PDB-5td5: Crystal Structure of Human APOBEC3B variant complexed with ssDNA

ID or keywords:

Entry

Database: PDB / ID: 5td5

Title

Crystal Structure of Human APOBEC3B variant complexed with ssDNA

Components

DNA (5'-D(P*TP*TP*CP*AP*T)-3')
DNA dC->dU-editing enzyme APOBEC-3B

Keywords

Hydrolase/DNA / Deaminase / DNA substrate complex / Hydrolase-DNA complex

Function / homology

Function and homology information

mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / transposable element silencing / P-body ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.718 Å

Authors

Shi, K. / Banerjee, S. / Kurahashi, K. / Aihara, H.

Citation

Journal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
Authors: Shi, K. / Carpenter, M.A. / Banerjee, S. / Shaban, N.M. / Kurahashi, K. / Salamango, D.J. / McCann, J.L. / Starrett, G.J. / Duffy, J.V. / Demir, O. / Amaro, R.E. / Harki, D.A. / Harris, R.S. / Aihara, H.

History

Deposition	Sep 16, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 22, 2017	Group: Database references
Revision 1.2	Mar 6, 2024	Group: Advisory / Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5td5.cif.gz	134.6 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	5td5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5td5_validation.pdf.gz	449.1 KB	Display	wwPDB validaton report
Full document	5td5_full_validation.pdf.gz	449.5 KB	Display
Data in XML	5td5_validation.xml.gz	10.6 KB	Display
Data in CIF	5td5_validation.cif.gz	14.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/td/5td5 ftp://data.pdbj.org/pub/pdb/validation_reports/td/5td5	HTTPS FTP

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Related structure data

Related structure data	5swwC C: citing same article (ref.)
Similar structure data	4hz5-2 5zdm-d 2akp-1 6nfk-d 2a6w-2 3opd-3 1kdt-1 5lb4-d 1g4e-2 4hz5-5 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: DNA dC->dU-editing enzyme APOBEC-3B

C: DNA (5'-D(P*TP*TP*CP*AP*T)-3')

hetero molecules

26.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	96.411, 96.411, 84.875
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	181
Space group name H-M	P6₄22

Components on special symmetry positions

ID	Model	Components
1	1	A-584- HOH

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein	DNA dC->dU-editing enzyme APOBEC-3B / A3B / Phorbolin-1-related protein / Phorbolin-2/3 Mass: 22393.342 Da / Num. of mol.: 1 Mutation: F200S, W228S, L230K, Y250S, E255A, F308K, Delta 205-207, Delta 242-249 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3B / Production host: Escherichia coli (E. coli) References: UniProt: Q9UH17, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: DNA chain	DNA (5'-D(PTPTPCPAPT)-3') Mass: 2078.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens* (human)

#1: Protein

DNA dC->dU-editing enzyme APOBEC-3B / A3B / Phorbolin-1-related protein / Phorbolin-2/3

Mass: 22393.342 Da / Num. of mol.: 1
Mutation: F200S, W228S, L230K, Y250S, E255A, F308K, Delta 205-207, Delta 242-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: APOBEC3B / Production host:

Escherichia coli (E. coli)
References: UniProt: Q9UH17, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines

#2: DNA chain

DNA (5'-D(P*TP*TP*CP*AP*T)-3')

Mass: 2078.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.)

Homo sapiens (human)

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Non-polymers , 5 types, 116 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.33 Å³/Da / Density % sol: 47.13 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: NaI, PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 10, 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: 1.718→83.494 Å / Num. obs: 50564 / % possible obs: 99.7 % / Redundancy: 12.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.054 / Net I/σ(I): 35.3
Reflection shell	Resolution: 1.718→1.78 Å / Redundancy: 11.8 % / R_merge(I) obs: 1.275 / Mean I/σ(I) obs: 2.1 / CC_1/2: 0.783 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
PHENIX	dev_2499	refinement
XDS		data reduction
XDS		data scaling
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.718→83.494 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.34

	R_factor	Num. reflection	% reflection
R_free	0.2089	2373	5.06 %
R_work	0.1801	-	-
obs	0.1816	46913	99.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.718→83.494 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1473	84	36	98	1691

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1643
X-RAY DIFFRACTION	f_angle_d	0.75	2232
X-RAY DIFFRACTION	f_dihedral_angle_d	17.819	945
X-RAY DIFFRACTION	f_chiral_restr	0.045	229
X-RAY DIFFRACTION	f_plane_restr	0.004	276

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 (%)
1.7184-1.7534	0.3014	122	0.321	2511	X-RAY DIFFRACTION	95
1.7534-1.7916	0.3461	132	0.2983	2642	X-RAY DIFFRACTION	100
1.7916-1.8333	0.2959	130	0.2784	2649	X-RAY DIFFRACTION	100
1.8333-1.8791	0.2445	136	0.2392	2622	X-RAY DIFFRACTION	100
1.8791-1.9299	0.2467	140	0.2298	2624	X-RAY DIFFRACTION	100
1.9299-1.9867	0.2431	131	0.2172	2619	X-RAY DIFFRACTION	100
1.9867-2.0508	0.2494	144	0.2059	2636	X-RAY DIFFRACTION	100
2.0508-2.1241	0.2549	159	0.1932	2605	X-RAY DIFFRACTION	100
2.1241-2.2092	0.214	150	0.1852	2615	X-RAY DIFFRACTION	100
2.2092-2.3097	0.1801	131	0.1766	2622	X-RAY DIFFRACTION	100
2.3097-2.4315	0.2235	128	0.1804	2659	X-RAY DIFFRACTION	100
2.4315-2.5839	0.2105	134	0.183	2609	X-RAY DIFFRACTION	100
2.5839-2.7834	0.2445	133	0.1822	2651	X-RAY DIFFRACTION	100
2.7834-3.0635	0.2213	165	0.1865	2590	X-RAY DIFFRACTION	100
3.0635-3.5068	0.2038	121	0.1727	2648	X-RAY DIFFRACTION	100
3.5068-4.4182	0.1775	167	0.1447	2613	X-RAY DIFFRACTION	100
4.4182-83.5932	0.1935	150	0.1726	2625	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	0.0244	0.0113	0.021	-0.0433	-0.0204	0.1159	-0.0552	-0.2048	0.4301	0.3492	-0.0734	0.5408	0.2633	-0.127	0.0882	0.2682	0.0563	0.0908	0.3522	-0.1905	0.6595	-0.9354	38.952	-8.352
2	0.5904	-0.6655	0.1922	0.4977	-0.2531	0.0102	0.0606	0.1521	0.1939	0.0335	-0.0929	0.2464	-0.0773	0.0768	-0.0058	0.324	0.0372	0.0462	0.3323	-0.0727	0.3423	5.1289	33.015	-13.6122
3	-0.0079	0.0388	0.045	-0.0088	0.0167	0.0648	-0.4216	0.3478	0.0965	0.3839	-0.3324	-0.0307	0.0343	-0.2478	-0	0.4507	-0.033	-0.0304	0.6784	-0.0745	0.8339	-4.1957	29.3605	-26.4111
4	0.3501	-0.0628	0.1122	0.1969	0.0166	0.1464	-0.2154	-0.3573	-0.1305	0.3627	-0.0888	0.1171	0.2189	-0.0867	-0.0426	0.3606	0.0167	0.1293	0.3541	-0.0123	0.3041	3.2022	24.0773	-7.4971
5	-0.0178	-0.0085	-0.0105	0.0436	-0.0376	0.0477	0.0204	0.2139	-0.3206	-0.668	-0.2177	0.4118	0.3333	0.1794	-0.0033	0.4287	-0.074	-0.0106	0.4508	-0.2179	0.4809	-1.6439	17.8628	-24.2153
6	0.2468	0.0524	0.14	0.2569	0.1901	-0.0038	-0.035	-0.0019	0.1863	0.0571	-0.136	0.1487	-0.0005	0.0516	-0.0362	0.307	0.0334	0.0327	0.2536	-0.0186	0.2079	10.6214	27.0855	-13.1764
7	0.0468	0.0317	0.0223	-0.0321	0.0216	0.0163	-0.0689	-0.1619	0.1604	-0.1008	-0.0096	0.1219	0.4986	0.1874	0	0.4102	0.0155	0.0978	0.3019	-0.0082	0.2696	11.8676	16.2306	-15.7999
8	0.1184	-0.0275	0.0472	-0.0047	0.0566	0.0667	-0.0497	-0.1328	0.0536	-0.1195	0.0145	0.0142	0.0383	-0.1576	-0.0001	0.3579	0.0013	0.0311	0.3211	-0.0331	0.2511	8.6674	23.8702	-22.4029
9	0.6431	0.8703	-0.0958	0.9219	0.5356	0.2007	-0.1192	0.0407	0.2615	-0.1424	0.0035	-0.0114	0.0047	0.0782	-0.0001	0.2926	0.0352	0.0167	0.2892	-0.0053	0.2865	13.7373	32.9717	-14.5298
10	0.1738	0.1195	-0.102	0.0751	-0.0723	0.5095	0.0567	0.0977	-0.3765	0.2762	0.016	0.427	-0.1936	-0.2096	-0.028	0.302	0.0873	0.0283	0.34	-0.1084	0.7239	0.5744	47.7735	-12.4073
11	0.0085	0.1026	-0.0167	0.078	0.0366	-0.0453	-0.1209	0.0636	0.3755	-0.2518	0.0665	-0.2811	0.0071	-0.0026	0	0.3291	-0.0265	0.0185	0.3313	-0.0125	0.4362	21.323	39.1421	-16.4593
12	0.691	-0.3089	0.3144	0.4238	-0.1513	0.1958	0.1042	0.0514	0.1643	0.4161	0.311	-0.4909	0.1498	-0.0599	0.1038	0.3922	0.0767	0.0751	0.3216	-0.0595	0.2383	12.2337	33.7244	1.9042

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 190 through 202 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 203 through 224 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 225 through 235 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 236 through 261 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 262 through 272 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 273 through 288 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 289 through 299 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 300 through 309 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 310 through 348 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 349 through 361 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 362 through 379 )
12	X-RAY DIFFRACTION	12	chain 'B' and resname CL and name 'CL ' and altloc ' ' and resid 2

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