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- PDB-3d3t: Crystal Structure of HIV-1 CRF01_AE in complex with the substrate... -

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Basic information

Entry
Database: PDB / ID: 3d3t
TitleCrystal Structure of HIV-1 CRF01_AE in complex with the substrate p1-p6
Components
  • HIV-1 protease
  • P1-P6 SUBSTRATE PEPTIDE
KeywordsHYDROLASE / HIV-1 protease / non-B clades / CRF01_AE / p1-p6 substrate / AIDS / Aspartyl protease
Function / homology
Function and homology information


viral budding via host ESCRT complex / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / symbiont-mediated suppression of host gene expression ...viral budding via host ESCRT complex / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / host cell cytoplasm / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...Retroviral nucleocapsid Gag protein p24, N-terminal / Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / 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 / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsBandaranayake, R.M. / Prabu-Jeyabalan, M. / Kakizawa, J. / Sugiura, W. / Schiffer, C.A.
CitationJournal: J.Virol. / Year: 2008
Title: Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6.
Authors: Bandaranayake, R.M. / Prabu-Jeyabalan, M. / Kakizawa, J. / Sugiura, W. / Schiffer, C.A.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 protease
B: HIV-1 protease
P: P1-P6 SUBSTRATE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)22,7873
Polymers22,7873
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-31.5 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.186, 62.186, 82.099
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsThe protein is homodimeric.

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Components

#1: Protein HIV-1 protease


Mass: 10806.804 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 484-582 / Mutation: D25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NH1 / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: Q90VT5, HIV-1 retropepsin
#2: Protein/peptide P1-P6 SUBSTRATE PEPTIDE


Mass: 1173.325 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 446-455 / Source method: obtained synthetically
Details: This sequence occurs naturally in HIV-1 gag poly-protein
References: UniProt: P12495
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Phosphate buffer, 63mM Sodium Citrate, 18-33% Ammonium Sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 12, 2006
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 4530 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.115 / Χ2: 1.134 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.911.40.4054451.0621100
2.9-3.02110.3394451.1161100
3.02-3.1511.10.274551.2611100
3.15-3.3211.20.1934541.3741100
3.32-3.5311.60.1474441.0271100
3.53-3.811.60.114511.0251100
3.8-4.1811.40.1054601.0321100
4.18-4.7811.30.0834481.1431100
4.78-6.0111.50.0774541.0861100
6.01-2511.10.0664741.2261100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.89 / SU B: 27.193 / SU ML: 0.325 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 312 7 %RANDOM
Rwork0.199 ---
obs0.203 4476 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.844 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 0 16 1494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221502
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9832052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02824.46847
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23115227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.913158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021108
X-RAY DIFFRACTIONr_nbd_refined0.2260.2561
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21011
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.232
X-RAY DIFFRACTIONr_mcbond_it0.4781.51029
X-RAY DIFFRACTIONr_mcangle_it0.82321616
X-RAY DIFFRACTIONr_scbond_it1.1173526
X-RAY DIFFRACTIONr_scangle_it1.8724.5436
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 27 -
Rwork0.248 303 -
all-330 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
111.06524.07985.02339.39528.037414.36260.5571-0.3425-0.76960.1944-0.4027-0.4183-0.32390.4815-0.1544-0.10040.06160.0167-0.01910.05740.059318.9914-30.82110.8586
28.041.77657.77493.6204-4.315718.7965-0.31460.3071-0.39630.02210.1825-0.24470.78690.07950.13210.02960.02410.0789-0.109-0.00740.066116.9479-31.9339-1.0422
315.279-3.29328.70986.5359-15.907638.7527-0.6646-0.7860.53430.3427-0.2374-1.4844-0.33430.50120.9020.0136-0.1025-0.0794-0.0177-0.0302-0.064821.3841-20.61636.0769
417.5542-2.7333-27.198915.160421.641162.7046-0.63250.4990.321-1.13990.19360.81020.1947-0.56010.43890.0631-0.0858-0.0340.0783-0.0158-0.09797.2747-28.8675-6.1362
55.2083-3.4894-1.86785.6239-0.26771.37210.0541-0.3226-0.1056-0.01310.01480.50340.0998-0.3723-0.06890.0704-0.05170.0067-0.01010.0216-0.060513.9365-19.0327-5.2876
618.75314.64042.08621.15360.893126.908-0.80330.7120.87060.62430.1837-0.0127-0.49130.7690.61960.08550.07670.0557-0.21470.11190.070917.3504-7.3869-16.3446
72.4184-1.6503-2.95887.2721-0.86364.9719-0.0620.04610.640.1193-0.02620.2016-0.07570.53380.0882-0.0546-0.01390.00230.0931-0.00850.02819.513-21.62165.184
89.373311.364111.725813.804513.385940.59010.41010.21020.6239-0.2376-0.49071.07950.4289-1.01430.0807-0.13930.13610.1284-0.1290.06950.1041-2.4069-18.905315.4553
922.40597.20241.21043.63142.90964.8921-0.45122.0888-0.7634-0.409-0.39310.9589-0.328-1.04590.8442-0.16350.14970.1220.1110.25370.1585.0263-10.5473-11.4559
1010.177423.56662.500954.57065.7910.61451.3808-1.45130.18770.7836-0.7516-1.0749-3.01152.0123-0.62920.34410.35210.15920.23860.41110.17795.9716-7.4759-8.3015
119.689-2.41857.58540.6037-1.89345.93851.5355-0.29751.10991.2728-0.6699-1.2807-3.86442.6277-0.86560.4882-0.26260.4710.00370.06090.43336.4589-9.769510.9976
1245.2938-6.5316-23.96056.4524-5.56427.43711.9640.20282.61161.41170.4971.2465-2.5728-0.0935-2.46090.1849-0.01060.2103-0.11740.013-0.04424.3623-8.48787.835
1314.7293-17.1313.480224.0236-10.363210.55210.1068-0.0658-0.33721.1580.6986-0.1912-0.2216-0.323-0.8053-0.14030.04050.01620.2550.10180.019714.4867-11.7535-18.875
1420.0484-24.344115.929730.634-21.1309100.19151.4022-1.4641-0.7142-0.1731-0.5837-1.30451.49620.8877-0.8186-0.1224-0.2048-0.113-0.25140.07430.099226.6533-20.6634-12.7885
1531.9915-23.2787-7.832221.56422.09154.7312-0.1125-0.1805-0.1517-0.14180.6614-0.30910.5567-0.3465-0.549-0.0688-0.170.02890.0841-0.0149-0.013319.298-19.2834-15.7976
164.9141-6.7771-5.657117.0546.13936.8710.62250.1912-0.88210.3954-0.0545-0.16150.05850.0812-0.56810.0624-0.03080.0705-0.0993-0.03060.04543.0089-18.393518.7775
1715.80686.12675.21593.5989-6.646163.0921-0.69770.8348-1.92160.5301-0.9137-1.45871.177-1.45921.6113-0.1977-0.0340.0820.1127-0.092-0.03784.5874-32.925612.7664
180.05160.6836-0.526532.8496-4.68135.59580.0079-0.2394-0.3687-0.0805-0.0662-0.34130.1610.11860.0583-0.0401-0.0974-0.0193-0.0440.1181-0.01737.0689-26.311515.6891
199.2174-0.0381-2.79081.2952.05444.068-0.20750.17620.55990.94370.83430.1486-0.7299-0.2974-0.62680.21940.03390.0499-0.02510.01360.035415.52-10.8343-5.5087
200.42581.6481-1.73566.3786-6.71737.07390.66990.34530.5603-0.5476-0.1919-0.1279-0.5127-0.6149-0.4780.1110.07880.00810.0927-0.0260.03381.6526-18.8225.4914
211.85024.9625-2.236316.0929-0.598113.181-0.71240.51130.3532-0.20.6986-0.87370.1859-0.39620.0138-0.11310.02210.02510.0795-0.02240.054815.9832-24.8647-10.773
228.8387-0.3891-7.60124.9406-2.78368.51190.0706-0.9263-0.3910.1425-0.2725-0.22870.1130.48230.2019-0.0099-0.071-0.01480.02280.04890.025913.5589-26.243710.6865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 51 - 5
2X-RAY DIFFRACTION1AA94 - 9994 - 99
3X-RAY DIFFRACTION2BB1 - 51 - 5
4X-RAY DIFFRACTION2BB94 - 9994 - 99
5X-RAY DIFFRACTION3AA6 - 106 - 10
6X-RAY DIFFRACTION4BB6 - 106 - 10
7X-RAY DIFFRACTION5AA22 - 3222 - 32
8X-RAY DIFFRACTION6AA33 - 4333 - 43
9X-RAY DIFFRACTION7BB22 - 3222 - 32
10X-RAY DIFFRACTION8BB33 - 4333 - 43
11X-RAY DIFFRACTION9AA44 - 4944 - 49
12X-RAY DIFFRACTION10AA52 - 5652 - 56
13X-RAY DIFFRACTION11BB44 - 4944 - 49
14X-RAY DIFFRACTION12BB52 - 5652 - 56
15X-RAY DIFFRACTION13AA57 - 6257 - 62
16X-RAY DIFFRACTION14AA63 - 6863 - 68
17X-RAY DIFFRACTION15AA69 - 7669 - 76
18X-RAY DIFFRACTION16BB57 - 6257 - 62
19X-RAY DIFFRACTION17BB63 - 6863 - 68
20X-RAY DIFFRACTION18BB69 - 7669 - 76
21X-RAY DIFFRACTION19AA77 - 8577 - 85
22X-RAY DIFFRACTION20BB77 - 8577 - 85
23X-RAY DIFFRACTION21AA86 - 9386 - 93
24X-RAY DIFFRACTION22BB86 - 9386 - 93

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