PDB-8cbt: HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Co...

ID or keywords:

Entry

Database: PDB / ID: 8cbt

Title

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor MUT872

Components

Integrase

Keywords

VIRAL PROTEIN / Integrase / HIV / ALLINI / Allosteric Inhibitor / Inhibitor / Retrovirus / INLAI / NCINI / MINI / LEDGIN / Mutabilis / MUT872

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

Integrase, C-terminal domain superfamily, retroviral / 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 ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.14 Å

Authors

Singer, M.R. / Pye, V.E. / Yu, Z. / Cherepanov, P.

Funding support

United Kingdom, 4items

Organization	Grant number	Country
Cancer Research UK	FC001061	United Kingdom
Medical Research Council (MRC, United Kingdom)	FC001061	United Kingdom
Wellcome Trust	FC001061	United Kingdom
The Francis Crick Institute	FC001061	United Kingdom

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2023
Title: Biological and Structural Analyses of New Potent Allosteric Inhibitors of HIV-1 Integrase.
Authors: Bonnard, D. / Le Rouzic, E. / Singer, M.R. / Yu, Z. / Le Strat, F. / Batisse, C. / Batisse, J. / Amadori, C. / Chasset, S. / Pye, V.E. / Emiliani, S. / Ledoussal, B. / Ruff, M. / Moreau, F. ...

History

Deposition	Jan 25, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 7, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 14, 2023	Group: Structure summary / Category: struct / struct_keywords / Item: _struct.title / _struct_keywords.text
Revision 1.2	Jun 21, 2023	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Jul 26, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4	Jun 19, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8cbt.cif.gz	217.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8cbt.ent.gz	141.1 KB	Display	PDB format
PDBx/mmJSON format	8cbt.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/cb/8cbt ftp://data.pdbj.org/pub/pdb/validation_reports/cb/8cbt	HTTPS FTP

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Related structure data

Related structure data	8bv2C 8cbrC 8cbsC 8cbuC 8cbvC 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	#163 - Jul 2013 HIV Capsid similarity (3) #135 - Mar 2011 Integrase similarity (1)

Deposited unit

A: Integrase

B: Integrase

C: Integrase

D: Integrase

hetero molecules

105 kDa, 4 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)	53.306, 64.470, 70.702
Angle α, β, γ (deg.)	90.000, 101.660, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Integrase / IN Mass: 25904.537 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The construct is of HIV-1 integrase with the following domain swap: The C-Terminal Domain of HIV-1 integrase (from residues 220 to 288) is followed by the Catalytic Core Domain of HIV-1 ...Details: The construct is of HIV-1 integrase with the following domain swap: The C-Terminal Domain of HIV-1 integrase (from residues 220 to 288) is followed by the Catalytic Core Domain of HIV-1 integrase (from residues 50 to 212). In addition, there are the following mutations: F185K and W243E. The residue numbers are correct in the structure. Because the linker is not defined in the electron density map, we do not know for sure which CTD is linked to which CCD in the lattice formation. We have therefore kept each domain as a separate chain. This chain is CTD There are 2 copies of CTD and CCD in the asymmetric unit. We cannot determine how they are connected in the crystal lattice.,The construct is of HIV-1 integrase with the following domain swap: The C-Terminal Domain of HIV-1 integrase (from residues 220 to 288) is followed by the Catalytic Core Domain of HIV-1 integrase (from residues 50 to 212). In addition, there are the following mutations: F185K and W243E. The residue numbers are correct in the structure. Because the linker is not defined in the electron density map, we do not know for sure which CTD is linked to which CCD in the lattice formation. We have therefore kept each domain as a separate chain. This chain is CTD There are 2 copies of CTD and CCD in the asymmetric unit. We cannot determine how they are connected in the crystal lattice. Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds

#1: Protein

Integrase / IN

Mass: 25904.537 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The construct is of HIV-1 integrase with the following domain swap: The C-Terminal Domain of HIV-1 integrase (from residues 220 to 288) is followed by the Catalytic Core Domain of HIV-1 ...
Source: (gene. exp.)

Human immunodeficiency virus 1 / Gene: gag-pol / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds

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Non-polymers , 6 types, 172 molecules

#2: Chemical	ChemComp-W2Q / (2~{S})-2-[3-cyclopropyl-2-(3,4-dihydro-2~{H}-chromen-6-yl)-6-methyl-phenyl]-2-cyclopropyloxy-ethanoic acid Mass: 378.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₄H₂₆O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 158 / 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 grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 8000, ethylene glycol, magnesium chloride, calcium chloride, imidazole, MES

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 5, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.14→64.47 Å / Num. obs: 26052 / % possible obs: 100 % / Redundancy: 36.95 % / B_iso Wilson estimate: 46.91 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.027 / Net I/σ(I): 13.6
Reflection shell	Resolution: 2.14→2.18 Å / Redundancy: 27.51 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1265 / CC_1/2: 0.931 / R_pim(I) all: 0.32 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
DIALS		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.14→52.21 Å / SU ML: 0.2876 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2534	1258	4.83 %
R_work	0.2073	24765	-
obs	0.2096	26023	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 58.49 Å²

Refinement step

Cycle: LAST / Resolution: 2.14→52.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2972	0	107	158	3237

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0015	3196
X-RAY DIFFRACTION	f_angle_d	0.4023	4312
X-RAY DIFFRACTION	f_chiral_restr	0.0418	480
X-RAY DIFFRACTION	f_plane_restr	0.0028	530
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3429	1185

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 (%)
2.14-2.23	0.3532	148	0.2884	2728	X-RAY DIFFRACTION	99.93
2.23-2.33	0.31	124	0.2662	2733	X-RAY DIFFRACTION	99.97
2.33-2.45	0.2879	122	0.2446	2760	X-RAY DIFFRACTION	99.97
2.45-2.6	0.2692	143	0.2298	2708	X-RAY DIFFRACTION	99.96
2.6-2.8	0.2971	155	0.2359	2753	X-RAY DIFFRACTION	100
2.8-3.09	0.3021	145	0.2263	2742	X-RAY DIFFRACTION	100
3.09-3.53	0.2419	133	0.202	2766	X-RAY DIFFRACTION	99.97
3.53-4.45	0.217	136	0.1811	2777	X-RAY DIFFRACTION	100
4.45-52.21	0.2357	152	0.194	2798	X-RAY DIFFRACTION	99.76

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	0.842527401158	-0.274989229237	-0.595918496735	1.59218050832	0.238888839715	1.28364940582	-0.0147248518144	0.0190141690637	0.150415284005	-0.265193022597	-0.0732538399087	0.188701239043	-0.192098450737	-0.234323987522	3.56398182644E-6	0.386453815928	0.0346133871504	-0.0157323077672	0.334564443478	0.043690663425	0.4303951788	17.7259208223	-9.40928653219	7.24090376798
2	0.409926567582	0.15370961291	-0.172391517854	0.392054776163	0.06480452626	0.0387047455974	0.21245866588	1.00261701875	0.129817603331	-0.863868058527	-0.26204475535	0.413999819344	-0.531815575895	-0.426401121484	0.00921660345409	0.488494265041	0.0688874880903	-0.0878436019322	0.488551946475	0.0353419059105	0.474005930998	10.2861362135	-10.5307548202	-2.05049777844
3	0.531575100234	-0.0881701173991	0.430229295102	0.849616951849	-0.383186547823	1.62876388115	0.155675869396	-0.271863390672	0.351653985159	0.276733344911	-0.0802315410548	-0.0470229410328	-0.235238302992	-0.0613430125678	-9.23095543274E-6	0.380696315899	-0.0285273423839	0.0420617518951	0.36848103356	-0.0810942387637	0.378532586308	19.1481276537	-9.17342623752	21.3250261922
4	0.169824115069	-0.0588424817235	-0.0203668642701	-0.145130162871	0.131081167612	0.290947706553	-0.168171793747	-0.596686153926	-0.068991426603	0.0905594139741	0.486891207203	-0.0920567119789	0.310289260895	0.169909856101	0.00110656047549	0.425260384659	0.0386996584619	0.0481949395837	0.397843625533	0.0593158435082	0.539721387012	17.9624026794	-32.3497689078	16.0035133214
5	0.737881369622	-0.413013485465	-0.575645296103	0.403916710185	0.0874240851703	0.441172041788	-1.89894278112E-5	-0.215185663311	-0.0543879111492	0.205425724	0.0167092043722	-0.0473189674191	0.196361658251	-0.0289185003735	-6.31771497014E-6	0.439345901551	0.0153618136311	0.0337633497348	0.367742253439	0.0341627800586	0.384611144175	21.4803833939	-27.8101102639	16.0481395698
6	0.030168197568	0.0353647745928	-0.0795681431225	0.0327589417072	-0.0662713824949	0.042557930084	0.64754508773	-0.967805295635	-0.210964640042	0.273927140163	-0.274737618291	-0.63163067423	0.201487830942	0.177816537202	0.00029650224548	0.562770506586	0.00380335254447	-0.0433090043109	0.531666097387	0.0606896771426	0.393121510503	28.832305313	-24.1585814922	26.756334847
7	0.288186333148	-0.0471934961308	-0.027008777452	0.10396170681	-0.015547397101	-0.0117416914009	-0.112319875209	-0.447694998637	0.358419106362	0.105830502224	-0.0784037818972	0.486561902735	0.680816355827	0.171330596459	-0.0129039831074	0.528062314429	0.0576452784016	0.0269800403736	0.652379506387	0.0894250780207	0.3844118784	20.5538232694	-32.5922637761	26.378366025
8	0.158721434926	0.0712061944706	-0.0419068963557	0.240741157388	0.199188710523	0.132058337233	0.188065701629	0.156319118173	-0.272416209254	-0.316350207722	0.230027745223	0.671283054145	0.568382867313	-0.555267412742	0.000489045074571	0.555460220048	-0.169514741356	-0.00966780423167	0.465931662383	-0.0478191145442	0.546275690469	13.1492152938	-34.3616490004	3.62785334137
9	0.103224304398	0.0639283320421	0.145168498553	0.767887109454	0.492375296265	0.227753941803	0.385253032729	-0.448364821933	0.227450989503	-0.175398764909	-0.0728377292897	0.145710687666	-0.0341196418909	0.240318970165	0.000384761601799	0.34760331716	-0.0344223445549	-0.00399272699354	0.329098286849	-0.015585638905	0.392934936016	9.96194232406	-25.7475511823	4.41234926733
10	0.0197884604605	-0.0119290650814	0.00354339427244	0.0223010333867	0.0271838559826	0.179045753077	0.0537926646424	-0.131822175149	-0.34640283776	0.247574687768	-0.211992214392	0.321095163765	0.954275931988	-1.00027662471	0.001413509664	0.399703130314	-0.0618084304738	0.0903730405967	0.746250088052	0.0385499320626	0.604506354213	2.92614490426	-21.4266853745	22.5840659288
11	0.783852790268	0.606440523881	-0.710230636773	0.92578950315	-0.524439115905	0.63770923699	-0.277553872216	0.2484316718	0.0249208645717	0.187429116622	0.0523339964502	-0.479494351764	-0.728755038892	-0.594207126477	-0.0515961588014	0.505808399672	0.135372304933	-0.139576664725	1.08714848618	-0.0829734556619	0.494588068065	36.5869845373	-21.5584256141	32.4178503506
12	0.0583694560146	-0.0225582020378	0.00930388292787	0.127566342005	-0.0328747159584	0.0238572343287	1.01950278558	0.111099565626	0.713822438292	0.208500364515	-0.941091017793	-0.589181619377	0.886636139834	0.341615929393	-0.00275969512118	0.703995032737	0.0367041269992	0.0858470233078	0.800234213892	0.029843963794	0.497600019154	41.7662780663	-27.5608239047	26.6356368479
13	1.39508473721	0.30076213526	1.07112579036	0.903561715723	0.304565955823	1.00213326033	-0.359358040947	-0.770598329988	0.17826823102	0.435571756567	-0.588657022162	0.512360027301	0.224453008127	-1.76616909633	-0.308880342509	0.604209023495	0.0976802494361	0.0586613512296	0.695892342991	-0.103992843606	0.394321039941	43.358065176	-18.6510835053	36.5733098423
14	0.37819057611	0.273423901435	-0.290206314894	0.623795202405	-0.191727614029	0.447809624476	-0.297144809417	0.0302393116675	0.535635470201	-0.262020330588	-0.506894042599	0.0976151818418	-0.143102302968	-0.821034509676	-0.00588516382977	0.486526978264	0.16756416344	-0.0713875180237	0.843152842099	-0.0412305846185	0.500320994509	42.9837849823	-19.2592219673	30.750625588
15	0.0260551883658	-0.0690030799222	-0.00289220263889	0.713691797222	-0.0219134488979	0.0192288583628	0.264039419008	-0.265480858574	-0.0554793646897	-0.73960667388	-0.563287442774	0.0658926400173	-0.579952289749	-0.473152955011	0.00150664583666	0.806820755019	-0.0401963942502	-0.121088647809	1.03938739296	0.0299676852119	0.520051082307	14.4229662305	-14.3643970118	-14.3931788059
16	0.96346026239	0.269540458129	-0.762566590218	0.334537582979	-0.288914404591	0.539929384481	-0.444126387903	0.137094437796	-0.472820147198	-1.05392676556	-0.866364836172	-0.183104799579	0.0497081631853	-0.485151347048	-0.106620473186	0.769522218879	-0.0486655147499	-0.168509678438	0.9595300661	0.021923450592	0.600521914001	7.2771608688	-17.6184296487	-21.3115762807
17	0.296905946371	-0.0392745278075	0.0516084747459	0.0363451117516	-0.228229915593	0.221728819308	-0.536308648567	-0.0597154840911	-0.650629080996	-0.405355413407	0.0605543220816	0.00636723235986	1.08275518183	0.128835941787	-0.00692718174484	0.838494586112	-0.0553521493401	-0.0378646012876	0.772792594731	-0.0284270701674	0.684941411263	10.486357657	-19.5652677108	-14.6874009099

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 57 through 123 )	B	C	57 - 123	1 - 67
2	2	chain 'B' and (resid 124 through 149 )	B	C	124 - 149	68 - 84
3	3	chain 'B' and (resid 150 through 208 )	B	C	150 - 208	85 - 140
4	4	chain 'D' and (resid 57 through 68 )	D	J	57 - 68	1 - 12
5	5	chain 'D' and (resid 69 through 123 )	D	J	69 - 123	13 - 67
6	6	chain 'D' and (resid 124 through 132 )	D	J	124 - 132	68 - 76
7	7	chain 'D' and (resid 133 through 149 )	D	J	133 - 149	77 - 85
8	8	chain 'D' and (resid 150 through 168 )	D	J	150 - 168	86 - 104
9	9	chain 'D' and (resid 169 through 195 )	D	J	169 - 195	105 - 127
10	10	chain 'D' and (resid 196 through 210 )	D	J	196 - 210	128 - 142
11	11	chain 'A' and (resid 223 through 227 )	A	A	223 - 227	1 - 5
12	12	chain 'A' and (resid 228 through 239 )	A	A	228 - 239	6 - 15
13	13	chain 'A' and (resid 240 through 255 )	A	A	240 - 255	16 - 31
14	14	chain 'A' and (resid 256 through 269 )	A	A	256 - 269	32 - 45
15	15	chain 'C' and (resid 222 through 239 )	C	F	222 - 239	1 - 16
16	16	chain 'C' and (resid 240 through 255 )	C	F	240 - 255	17 - 32
17	17	chain 'C' and (resid 256 through 273 )	C	F	256 - 273	33 - 50

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Protein , 1 types, 4 molecules ABCD

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