PDB-4f74: Crystal Structure of active HIV-1 Protease in Complex with the N ...

ID or keywords:

Entry

Database: PDB / ID: 4f74

Title

Crystal Structure of active HIV-1 Protease in Complex with the N terminal product of the substrate MA-CA.

Components

N terminal product of substrate MA-CA
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 / 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 / viral penetration into host nucleus ...
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 /

molecular replacement / Resolution: 2.2 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 MA-CA.
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 / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4f74.cif.gz	91 KB	Display	PDBx/mmCIF format
PDB format	pdb4f74.ent.gz	71.6 KB	Display	PDB format
PDBx/mmJSON format	4f74.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4f74_validation.pdf.gz	426 KB	Display	wwPDB validaton report
Full document	4f74_full_validation.pdf.gz	426.7 KB	Display
Data in XML	4f74_validation.xml.gz	10.2 KB	Display
Data in CIF	4f74_validation.cif.gz	13.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/4f74 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/4f74	HTTPS FTP

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Related structure data

Related structure data	4f73 4f75 4f76
Similar structure data	6dgx-d 6dgz-d 4eq0-d 2nxd-d 3sa6-d 3o9c-d 6pjd-d 6pji-d 4m8y-d 4q1y-d 3i7e-d 2nxl-d 2nxm-d 2psv-d 3sa9-d 6opu-d 3dox-d 4hvp-d 4rvx-1 2r3w-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	#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 MA-CA

22.2 kDa, 3 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)	50.675, 58.240, 61.600
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.

#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
#2: Protein/peptide	N terminal product of substrate MA-CA Mass: 609.629 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: synthetic peptide corresponding to MA-CA cleavage site Source: (synth.) Human immunodeficiency virus 1
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.05 Å³/Da / Density % sol: 39.88 %
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: 2.2→50 Å / Num. obs: 9711 / % possible obs: 100 % / Redundancy: 7.6 % / R_merge(I) obs: 0.084 / Χ²: 1.04 / Net I/σ(I): 10.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.2-2.28	7.9	0.23	944	1.095	1	100
2.28-2.37	7.9	0.208	927	1.004	1	100
2.37-2.48	7.9	0.183	958	1.002	1	100
2.48-2.61	7.8	0.157	947	1.068	1	100
2.61-2.77	7.8	0.131	974	1.063	1	100
2.77-2.99	7.7	0.11	956	1.038	1	100
2.99-3.29	7.7	0.093	967	1.091	1	100
3.29-3.76	7.6	0.078	976	1.011	1	100
3.76-4.74	7.2	0.047	1000	1.005	1	100
4.74-50	7	0.037	1062	1.018	1	99.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→42.32 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.931 / WR_factor R_free: 0.1926 / WR_factor R_work: 0.1624 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.859 / SU B: 10.066 / SU ML: 0.133 / SU R Cruickshank DPI: 0.2881 / SU R_free: 0.1951 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2069	463	4.8 %	RANDOM
R_work	0.1653	-	-	-
obs	0.1672	9627	99.35 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 66 Å² / B_iso mean: 23.3631 Å² / B_iso min: 10.58 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.11 Å²	0 Å²	0 Å²
2-	-	0.42 Å²	0 Å²
3-	-	-	0.69 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→42.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1524	0	0	97	1621

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1552
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1037
X-RAY DIFFRACTION	r_angle_refined_deg	1.479	1.983	2114
X-RAY DIFFRACTION	r_angle_other_deg	0.894	3	2555
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.58	5	199
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.079	24.912	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.881	15	259
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.891	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	252
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	1705
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	275

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.272	40	-
R_work	0.148	620	-
all	-	660	-
obs	-	-	97.2 %

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	5.765	2.695	-3.7661	8.7475	-3.8007	8.0455	-0.1014	0.5687	0.0513	-0.2709	0.1274	0.0596	-0.0968	-0.1061	-0.0261	0.1737	-0.0281	-0.0296	0.1425	-0.0226	0.0616	20.7368	1.7562	-1.989
2	18.5199	-3.7669	5.9511	0.7697	-1.2078	1.9159	0.2204	0.1934	-0.9627	-0.0167	0.0293	0.1902	0.0792	0.0742	-0.2497	0.29	-0.0038	0.033	0.156	-0.0356	0.1786	26.8702	-3.702	3.6629
3	30.8408	-12.0369	11.2174	7.3972	0.8093	14.6023	0.2531	0.7216	0.4478	-0.3122	-0.0068	-0.5948	-0.1279	0.7417	-0.2463	0.179	-0.0264	0.1424	0.0886	-0.0191	0.358	41.6181	-0.9419	8.9379
4	21.8374	-7.6709	-1.9202	6.6569	-1.9487	1.9076	-0.151	-0.1094	-0.35	-0.3876	0.0802	0.0104	0.307	-0.0397	0.0708	0.219	0.0039	-0.0261	0.1066	-0.0143	0.1373	32.2973	-3.2641	7.3669
5	3.8627	-2.4885	3.9615	3.6971	0.395	8.2132	0.0096	-0.0978	0.0327	0.1061	0.0964	-0.1168	0.1886	-0.0301	-0.106	0.0606	0.0042	0.0288	0.0728	-0.0032	0.0514	23.6385	4.6946	14.9314
6	12.273	-9.7101	2.0054	34.3497	-5.7748	7.145	0.0095	-0.2239	-0.4017	0.2815	-0.091	-0.2257	0.4555	0.1358	0.0815	0.0591	-0.0212	-0.0063	0.0801	0.0046	0.0471	32.8829	-3.7299	17.2345
7	6.8274	3.6904	-1.807	5.6964	5.1652	10.7868	0.1309	-0.2232	-0.0599	0.0015	0.1843	-0.3218	-0.0794	0.6604	-0.3152	0.065	0.0684	0.024	0.1544	0.0817	0.2526	42.2144	-1.0254	21.8573
8	8.4308	3.8921	2.2216	2.7808	0.4447	2.466	-0.0345	-0.2646	-0.2066	0.0434	-0.0247	-0.1909	0.0072	-0.0873	0.0592	0.0915	0.0092	0.0106	0.0677	-0.0044	0.0558	25.7924	-0.6287	26.017
9	12.4253	4.8943	-4.2483	3.619	-2.1651	4.2494	0.2194	-0.1419	-0.1555	0.3042	-0.1661	-0.1087	0.0092	0.2105	-0.0533	0.092	0.0004	-0.0197	0.0571	-0.005	0.0328	30.5122	-1.5096	26.3941
10	4.4837	2.7229	-0.0152	5.2564	-0.4111	10.5195	0.0512	-0.3292	0.1382	0.1849	-0.1502	-0.0203	-0.4506	0.4137	0.099	0.0559	0.0066	-0.0093	0.0628	-0.0093	0.0923	39.7609	6.1755	17.4453
11	19.3885	0.1253	3.6403	12.6548	-0.3141	11.6601	-0.1391	0.9639	0.1938	-0.7098	0.0816	-0.2353	-0.0565	0.746	0.0574	0.0828	0.0102	0.0507	0.1254	0	0.0712	36.6229	6.5197	3.7102
12	1.2003	0.923	-0.4104	5.2493	-0.0056	0.1618	0.054	-0.2314	0.1098	0.3042	-0.0124	-0.0062	-0.0034	0.0936	-0.0417	0.052	-0.013	-0.0188	0.0903	-0.0024	0.0918	35.7126	5.0443	17.1579
13	3.965	1.5225	-1.6269	4.5963	1.9209	2.3784	-0.2007	0.0718	-0.1186	0.111	0.1558	0.0329	0.4188	-0.0071	0.0449	0.459	-0.0599	-0.1205	0.0989	0.0551	0.1716	28.7144	-6.6121	16.9
14	4.1276	1.5927	1.0926	1.1715	1.094	1.101	0.0249	0.0759	0.0802	0.0019	0.0376	-0.0406	-0.0045	0.0262	-0.0625	0.0618	-0.0019	0.0089	0.0558	0.0001	0.053	29.1217	8.1194	11.0875
15	17.2327	5.5683	9.0001	3.6931	-0.7859	11.9088	-0.1361	-0.1806	0.5473	-0.1424	0.0066	0.268	0.1199	-0.2153	0.1294	0.1573	-0.0009	0.0123	0.0258	-0.0307	0.1067	18.5721	10.503	2.8588
16	4.0158	4.0996	2.6452	4.2562	3.127	4.9439	-0.402	-0.0496	0.6149	-0.4995	-0.052	0.5815	-0.6364	-0.2915	0.454	0.2318	0.0569	-0.0387	0.1808	-0.0117	0.2831	20.3526	14.7859	7.5985
17	11.6226	0.7836	-0.99	0.4073	0.9566	3.0412	0.1038	-0.3665	-0.0478	0.0455	-0.005	-0.0292	0.0957	0.1157	-0.0988	0.1189	0.0212	0.013	0.0609	-0.0051	0.1431	14.3587	10.7168	13.8901
18	20.8675	6.1545	-16.0201	20.4079	-2.2936	12.617	-0.0389	0.2602	0.1658	-0.1289	-0.0948	1.6015	0.0672	-0.2281	0.1337	0.1212	0.023	-0.0145	0.2963	0.0104	0.1599	-0.2925	5.2515	12.2997
19	26.2039	-4.972	-7.667	1.9199	1.134	6.8415	0.0789	-0.6325	0.8095	0.3173	-0.0178	-0.1352	-0.4687	-0.0526	-0.0611	0.2039	0.0301	0.0262	0.1432	-0.0734	0.1595	8.4547	7.6791	13.9728
20	5.1622	4.0466	-1.2509	8.1933	0.0289	10.058	0.0871	-0.238	-0.5994	0.0914	-0.1362	-0.1088	0.463	0.0708	0.049	0.0491	0.009	-0.0083	0.0614	0.0011	0.1294	17.0602	-2.3563	9.5036
21	17.6967	-1.4729	-14.5069	7.6197	2.4979	24.0888	0.2229	-0.4817	0.41	0.248	0.241	0.1214	-0.468	-0.3624	-0.4639	0.0713	0.006	-0.0212	0.0768	0.0142	0.054	7.0746	-1.3918	17.5358
22	4.9598	2.3441	2.747	12.6489	5.4108	6.6408	0.2326	-0.1496	-0.2113	0.3027	-0.2754	0.5162	-0.0072	-0.2452	0.0428	0.1555	0.0243	-0.0134	0.2069	0.0703	0.1775	-2.9349	-5.0668	16.5116
23	27.6432	-2.6569	3.3367	3.1729	0.1927	5.8624	0.0664	-0.6307	-0.248	-0.1168	0.1646	0.4288	0.1163	-0.4758	-0.231	0.1015	0.0003	-0.0225	0.0574	0.0495	0.0999	5.8367	-13.7195	16.5497
24	11.3763	4.9549	-3.3069	4.5706	-0.2699	1.5292	-0.0054	-0.0612	-0.0315	0.0135	-0.07	0.1242	0.0055	-0.0027	0.0754	0.0877	-0.0107	-0.0162	0.052	0.012	0.0726	18.9549	-8.7233	19.9287
25	12.1396	0.9495	4.6085	6.7076	2.5219	7.3856	0.2719	-0.4428	-0.3354	0.1398	0.1271	0.1927	0.4542	-0.3518	-0.399	0.0675	-0.0257	0.0088	0.0399	0.0184	0.0887	7.4748	-10.1798	18.7827
26	13.6573	-7.0838	3.5353	9.5528	-9.103	14.6226	0.4083	0.212	-0.5139	-0.6765	-0.264	0.0994	0.3468	0.2114	-0.1443	0.1072	-0.0324	-0.0168	0.1042	0.0153	0.1102	0.6669	-5.9492	8.3776
27	2.1708	2.0225	-3.7594	11.2969	-8.4083	17.4328	-0.0701	-0.3484	0.2805	-0.3828	-0.0581	0.2013	-0.2776	0.2143	0.1282	0.0828	0.0129	-0.0348	0.0906	-0.0291	0.1562	4.9436	7.66	4.6877
28	2.4698	-0.5846	3.075	12.3891	-9.5338	10.1698	0.073	-0.0031	-0.1057	0.1781	0.2007	0.2989	-0.0762	-0.1353	-0.2738	0.0661	0.0067	0.0012	0.0927	0.0002	0.1312	3.6009	-1.4545	5.0207
29	1.1787	0.596	-1.1065	8.169	0.4582	1.1724	0.2028	-0.271	-0.1542	0.4671	-0.2892	-0.1322	-0.1858	0.2422	0.0864	0.1603	-0.0441	0.0039	0.2128	0.0259	0.1477	9.0464	-3.6906	19.9171
30	4.2973	0.5857	-2.9855	3.914	2.2065	3.8571	0.0516	-0.1721	0.2083	0.2525	0.1349	-0.0283	0.1418	0.2193	-0.1865	0.0751	0.0165	-0.0096	0.0736	0.0261	0.0643	12.8074	0.7382	11.9979
31	1.4835	-0.2544	1.4563	3.9645	-1.3073	1.9425	-0.1849	0.0962	0.1327	-0.0764	0.1945	0.3733	-0.0709	-0.0625	-0.0096	0.0996	-0.0319	-0.0137	0.1561	0.0217	0.0793	10.7831	1.0674	2.2953
32	23.0971	8.3553	0.2694	4.9283	-2.524	4.2865	-0.2993	0.0193	0.0325	-0.1285	0.1761	-0.1142	0.0441	0.1805	0.1232	0.1156	0.0025	0.0057	0.2342	-0.0423	0.0718	22.8633	7.4108	0.7449

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 - 12
3	X-RAY DIFFRACTION	3	A	13 - 18
4	X-RAY DIFFRACTION	4	A	19 - 24
5	X-RAY DIFFRACTION	5	A	25 - 30
6	X-RAY DIFFRACTION	6	A	31 - 35
7	X-RAY DIFFRACTION	7	A	36 - 42
8	X-RAY DIFFRACTION	8	A	43 - 52
9	X-RAY DIFFRACTION	9	A	53 - 58
10	X-RAY DIFFRACTION	10	A	59 - 64
11	X-RAY DIFFRACTION	11	A	65 - 70
12	X-RAY DIFFRACTION	12	A	71 - 77
13	X-RAY DIFFRACTION	13	A	78 - 83
14	X-RAY DIFFRACTION	14	A	84 - 94
15	X-RAY DIFFRACTION	15	A	95 - 99
16	X-RAY DIFFRACTION	16	B	1 - 6
17	X-RAY DIFFRACTION	17	B	7 - 12
18	X-RAY DIFFRACTION	18	B	13 - 18
19	X-RAY DIFFRACTION	19	B	19 - 24
20	X-RAY DIFFRACTION	20	B	25 - 30
21	X-RAY DIFFRACTION	21	B	31 - 35
22	X-RAY DIFFRACTION	22	B	36 - 41
23	X-RAY DIFFRACTION	23	B	42 - 46
24	X-RAY DIFFRACTION	24	B	47 - 53
25	X-RAY DIFFRACTION	25	B	54 - 58
26	X-RAY DIFFRACTION	26	B	59 - 63
27	X-RAY DIFFRACTION	27	B	64 - 69
28	X-RAY DIFFRACTION	28	B	70 - 75
29	X-RAY DIFFRACTION	29	B	76 - 81
30	X-RAY DIFFRACTION	30	B	82 - 87
31	X-RAY DIFFRACTION	31	B	88 - 94
32	X-RAY DIFFRACTION	32	B	95 - 99

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