PDB-4f75: Crystal Structure of active HIV-1 Protease in Complex with the N ...

ID or keywords:

Entry

Database: PDB / ID: 4f75

Title

Crystal Structure of active HIV-1 Protease in Complex with the N terminal product of the substrate RH-IN

Components

C terminal product of substrate RH-IN
N terminal product of substrate RH-IN
Protease

Keywords

hydrolase/hydrolase product / HIV-1 protease / substrate complex / AIDS / product complex / Aspartyl protease / HYDROLASE / hydrolase-hydrolase product complex

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

HIV-1 M:B_ARV2/SF2 (virus)

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Schiffer, C.A. / Mittal, S. / Nalam, M.N.L.

Citation

Journal: To be Published
Title: Crystal Structure of active HIV-1 Protease in Complex with the N terminal product of the substrate RH-IN
Authors: Mittal, S. / Nalam, M.N.L. / Schiffer, C.A.

History

Deposition	May 15, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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Download

PDBx/mmCIF format	4f75.cif.gz	99.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4f75.ent.gz	78.6 KB	Display	PDB format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/4f75 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/4f75	HTTPS FTP

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Related structure data

Related structure data	4f73 4f74 4f76
Similar structure data	2nxl-d 6oxz-d 3r4b-d 3bgc-d 6dh7-d 2rkg-d 6uwc-d 5kr2-3 6pjf-d 1zpa-1 3bgb-d 4mc1-d 2nxd-d 6oot-d 2psv-d 4rvx-1 4q1y-d 4q1x-d 4i8z-d 2zga-1 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	#6 - Jun 2000 HIV-1 Protease similarity (2) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Protease

B: Protease

C: N terminal product of substrate RH-IN

D: C terminal product of substrate RH-IN

hetero molecules

23 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)	50.783, 58.108, 61.797
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

biological unit is the same as asym.

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Protein , 1 types, 2 molecules AB

#1: Protein	Protease Mass: 10801.763 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: SF2 / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: P03369, HIV-1 retropepsin

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Protein/peptide , 2 types, 2 molecules CD

#2: Protein/peptide	N terminal product of substrate RH-IN Mass: 643.862 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: N-terminal of the synthetic peptide corresponding to RH-IN cleavage site Source: (synth.) Human immunodeficiency virus 1
#3: Protein/peptide	C terminal product of substrate RH-IN Mass: 563.644 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: C-terminal of the synthetic peptide corresponding to RH-IN cleavage site Source: (synth.) Human immunodeficiency virus 1

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Non-polymers , 3 types, 122 molecules

#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 120 / 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 Å³/Da / Density % sol: 38.46 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-31% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 14-BM-C / Wavelength: 0.9 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection

Resolution: 1.65→50 Å / Num. obs: 22603 / % possible obs: 99.7 % / Redundancy: 7.8 % / R_merge(I) obs: 0.058 / Χ²: 1.037 / Net I/σ(I): 11.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.65-1.71	7.9	0.525	2219	1.137	1	99.7
1.71-1.78	8	0.364	2223	1.063	1	99.9
1.78-1.86	8	0.261	2221	1.056	1	99.9
1.86-1.96	7.9	0.169	2229	1.022	1	100
1.96-2.08	7.9	0.114	2241	1.008	1	100
2.08-2.24	7.9	0.085	2260	1.004	1	100
2.24-2.46	7.9	0.071	2243	1.023	1	100
2.46-2.82	7.8	0.058	2286	1.016	1	100
2.82-3.55	7.7	0.049	2295	1.033	1	100
3.55-50	7.1	0.027	2386	1.004	1	97.9

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→42.33 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.957 / WR_factor R_free: 0.1933 / WR_factor R_work: 0.1716 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.881 / SU B: 4.433 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1104 / SU R_free: 0.1006 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1934	1053	5.1 %	RANDOM
R_work	0.1699	-	-	-
obs	0.1711	20581	99.35 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 57.87 Å² / B_iso mean: 23.0717 Å² / B_iso min: 10.29 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1 Å²	0 Å²	0 Å²
2-	-	-0.11 Å²	0 Å²
3-	-	-	1.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→42.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1540	0	10	120	1670

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1670
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1137
X-RAY DIFFRACTION	r_angle_refined_deg	1.344	1.994	2277
X-RAY DIFFRACTION	r_angle_other_deg	0.835	3	2800
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.434	5	219
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.606	24.237	59
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.19	15	289
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.06	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	267
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	1864
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	307
X-RAY DIFFRACTION	r_mcbond_it	0.581	1.5	1067
X-RAY DIFFRACTION	r_mcbond_other	0.177	1.5	444
X-RAY DIFFRACTION	r_mcangle_it	0.973	2	1736
X-RAY DIFFRACTION	r_scbond_it	1.676	3	603
X-RAY DIFFRACTION	r_scangle_it	2.651	4.5	541

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.215	58	-
R_work	0.196	1423	-
all	-	1481	-
obs	-	-	99.53 %

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	6.1856	5.7179	-3.7208	11.085	-4.7818	6.5306	-0.1849	0.4039	-0.2001	-0.5682	0.1604	-0.2358	0.0004	-0.0154	0.0245	0.1676	-0.0115	-0.0272	0.1471	-0.0423	0.0467	20.7857	1.5511	-1.8274
2	20.4702	-0.2674	8.7705	3.934	3.6612	7.4045	0.0099	0.4203	-0.7773	-0.0465	0.062	0.2344	0.0178	0.2228	-0.0719	0.2248	-0.0093	0.0903	0.0595	-0.0488	0.1206	24.8291	-4.4525	3.7459
3	16.3933	2.9933	14.3606	0.6125	2.9585	14.6804	-0.1863	0.7123	0.3252	-0.0662	0.1021	-0.042	-0.2229	0.4665	0.0842	0.0789	0.0247	0.1229	0.064	0.0401	0.424	39.9635	-0.3436	8.0521
4	24.4078	-4.4846	-3.9288	2.96	1.7777	2.8416	0.0356	-0.0391	-0.5563	-0.0492	0.0105	-0.3695	0.2711	0.1881	-0.0461	0.1387	0.0154	0.0227	0.0435	-0.0052	0.1353	35.4611	-4.4083	8.3197
5	7.871	-2.3541	-1.7576	3.5138	1.9506	9.99	-0.075	-0.0534	-0.0396	0.1385	0.0389	-0.0733	0.2165	0.0712	0.0361	0.0359	-0.0041	0.0121	0.0023	-0.0032	0.0105	23.3926	4.153	12.6315
6	15.2124	-12.2474	0.7369	27.09	-5.1741	4.172	-0.1966	-0.4694	-0.255	0.4456	0.2617	-0.2727	0.1487	0.1038	-0.0651	0.0365	-0.0158	-0.0203	0.0921	0.0082	0.0287	32.1957	-1.943	17.6658
7	5.9285	-0.4288	-5.0551	6.2076	4.9047	9.2578	-0.0076	-0.4646	-0.0815	0.0661	0.0486	-0.404	0.03	0.6595	-0.041	0.1118	0.0164	-0.0425	0.2235	0.0601	0.1751	41.136	-0.015	23.5312
8	17.443	3.98	10.5369	7.2818	5.4532	13.2446	-0.4132	0.0952	0.9415	-0.1663	0.1269	0.3481	-0.2083	0.1124	0.2863	0.1207	-0.0337	0.0065	0.0605	0.011	0.0906	24.6848	0.347	25.503
9	12.9896	6.8739	0.418	7.3718	-2.5269	6.2727	-0.0333	-0.1007	-0.4268	0.2351	-0.0211	-0.0718	0.0077	0.1742	0.0543	0.1126	0.0184	-0.0086	0.063	-0.0135	0.049	28.1531	-2.744	26.6303
10	3.0273	3.652	-4.0732	7.1809	-8.6651	14.2527	0.2191	-0.2779	0.1327	0.3252	-0.3213	-0.0872	-0.305	0.3205	0.1022	0.0286	-0.0251	-0.0275	0.1044	-0.0034	0.1231	39.3599	6.4	19.6528
11	7.2704	-1.4388	4.1151	14.7771	-7.9117	14.8319	0.0295	0.777	-0.1528	-0.5285	-0.0349	-0.25	-0.2395	0.5305	0.0054	0.096	0.0143	0.0615	0.1313	-0.0354	0.1098	36.8728	6.271	4.6009
12	1.2617	2.514	-2.8983	8.3109	-6.7853	6.9736	-0.0398	-0.0704	0.0396	-0.0109	0.0403	-0.1429	0.0683	0.0994	-0.0005	0.0265	-0.0124	-0.038	0.065	-0.0095	0.0974	35.5116	4.4432	17.5736
13	0.5922	2.4703	-1.7439	11.7104	-4.9809	9.0141	-0.0669	0.0185	0.0922	-0.1032	0.1453	0.5538	0.6101	-0.0302	-0.0784	0.0619	0.0121	0.0134	0.0614	0.0483	0.1149	28.422	-5.4705	16.2281
14	5.6512	1.7505	-2.046	5.5618	-1.7586	3.4601	-0.0492	-0.01	0.22	-0.0834	0.0091	-0.1673	-0.2518	0.0369	0.0402	0.0367	-0.0085	-0.0021	0.0265	-0.0026	0.0305	29.3112	9.1247	10.7679
15	13.1231	5.0349	4.9513	4.799	2.9306	6.723	-0.2738	0.1287	0.1766	-0.158	0.0388	0.3168	-0.2167	-0.1304	0.235	0.1284	-0.013	-0.018	0.0668	0.0145	0.045	18.6065	10.4451	2.7808
16	8.9075	3.845	10.6022	3.1923	3.3094	13.7032	-0.6605	-0.1605	0.6041	-0.5162	0.122	0.488	-0.685	-0.3931	0.5384	0.2352	0.0686	-0.0446	0.1383	-0.0062	0.121	20.4956	14.781	7.4328
17	17.9489	2.7872	2.2764	1.6038	1.259	0.9921	-0.1318	-0.1349	0.5492	0.0313	-0.068	0.2494	0.0073	-0.0687	0.1998	0.1011	0.0344	0.0067	0.0779	-0.0111	0.1033	12.9574	10.3567	13.5548
18	16.8555	5.7786	-0.308	2.5416	1.1973	3.065	0.1205	-0.4961	0.5943	0.1164	-0.4835	0.4007	0.0717	-0.7119	0.363	0.2533	0.0655	0.111	0.2613	0.024	0.3343	-1.1762	6.0488	12.9205
19	13.4347	-6.233	-5.923	4.3512	2.8257	6.3374	-0.1139	-0.2647	0.2222	0.1945	0.1198	0.187	-0.0063	-0.1825	-0.006	0.0552	-0.0152	0.0048	0.0443	-0.0034	0.0782	12.3915	5.7989	12.7977
20	15.4809	-0.525	-9.4194	2.4314	-0.8187	6.5776	0.0108	-0.1315	-0.2357	0.0533	0.0063	0.0985	0.1152	-0.0015	-0.0172	0.0861	-0.0196	-0.0478	0.0573	0.0326	0.0593	11.7635	-2.4945	13.4584
21	19.8826	9.8477	16.6653	8.1029	7.7828	18.5957	0.0245	-0.467	0.3054	0.0139	-0.2254	0.7515	0.0282	-0.4782	0.2008	0.1406	0.0379	0.0309	0.2257	0.0209	0.1939	-1.2902	-2.9539	19.0109
22	9.1552	-3.8496	6.0321	8.828	2.1814	7.0929	0.0942	-0.2418	-0.5723	0.0072	-0.0887	0.7514	0.0929	-0.3534	-0.0055	0.0853	-0.0526	-0.0376	0.178	0.0432	0.1855	2.5036	-12.786	15.8673
23	23.9476	15.0503	7.081	11.9785	7.78	6.4994	-0.1613	0.1846	-0.0978	-0.0423	0.2122	-0.0515	0.0009	0.2458	-0.0508	0.0942	-0.0496	-0.0186	0.1143	-0.0033	0.0527	18.0693	-8.6434	19.7884
24	12.0202	-1.0093	3.0899	4.9338	-3.5156	3.2384	0.1945	-0.2362	0.0233	0.0338	-0.0783	0.1025	-0.067	-0.0837	-0.1162	0.0522	0.0057	0.0185	0.0636	-0.0124	0.0555	10.3344	-10.2163	20.7698
25	6.1435	-4.2698	6.2187	9.2483	-7.359	11.627	0.2013	0.2424	-0.3308	-0.485	0.0184	0.088	0.3578	-0.1586	-0.2197	0.0503	-0.0364	-0.0265	0.0951	0.0306	0.1209	1.3968	-6.7198	9.2754
26	13.0883	4.8803	-8.0105	3.4989	-7.0757	17.0891	0.0835	0.0323	0.5002	-0.1907	-0.0666	0.3212	-0.2815	-0.189	-0.0169	0.3489	0.0759	-0.1998	0.1533	-0.1015	0.2476	5.0257	7.6645	4.6467
27	4.5055	-1.5481	5.503	4.3428	-5.7933	10.7193	-0.0955	-0.1412	0.0797	0.0217	0.2319	0.2014	-0.114	-0.3654	-0.1364	0.0669	-0.0008	0.0031	0.0679	0.0056	0.0709	4.2739	-2.2032	6.7127
28	2.431	2.4611	-1.9258	6.8184	-2.4083	1.7032	0.3374	-0.3704	0.0297	0.61	-0.2122	0.0256	-0.3285	0.3134	-0.1253	0.1164	-0.0384	0.0237	0.1396	-0.005	0.095	10.37	-0.4947	19.6592
29	4.0598	-0.3006	0.3682	3.2446	-0.261	3.933	-0.0515	0.299	-0.0406	-0.2253	-0.0229	0.3507	0.0412	-0.1535	0.0744	0.0543	-0.0241	-0.0261	0.0528	0.0009	0.0451	11.8841	0.4218	3.9279
30	26.3018	8.1913	5.0154	8.4641	-1.0128	2.0798	-0.3054	0.3842	-0.0787	-0.4698	0.2481	-0.2027	0.103	0.0348	0.0573	0.1416	-0.0413	0.0129	0.1512	-0.0364	0.0159	22.9496	7.2771	0.732

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 6
2	X-RAY DIFFRACTION	2	A	7 - 11
3	X-RAY DIFFRACTION	3	A	12 - 17
4	X-RAY DIFFRACTION	4	A	18 - 23
5	X-RAY DIFFRACTION	5	A	24 - 29
6	X-RAY DIFFRACTION	6	A	30 - 35
7	X-RAY DIFFRACTION	7	A	36 - 44
8	X-RAY DIFFRACTION	8	A	45 - 50
9	X-RAY DIFFRACTION	9	A	51 - 57
10	X-RAY DIFFRACTION	10	A	58 - 63
11	X-RAY DIFFRACTION	11	A	64 - 70
12	X-RAY DIFFRACTION	12	A	71 - 78
13	X-RAY DIFFRACTION	13	A	79 - 84
14	X-RAY DIFFRACTION	14	A	85 - 94
15	X-RAY DIFFRACTION	15	A	95 - 99
16	X-RAY DIFFRACTION	16	B	1 - 6
17	X-RAY DIFFRACTION	17	B	7 - 13
18	X-RAY DIFFRACTION	18	B	14 - 19
19	X-RAY DIFFRACTION	19	B	20 - 26
20	X-RAY DIFFRACTION	20	B	27 - 34
21	X-RAY DIFFRACTION	21	B	35 - 39
22	X-RAY DIFFRACTION	22	B	40 - 45
23	X-RAY DIFFRACTION	23	B	46 - 52
24	X-RAY DIFFRACTION	24	B	53 - 57
25	X-RAY DIFFRACTION	25	B	58 - 63
26	X-RAY DIFFRACTION	26	B	64 - 69
27	X-RAY DIFFRACTION	27	B	70 - 76
28	X-RAY DIFFRACTION	28	B	77 - 84
29	X-RAY DIFFRACTION	29	B	85 - 94
30	X-RAY DIFFRACTION	30	B	95 - 99

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