PDB-4ig0: HIV-1 reverse transcriptase with bound fragment at the 507 site

ID or keywords:

Entry

Database: PDB / ID: 4ig0

Title

HIV-1 reverse transcriptase with bound fragment at the 507 site

Components

P51 RT
Reverse transcriptase/ribonuclease H

Keywords

transferase/transferase inhibitor / RNA-DIRECTED DNA POLYMERASE / DNA POLYMERASE / ENDONUCLEASE / HYDROLASE / MULTIFUNCTIONAL ENZYME / transferase-transferase inhibitor complex

Function / homology

Function and homology information

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

HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus type 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Bauman, J.D. / Patel, D. / Arnold, E.

Citation

Journal: J.Med.Chem. / Year: 2013
Title: Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-ray Crystallographic Fragment Screening.
Authors: Bauman, J.D. / Patel, D. / Dharia, C. / Fromer, M.W. / Ahmed, S. / Frenkel, Y. / Vijayan, R.S. / Eck, J.T. / Ho, W.C. / Das, K. / Shatkin, A.J. / Arnold, E.

History

Deposition	Dec 15, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 24, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ig0.cif.gz	418.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ig0.ent.gz	346.3 KB	Display	PDB format
PDBx/mmJSON format	4ig0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ig0_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4ig0_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4ig0_validation.xml.gz	36.3 KB	Display
Data in CIF	4ig0_validation.cif.gz	49.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ig/4ig0 ftp://data.pdbj.org/pub/pdb/validation_reports/ig/4ig0	HTTPS FTP

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Related structure data

Related structure data	4iclC 4id5C 4idkC 4ifvC 4ifyC 4ig3C 4kfbC C: citing same article (ref.)
Similar structure data	4o4g-d 4kko-d 1s6q-d 5cym-d 4lsn-d 1s6p-d 4rw8-d 3qlh-d 6dug-d 3qo9-d 6duh-d 4lsl-d 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	#33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #227 - Nov 2018 Telomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Reverse transcriptase/ribonuclease H

B: P51 RT

hetero molecules

115 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)	162.336, 73.351, 108.793
Angle α, β, γ (deg.)	90.00, 99.67, 90.00
Int Tables number	5
Space group name H-M	C121

Details

Heterodimer of p66 and p51 subunits

#1: Protein	Reverse transcriptase/ribonuclease H / EXORIBONUCLEASE H / P66 RT Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: P66 (unp residues 600-1154) / Mutation: K771A, K772A, C879S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol, POL / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein	P51 RT / Gag-Pol polyprotein Mass: 50096.539 Da / Num. of mol.: 1 / Fragment: P51 (unp residues 600-1027) / Mutation: C879S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol, POL / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#3: Chemical	ChemComp-1FG / 2-({[2-(3,4-dihydroquinolin-1(2H)-yl)-2-oxoethyl](methyl)amino}methyl)quinazolin-4(1H)-one Mass: 362.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₂N₄O₂
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.8 Å³/Da / Density % sol: 56.05 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 11% PEG 8000, 4% PEG 400, 50 MM IMIDAZOLE, 10 MM SPERMINE, 15 MM MGSO4, 100 MM AMMONIUM SULFATE,AND 5 MM TRIS(2-CARBOXYETHYL)PHOSPHINE, PH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X25 / Wavelength: 0.917 / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2009

Radiation

Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.917	1
2	1.075	1

Reflection

Resolution: 2.5→50 Å / Num. all: 44020 / Num. obs: 43932 / % possible obs: 99.8 % / Observed criterion σ(F): -2 / R_merge(I) obs: 0.063 / Net I/σ(I): 33.56

Reflection shell

Resolution (Å)	R_merge(I) obs	Diffraction-ID	% possible all
2.5-2.54	0.609	1	100
2.54-2.59	0.539	1	100
2.59-2.64	0.471	1	100
2.64-2.69	0.425	1	100
2.69-2.75	0.343	1	100
2.75-2.82	0.293	1	100

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Processing

Software

Name	Version	Classification
CBASS		data collection
PHENIX	(phenix.refine: dev_1233)	model building
PHENIX	(phenix.refine: dev_1233)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	dev_1233	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→43.141 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 26.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2432	2206	5.03 %	2%
R_work	0.2009	-	-	-
obs	0.2032	43820	99.69 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→43.141 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7955	0	70	66	8091

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	8259
X-RAY DIFFRACTION	f_angle_d	1.027	11228
X-RAY DIFFRACTION	f_dihedral_angle_d	14.277	3140
X-RAY DIFFRACTION	f_chiral_restr	0.075	1208
X-RAY DIFFRACTION	f_plane_restr	0.005	1410

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 (%)
2.4988-2.5531	0.2809	142	0.2629	2558	X-RAY DIFFRACTION	99
2.5531-2.6125	0.2973	128	0.2473	2594	X-RAY DIFFRACTION	100
2.6125-2.6778	0.3052	132	0.2404	2582	X-RAY DIFFRACTION	100
2.6778-2.7502	0.2849	137	0.2507	2575	X-RAY DIFFRACTION	100
2.7502-2.8311	0.317	122	0.2456	2604	X-RAY DIFFRACTION	100
2.8311-2.9225	0.3077	110	0.2371	2634	X-RAY DIFFRACTION	100
2.9225-3.0269	0.3072	140	0.2436	2579	X-RAY DIFFRACTION	100
3.0269-3.1481	0.2834	140	0.2429	2587	X-RAY DIFFRACTION	100
3.1481-3.2913	0.2912	145	0.2364	2599	X-RAY DIFFRACTION	100
3.2913-3.4647	0.2339	143	0.2238	2596	X-RAY DIFFRACTION	100
3.4647-3.6817	0.2251	130	0.2057	2621	X-RAY DIFFRACTION	100
3.6817-3.9658	0.2347	145	0.1752	2596	X-RAY DIFFRACTION	100
3.9658-4.3645	0.2096	151	0.1718	2602	X-RAY DIFFRACTION	100
4.3645-4.9953	0.2039	138	0.1641	2626	X-RAY DIFFRACTION	100
4.9953-6.2904	0.232	157	0.1946	2619	X-RAY DIFFRACTION	100
6.2904-43.1477	0.2338	146	0.1836	2642	X-RAY DIFFRACTION	98

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	3.0332	1.0657	-1.9121	1.8771	-0.2782	3.3276	0.3465	-0.1823	-0.039	0.5524	-0.1747	0.1825	0.0902	0.0669	-0.1427	1.1107	-0.0097	0.0611	0.6701	0.0868	0.4793	47.9985	-15.3112	70.1468
2	0.4142	0.2042	-1.1446	-0.4071	1.7683	8.354	0.1954	-0.0953	-0.1991	0.0817	0.1276	0.2205	0.4472	-0.3689	-0.2259	0.9309	0.018	-0.0162	0.6772	0.1532	0.6609	45.9558	-18.0797	60.5947
3	3.0488	-0.0463	2.7916	2.1275	-0.1693	4.7093	0.6257	-0.5603	-1.1655	0.2145	0.2397	0.5397	0.5573	-0.7816	-0.8388	0.9005	-0.0694	-0.119	0.6941	0.2754	0.9095	42.6741	-25.8091	39.9838
4	3.319	-1.3978	1.6556	3.5611	-1.0871	4.04	0.358	-0.2749	-0.8537	0.0214	0.2413	0.5723	0.5428	-0.2548	-0.4378	0.4939	-0.0467	-0.1232	0.357	0.0061	0.6658	35.2686	-15.7604	17.6456
5	4.3249	-1.2833	2.4614	2.191	-0.4952	0.9699	-0.0616	-0.4393	-0.1708	0.2106	0.1237	0.1709	0.0753	-0.3182	-0.0927	0.3198	-0.0336	0.0419	0.5357	0.0203	0.4623	13.0131	6.7423	6.7134
6	4.495	2.5779	-0.9636	2.6193	-2.6573	3.8381	0.3114	0.3044	0.7625	-0.4019	-0.696	1.6501	-1.4377	-1.4317	0.3989	0.5208	0.1746	-0.0791	0.7685	-0.1285	0.8601	13.2563	17.2425	4.0824
7	6.0004	-0.4127	0.9442	5.2597	0.6085	6.476	-0.1158	-0.4655	-0.0504	0.6882	0.1101	-0.1554	-0.3393	0.3865	-0.0048	0.5618	-0.006	-0.0631	0.4459	0.1084	0.3089	57.3222	0.3703	39.8159
8	2.9564	-0.0754	1.6239	6.3035	-2.1859	3.6145	-0.2488	0.1201	0.4721	0.7366	0.0921	-0.2837	-0.6241	0.4523	0.094	0.6395	-0.1443	-0.1022	0.5597	0.0515	0.439	58.8224	10.2386	34.941
9	4.7672	3.3827	-1.4053	8.9065	-0.052	6.1115	-0.2106	0.6413	-0.5166	-0.3869	0.1994	-1.6276	0.1026	2.1241	-0.0232	0.7551	-0.3795	-0.0957	1.5227	0.2142	1.118	68.5919	20.8596	22.6215
10	4.142	0.074	3.0853	3.5014	-0.8038	5.2223	-0.3473	0.2153	0.6359	0.2406	-0.1599	-0.0557	-0.6777	0.125	0.565	0.4098	-0.0735	0.0697	0.3942	0.0335	0.4357	32.8191	24.9971	7.579
11	4.0914	-0.3516	1.6411	6.631	0.9654	2.6217	0.1648	-0.0433	0.1063	0.4572	-0.2807	0.0786	-0.1262	0.1523	0.1214	0.432	-0.0662	0.0723	0.4335	0.0302	0.3219	43.5326	10.4365	20.1565

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 59 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 60 through 155 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 156 through 296 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 297 through 421 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 422 through 527 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 528 through 554 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 5 through 59 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 60 through 167 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 168 through 238 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 239 through 363 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 364 through 428 )

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