0904	-0.2401	-0.3559	0.2297	-0.194	-0.5893	0.3804	0.3546	0.1247	0.9024	0.2094	0.0337	-0.1364	-0.0861	0.4565	-43.5604	175.7222	-15.6287
7	2.1654	-1.5384	-0.0536	2.843	-0.6528	0.2616	-0.062	0.4762	-0.2523	-0.1739	-0.0726	-0.8382	0.3686	0.4226	0.0222	1.084	0.2595	0.3004	0.5049	-0.0621	0.7254	-35.0621	178.2487	-27.8205
8	2.5264	-0.0459	-0.2949	0.6317	1.1805	2.4973	0.1414	0.5693	-0.2844	-0.4972	-0.0256	-0.3449	0.3952	0.1485	-0.1597	1.6784	0.028	0.0714	0.5071	-0.1154	0.3502	-46.3104	179.9542	-39.7221
9	1.8061	0.0131	0.2854	2.4115	0.3504	0.1588	0.1358	0.5171	0.1031	-1.1743	0.0008	-0.0853	0.5882	-0.1465	-0.0726	0.8804	-0.0754	-0.1808	0.3134	0.0234	0.2739	-52.109	201.134	-31.783
10	1.2195	1.2212	0.3542	3.9538	1.5119	3.4349	-0.2126	0.0061	0.8933	-0.394	0.0291	-0.3842	-0.596	0.2796	0.155	0.4661	-0.0784	-0.2558	0.3398	0.0229	0.8139	-38.1919	219.6299	-16.0051
11	1.6527	-2.8375	1.9021	5.584	-1.4566	6.7824	0.0199	-0.1624	-0.2462	0.1664	0.0895	0.1544	0.2252	-0.1808	-0.0785	0.2235	0.0171	0.0032	0.494	-0.0941	0.2923	-9.5843	233.851	16.8757
12	4.2542	-0.7577	0.5135	0.864	1.6406	4.178	-0.0162	0.0476	0.2812	-0.1319	0.089	-0.2549	-0.211	0.2509	-0.0454	0.8345	0.1101	-0.0425	0.2645	-0.0044	0.3463	-45.7763	191.2838	-28.8897
13	0.416	0.0519	-0.0496	0.0064	-0.0061	0.0059	-0.1721	-0.0449	-0.5322	0.152	-0.0296	-0.0815	0.2036	0.051	0.1319	0.9345	-0.0774	-0.1057	0.1736	-0.007	0.3533	-50.4633	178.4147	-25.1969
14	2.0228	0.6721	-0.3656	0.9419	-0.6147	0.4105	-0.0871	-0.1484	0.0404	0.1217	-0.2296	-0.2708	-0.0721	0.2714	0.1952	0.2445	-0.019	-0.0227	0.5276	-0.2505	0.3724	2.8744	238.7084	12.3228

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 9 THROUGH 192 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 193 THROUGH 264 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 265 THROUGH 373 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 374 THROUGH 469 )
5	X-RAY DIFFRACTION	5	CHAIN 'C' AND (RESID 9 THROUGH 153 )
6	X-RAY DIFFRACTION	6	CHAIN 'C' AND (RESID 154 THROUGH 192 )
7	X-RAY DIFFRACTION	7	CHAIN 'C' AND (RESID 193 THROUGH 245 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 246 THROUGH 284 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 285 THROUGH 412 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 413 THROUGH 469 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 2 THROUGH 4 )
12	X-RAY DIFFRACTION	12	CHAIN 'D' AND (RESID 2 THROUGH 4 )
13	X-RAY DIFFRACTION	13	CHAIN 'D' AND RESID ' 1 '
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND RESID ' 1 '

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