PDB-5w3v: Crystal Structure of macaque APOBEC3H in complex with RNA

ID or keywords:

Entry

Database: PDB / ID: 5w3v

Title

Crystal Structure of macaque APOBEC3H in complex with RNA

Components

(Apobec3H) x 2
RNA (5'-R(P*AP*AP*CP*CP*CP*CP*GP*GP*GP*C)-3')
RNA (5'-R(P*AP*AP*CP*CP*CP*GP*GP*GP*GP*A)-3')

Keywords

ANTIVIRAL PROTEIN/RNA / cytidine deaminase / protein-RNA complex / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-RNA complex

Function / homology

Function and homology information

single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / cytidine deaminase activity / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleus
Similarity search - Function

Biological species

Macaca nemestrina (pig-tailed macaque)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.243 Å

Authors

Bohn, J.A. / Thummar, K. / York, A. / Raymond, A. / Brown, W.C. / Bieniasz, P.D. / Hatziioannou, T. / Smith, J.L.

Citation

Journal: Nat Commun / Year: 2017
Title: APOBEC3H structure reveals an unusual mechanism of interaction with duplex RNA.
Authors: Bohn, J.A. / Thummar, K. / York, A. / Raymond, A. / Brown, W.C. / Bieniasz, P.D. / Hatziioannou, T. / Smith, J.L.

History

Deposition	Jun 8, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 1, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 23, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5w3v.cif.gz	374 KB	Display	PDBx/mmCIF format
PDB format	pdb5w3v.ent.gz	306 KB	Display	PDB format
PDBx/mmJSON format	5w3v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5w3v_validation.pdf.gz	478.7 KB	Display	wwPDB validaton report
Full document	5w3v_full_validation.pdf.gz	483.2 KB	Display
Data in XML	5w3v_validation.xml.gz	36.5 KB	Display
Data in CIF	5w3v_validation.cif.gz	47.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w3/5w3v ftp://data.pdbj.org/pub/pdb/validation_reports/w3/5w3v	HTTPS FTP

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Related structure data

Similar structure data	4uaf-d 4ypi-3 4ypi-4 1xl3-1 1j1j-2 1pdu-d 7ba2-2 6mk6-5 7b7p-1 6w33-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Apobec3H

B: Apobec3H

C: Apobec3H

D: Apobec3H

E: RNA (5'-R(P*AP*AP*CP*CP*CP*GP*GP*GP*GP*A)-3')

F: RNA (5'-R(P*AP*AP*CP*CP*CP*CP*GP*GP*GP*C)-3')

G: RNA (5'-R(P*AP*AP*CP*CP*CP*CP*GP*GP*GP*C)-3')

H: RNA (5'-R(P*AP*AP*CP*CP*CP*GP*GP*GP*GP*A)-3')

hetero molecules

112 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Apobec3H

B: Apobec3H

E: RNA (5'-R(P*AP*AP*CP*CP*CP*GP*GP*GP*GP*A)-3')

F: RNA (5'-R(P*AP*AP*CP*CP*CP*CP*GP*GP*GP*C)-3')

hetero molecules

defined by author&software
Evidence: gel filtration
56.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Apobec3H

D: Apobec3H

G: RNA (5'-R(P*AP*AP*CP*CP*CP*CP*GP*GP*GP*C)-3')

H: RNA (5'-R(P*AP*AP*CP*CP*CP*GP*GP*GP*GP*A)-3')

hetero molecules

defined by author&software
56.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.960, 89.310, 134.370
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

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Protein , 2 types, 4 molecules ABCD

#1: Protein	Apobec3H / APOBEC3H Mass: 24742.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca nemestrina (pig-tailed macaque) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pGro7 / References: UniProt: A0A1B2AH37*PLUS
#2: Protein	Apobec3H Mass: 24774.287 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca nemestrina (pig-tailed macaque) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pGro7 / References: UniProt: A0A1B2AH37*PLUS

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RNA chain , 2 types, 4 molecules EHFG

#3: RNA chain	RNA (5'-R(PAPAPCPCPCPGPGPGPGPA)-3') Mass: 3239.029 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain	RNA (5'-R(PAPAPCPCPCPCPGPGPGPC)-3') Mass: 3174.981 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 254 molecules

#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: Zn
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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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: 47.89 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris:HCl pH 8.5 0.1M MgCl2 28% PEG 4000

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	23-ID-B	1	1.283
SYNCHROTRON	APS	23-ID-B	2	1.033

Detector

Type	ID	Detector	Date
DECTRIS EIGER X 16M	1	PIXEL	Feb 8, 2017
DECTRIS EIGER X 16M	2	PIXEL	Mar 7, 2017

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.283	1
2	1.033	1

Reflection

Entry-ID: 5W3V / CC_1/2: 1 / % possible obs: 100 %

Resolution (Å)	Num. obs	Redundancy (%)	R_merge(I) obs	Diffraction-ID	Net I/σ(I)
2.59-45.8	69877	7.1	0.086	1	15.7
2.24-44.6	51349	27.1	0.128	2	15.8

Reflection shell

R_merge(I) obs: 1.08 / CC_1/2: 0.64

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Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
Coot		model building
XDS		data scaling
AutoSol		phasing
XDS		data reduction

Refinement

Resolution: 2.243→44.655 Å / SU ML: 0.38 / σ(F): 1.33 / Phase error: 26.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2215	5320	5.44 %
R_work	0.1818	-	-
obs	0.1839	97735	99.82 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.243→44.655 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6047	830	4	250	7131

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7231
X-RAY DIFFRACTION	f_angle_d	0.527	9968
X-RAY DIFFRACTION	f_dihedral_angle_d	12.488	4294
X-RAY DIFFRACTION	f_chiral_restr	0.038	1096
X-RAY DIFFRACTION	f_plane_restr	0.004	1145

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 (%)
2.2431-2.2686	0.3992	180	0.37	2894	X-RAY DIFFRACTION	96
2.2686-2.2953	0.3401	172	0.3286	3107	X-RAY DIFFRACTION	100
2.2953-2.3233	0.3436	181	0.325	3073	X-RAY DIFFRACTION	100
2.3233-2.3527	0.3265	173	0.3152	3089	X-RAY DIFFRACTION	100
2.3527-2.3836	0.3359	184	0.3155	3080	X-RAY DIFFRACTION	100
2.3836-2.4163	0.3351	190	0.3067	3082	X-RAY DIFFRACTION	100
2.4163-2.4508	0.3212	179	0.3023	3099	X-RAY DIFFRACTION	100
2.4508-2.4874	0.3216	172	0.2824	3081	X-RAY DIFFRACTION	100
2.4874-2.5262	0.2865	159	0.2768	3084	X-RAY DIFFRACTION	100
2.5262-2.5677	0.3654	184	0.2906	3073	X-RAY DIFFRACTION	100
2.5677-2.6119	0.331	188	0.2827	3106	X-RAY DIFFRACTION	100
2.6119-2.6594	0.3199	179	0.2643	3065	X-RAY DIFFRACTION	100
2.6594-2.7106	0.3028	180	0.2691	3094	X-RAY DIFFRACTION	100
2.7106-2.7659	0.3919	166	0.2577	3100	X-RAY DIFFRACTION	100
2.7659-2.826	0.3422	177	0.2536	3117	X-RAY DIFFRACTION	100
2.826-2.8917	0.2902	174	0.2345	3047	X-RAY DIFFRACTION	100
2.8917-2.964	0.3156	175	0.2373	3109	X-RAY DIFFRACTION	100
2.964-3.0442	0.2721	190	0.2448	3074	X-RAY DIFFRACTION	100
3.0442-3.1337	0.3016	162	0.2361	3106	X-RAY DIFFRACTION	100
3.1337-3.2348	0.2502	177	0.2075	3066	X-RAY DIFFRACTION	100
3.2348-3.3504	0.2402	172	0.1902	3108	X-RAY DIFFRACTION	100
3.3504-3.4845	0.2123	188	0.1811	3085	X-RAY DIFFRACTION	100
3.4845-3.643	0.2309	175	0.1736	3071	X-RAY DIFFRACTION	100
3.643-3.835	0.1631	194	0.1599	3083	X-RAY DIFFRACTION	100
3.835-4.0751	0.219	168	0.1493	3087	X-RAY DIFFRACTION	100
4.0751-4.3895	0.1571	180	0.1309	3086	X-RAY DIFFRACTION	100
4.3895-4.8308	0.1248	176	0.1234	3106	X-RAY DIFFRACTION	100
4.8308-5.5287	0.1902	172	0.1352	3077	X-RAY DIFFRACTION	100
5.5287-6.9613	0.189	180	0.1588	3088	X-RAY DIFFRACTION	100
6.9613-44.6638	0.191	173	0.1503	3078	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	4.643	2.4767	-1.5757	6.861	-1.5846	6.805	-0.0334	0.384	0.0645	-0.2113	0.3196	0.2849	-0.5279	0.0092	-0.235	0.5658	0.0693	0.0469	0.5223	0.0142	0.4741	30.768	60.3415	11.8012
2	3.8071	2.5117	-1.6513	6.9405	-3.4077	3.3842	0.1132	-0.1833	0.1299	0.0752	-0.2187	-0.4146	-0.4586	0.6755	0.1328	0.4976	-0.118	0.0067	0.5861	-0.0833	0.3534	44.4355	56.8495	14.3035
3	5.8208	-1.5099	1.5882	6.8404	-4.0676	8.4219	0.2118	-0.3241	0.664	0.7768	0.1201	0.5928	-0.993	-0.4122	-0.3601	0.6786	-0.0806	0.1584	0.5127	-0.1357	0.5145	28.976	60.6474	22.8038
4	7.6959	3.3179	2.3578	8.53	2.242	3.957	0.6137	-0.4549	0.2398	1.6129	-0.3769	0.3386	0.3866	-0.3059	-0.2841	0.9359	-0.2272	0.127	0.818	-0.0345	0.6494	8.0009	28.0958	56.3229
5	4.5049	1.0223	-1.0002	6.6121	-1.2454	3.8229	0.3605	-0.4978	-0.3742	0.9001	-0.4083	0.4585	0.4589	-0.4837	0.0709	0.7462	-0.2747	-0.0295	0.8166	0.0134	0.5968	9.0209	18.9387	51.246
6	4.2549	-3.9015	-3.5679	4.2925	3.1582	6.6313	0.4028	0.7677	0.3325	-0.4083	-0.526	0.3909	-0.2403	-0.4359	0.0757	0.5889	-0.1385	-0.0561	0.7743	0.0465	0.7016	12.2096	31.1962	40.555
7	3.8079	1.5588	-4.9747	7.3832	-4.0198	7.8944	-0.2394	0.8139	-0.4497	-0.4256	0.6008	-0.4964	0.3208	-0.0435	-0.3618	0.4787	-0.071	-0.1013	0.8189	-0.077	0.696	11.5073	25.9486	10.4758
8	8.6899	4.111	0.5192	4.8098	2.9627	4.4289	-0.249	0.4231	0.1124	-0.1782	0.2704	0.4364	0.4313	-0.8681	0.0559	0.5618	-0.138	-0.1196	0.9381	0.1326	0.7047	-4.7571	26.1121	14.5912
9	8.065	-3.2954	-3.754	4.4578	3.2202	7.3847	-0.4004	-0.1353	-1.003	0.5136	0.4772	-0.3278	1.1058	0.3954	-0.0026	0.7653	-0.1405	-0.1308	0.6986	0.0733	0.8286	11.8812	20.9346	19.0753
10	4.027	1.9364	-0.2848	7.3035	-0.2887	5.8669	0.2414	-0.0739	-0.6606	0.2406	0.1384	-0.1172	0.2646	0.2636	-0.3139	0.5507	0.048	-0.0844	0.4903	0.013	0.4806	41.0791	50.1229	55.6675
11	2.5643	0.9422	1.5817	4.7156	1.3528	4.9928	0.0315	-0.0827	0.121	-0.1885	-0.1258	-0.1316	-0.7989	0.2878	0.1043	0.5473	-0.0621	0.0021	0.4699	0.0372	0.3585	41.8148	63.7103	54.0905
12	3.5414	-2.2072	3.3001	6.0835	-1.085	4.2174	0.056	1.0332	-0.704	-0.8316	-0.0578	0.2487	0.3286	0.3526	-0.0681	0.7833	-0.0905	0.0882	0.6843	-0.062	0.5792	38.2661	52.154	41.1927
13	6.2174	1.1717	3.7994	2.8931	1.7951	7.8149	-0.0994	-0.2998	-0.3203	0.0685	-0.2946	0.2878	0.1064	-0.2563	0.3494	0.5127	-0.1823	0.058	0.6586	0.0888	0.6487	21.3233	42.0941	22.3511
14	7.1385	5.4342	-8.0414	8.1694	-7.5253	9.7303	0.2365	-0.6237	0.0999	0.0338	-0.335	0.396	-0.0385	-0.3206	0.0429	0.5119	-0.1784	-0.0775	0.7308	-0.0435	0.6212	20.0099	39.4939	22.2802
15	2.3285	1.1813	2.6204	8.1948	7.8356	8.5053	-0.4548	0.0587	-0.1203	-0.1822	-0.0101	-0.0472	0.2572	0.095	0.409	0.6845	-0.1863	0.0806	0.5485	0.087	0.617	23.7526	40.9047	45.0735
16	1.6114	1.3509	-2.3133	8.0808	-4.9637	4.6298	-0.0104	-0.1925	-0.193	-0.4646	-0.1774	0.2423	0.4339	-0.4208	0.1051	0.8163	-0.2536	-0.1033	0.6947	-0.0581	0.5947	26.1913	42.2735	45.0409

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 56 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 57 through 139 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 140 through 186 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 5 through 56 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 57 through 160 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 161 through 183 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 4 through 38 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 39 through 139 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 140 through 185 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 4 through 38 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 39 through 160 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 161 through 184 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 1 through 5 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 1 through 5 )
15	X-RAY DIFFRACTION	15	chain 'G' and (resid 1 through 10 )
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 1 through 5 )

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Protein , 2 types, 4 molecules ABCD

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RNA chain , 2 types, 4 molecules EHFG

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-Non-polymers , 2 types, 254 molecules

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Protein , 2 types, 4 molecules ABCD

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RNA chain , 2 types, 4 molecules EHFG

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Non-polymers , 2 types, 254 molecules

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