PDB-8x20: HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:E-C...

ID or keywords:

Entry

Database: PDB / ID: 8x20

Title

HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:E-CFCP-TP ternary complex

Components

DNA/RNA (38-MER)
HIV-1 RT p51 subunit
Pol protein (Fragment)

Keywords

TRANSFERASE / reverse transcriptase / HIV-1 / HBV / drug resistance / nucleoside analogue / E-CFCP

Function / homology

Function and homology information

HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...
Similarity search - Function

Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus 1
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Yasutake, Y. / Hattori, S.I. / Mitsuya, H.

Funding support

Japan, 1items

Citation

Journal: Sci Rep / Year: 2024
Title: Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations.
Authors: Yasutake, Y. / Hattori, S.I. / Kumamoto, H. / Tamura, N. / Maeda, K. / Mitsuya, H.

History

Deposition	Nov 9, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8x20.cif.gz	892.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8x20.ent.gz	734.4 KB	Display	PDB format
PDBx/mmJSON format	8x20.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/x2/8x20 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/8x20	HTTPS FTP

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Related structure data

Related structure data	8x1zC 8x21C 8x22C 6kdnS S: Starting model for refinement 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #163 - Jul 2013 HIV Capsid similarity (3) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #227 - Nov 2018 Telomerase similarity (2) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#163 - Jul 2013
HIV Capsid
similarity (3)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#227 - Nov 2018
Telomerase
similarity (2)
#253 - Jan 2021
Expressome
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Pol protein (Fragment)

B: HIV-1 RT p51 subunit

E: DNA/RNA (38-MER)

C: Pol protein (Fragment)

D: HIV-1 RT p51 subunit

F: DNA/RNA (38-MER)

hetero molecules

257 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pol protein (Fragment)

B: HIV-1 RT p51 subunit

E: DNA/RNA (38-MER)

hetero molecules

defined by author&software
Evidence: gel filtration
128 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Pol protein (Fragment)

D: HIV-1 RT p51 subunit

F: DNA/RNA (38-MER)

hetero molecules

defined by author&software
128 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	284.069, 284.069, 95.605
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

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Protein , 2 types, 4 molecules ACBD

#1: Protein	Pol protein (Fragment) Mass: 64019.363 Da / Num. of mol.: 2 / Mutation: L74V, Y115F, F116Y, Q151M, C162S, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: D3XFN5
#2: Protein	HIV-1 RT p51 subunit / HIV-1 reverse transcriptase p51 subunit / p51 RT Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C162S, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497

#1: Protein

Pol protein (Fragment)

Mass: 64019.363 Da / Num. of mol.: 2 / Mutation: L74V, Y115F, F116Y, Q151M, C162S, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: D3XFN5

#2: Protein

HIV-1 RT p51 subunit / HIV-1 reverse transcriptase p51 subunit / p51 RT

Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C162S, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus 1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497

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DNA chain , 1 types, 2 molecules EF

#3: DNA chain	DNA/RNA (38-MER) Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 256 molecules

#4: Chemical	ChemComp-XTE / E-CFCP-triphosphate / [[(1~{S},2~{E},3~{S},5~{S})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-1-cyano-2-(fluoranylmethylidene)-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate Mass: 560.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₁₆FN₆O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.91 Å³/Da / Density % sol: 57.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, sucrose, glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 11, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 78960 / % possible obs: 100 % / Redundancy: 5.5 % / B_iso Wilson estimate: 63.3 Å² / R_rim(I) all: 0.105 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2.7→2.75 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4494 / R_rim(I) all: 0.878

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6KDN

6kdn

Resolution: 2.7→48.602 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2313	4023	5.1 %
R_work	0.1735	-	-
obs	0.1764	78952	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.7→48.602 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15688	1495	101	248	17532

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	17888
X-RAY DIFFRACTION	f_angle_d	0.849	24607
X-RAY DIFFRACTION	f_dihedral_angle_d	24.891	6845
X-RAY DIFFRACTION	f_chiral_restr	0.112	2662
X-RAY DIFFRACTION	f_plane_restr	0.005	2835

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 (%)
2.7001-2.7318	0.3184	135	0.265	2559	X-RAY DIFFRACTION	100
2.7318-2.7651	0.3314	129	0.2468	2586	X-RAY DIFFRACTION	100
2.7651-2.8001	0.294	144	0.2345	2595	X-RAY DIFFRACTION	100
2.8001-2.837	0.2995	140	0.2184	2589	X-RAY DIFFRACTION	100
2.837-2.8758	0.2868	162	0.2237	2552	X-RAY DIFFRACTION	100
2.8758-2.9169	0.306	142	0.2228	2598	X-RAY DIFFRACTION	100
2.9169-2.9605	0.2951	143	0.2097	2556	X-RAY DIFFRACTION	100
2.9605-3.0067	0.3106	162	0.2147	2565	X-RAY DIFFRACTION	100
3.0067-3.056	0.2487	148	0.1997	2586	X-RAY DIFFRACTION	100
3.056-3.1087	0.2446	105	0.194	2599	X-RAY DIFFRACTION	100
3.1087-3.1652	0.2532	152	0.193	2558	X-RAY DIFFRACTION	100
3.1652-3.2261	0.3214	152	0.1942	2627	X-RAY DIFFRACTION	100
3.2261-3.2919	0.2352	128	0.1932	2579	X-RAY DIFFRACTION	100
3.2919-3.3635	0.271	123	0.1849	2575	X-RAY DIFFRACTION	100
3.3635-3.4417	0.2676	153	0.1785	2562	X-RAY DIFFRACTION	100
3.4417-3.5277	0.2375	144	0.1788	2613	X-RAY DIFFRACTION	100
3.5277-3.6231	0.269	134	0.1761	2575	X-RAY DIFFRACTION	100
3.6231-3.7297	0.2225	126	0.1764	2589	X-RAY DIFFRACTION	100
3.7297-3.85	0.2242	138	0.1755	2608	X-RAY DIFFRACTION	100
3.85-3.9875	0.2178	164	0.1603	2566	X-RAY DIFFRACTION	100
3.9875-4.1471	0.1925	128	0.1533	2567	X-RAY DIFFRACTION	100
4.1471-4.3357	0.2373	128	0.1508	2608	X-RAY DIFFRACTION	100
4.3357-4.5642	0.1936	148	0.1489	2581	X-RAY DIFFRACTION	100
4.5642-4.8499	0.1836	134	0.151	2577	X-RAY DIFFRACTION	100
4.8499-5.224	0.2102	144	0.1469	2589	X-RAY DIFFRACTION	100
5.224-5.7489	0.2044	127	0.1665	2587	X-RAY DIFFRACTION	100
5.7489-6.579	0.2374	130	0.1774	2590	X-RAY DIFFRACTION	100
6.579-8.2822	0.1972	150	0.1634	2575	X-RAY DIFFRACTION	100
8.2822-48.602	0.2109	110	0.1691	2618	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	1.1312	-0.0784	-0.2699	0.5704	0.0524	3.0462	-0.0462	-0.0985	0.1463	0.0213	0.0158	-0.0771	0.1763	0.0224	0.0169	0.2752	0.0003	0.0347	0.3631	-0.0349	0.4008	178.1131	275.3178	-145.9297
2	5.1541	0.0293	-0.8742	4.6426	-0.1311	2.8082	0.145	-0.5845	0.6359	0.5697	-0.2343	-0.2259	-0.2003	0.1451	0.0905	1.5174	-0.2528	0.1221	1.8234	-0.3339	0.9328	182.5778	277.3192	-122.4028
3	2.4447	0.2852	-0.1846	0.9286	0.3434	1.4244	-0.0544	0.2979	0.1964	-0.1383	-0.0522	0.3263	-0.1728	-0.6782	0.1242	0.3466	0.087	-0.0338	0.7432	-0.0324	0.5957	145.7856	275.8962	-154.815
4	2.4723	1.2394	1.1151	5.2728	3.5881	6.5401	-0.1686	-0.3974	-0.1949	-0.2627	-0.0634	0.357	0.2126	-0.7424	0.2089	0.3892	-0.0224	0.0558	0.4497	0.022	0.3689	174.5638	264.1895	-147.5563
5	1.6833	0.066	-0.2441	1.467	-0.3499	0.9655	-0.0958	0.1156	0.1973	-0.1484	0.1041	0.1343	-0.0863	-0.0639	-0.0112	0.3183	-0.0473	0.0006	0.4244	0.0082	0.3494	211.0622	281.7057	-183.022
6	9.8852	-5.8753	-0.7337	3.4948	0.5785	8.1754	-0.0618	-0.1138	1.3029	-0.3519	0.0095	-0.2228	-1.2061	0.037	0.0783	1.3731	-0.1424	-0.1031	0.9005	0.2747	1.4116	212.4658	300.8705	-197.6322
7	1.1407	-0.1786	-0.1013	2.4384	-0.9668	1.3186	-0.1107	-0.024	-0.0827	-0.1382	0.0469	-0.1025	0.1553	0.3106	0.0813	0.3347	-0.0447	0.0508	0.5004	0.0157	0.3622	238.4855	262.2566	-182.1093
8	4.8959	0.2204	0.3594	2.9965	-1.1086	3.7577	0.1824	0.5841	-0.3088	-0.1559	-0.4212	-0.0828	0.3736	0.2039	0.2333	0.4353	-0.0369	0.0525	0.503	-0.0287	0.3253	207.2376	273.7985	-190.9547

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 1 through 553)
2	X-RAY DIFFRACTION	2	(chain 'A' and resid 601 through 601)
3	X-RAY DIFFRACTION	3	(chain 'B' and resid 5 through 427)
4	X-RAY DIFFRACTION	4	(chain 'E' and resid -1 through 33)
5	X-RAY DIFFRACTION	5	(chain 'C' and resid 1 through 553)
6	X-RAY DIFFRACTION	6	(chain 'C' and resid 601 through 601)
7	X-RAY DIFFRACTION	7	(chain 'D' and resid 5 through 427)
8	X-RAY DIFFRACTION	8	(chain 'F' and resid -4 through 33)

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