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- PDB-5cym: HIV-1 reverse transcriptase complexed with 4-iodopyrazole -

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Basic information

Entry
Database: PDB / ID: 5cym
TitleHIV-1 reverse transcriptase complexed with 4-iodopyrazole
Components(HIV-1 reverse transcriptase, ...) x 2
KeywordsTRANSFERASE / 4-bromopyrazole / phasing / influenza endonuclease / fragment screening
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 ...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 / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
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. ...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. / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / 4-IODOPYRAZOLE / Chem-T27 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.1 Å
AuthorsBauman, J.D. / Arnold, E.
CitationJournal: Iucrj / Year: 2016
Title: Rapid experimental SAD phasing and hot spot identification with halogenated fragments
Authors: Bauman, J.D. / Harrison, J.J.E.K. / Arnold, E.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2017Group: Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn_detector / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 reverse transcriptase, p66 subunit
B: HIV-1 reverse transcriptase, p51 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,35936
Polymers114,0292
Non-polymers4,33034
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12800 Å2
ΔGint-53 kcal/mol
Surface area44970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.842, 73.483, 109.582
Angle α, β, γ (deg.)90.00, 100.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

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HIV-1 reverse transcriptase, ... , 2 types, 2 molecules AB

#1: Protein HIV-1 reverse transcriptase, p66 subunit / p66 RT


Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein HIV-1 reverse transcriptase, p51 subunit / p51 RT


Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03366, RNA-directed DNA polymerase

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Non-polymers , 7 types, 270 molecules

#3: Chemical ChemComp-T27 / 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile / Rilpivirine


Mass: 366.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N6 / Comment: medication*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#7: Chemical
ChemComp-PYZ / 4-IODOPYRAZOLE


Mass: 193.974 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H3IN2
#8: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 50 mM Imidazole pH 6.6, 10% PEG 8k, 5%PEG400, 100 mM A/S, 15 mM MgSO4, 10 mM Spermine, 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 144235 / Num. obs: 144235 / % possible obs: 98.39 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIXdev_1988refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.168 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 7334 5.08 %Random selection
Rwork0.1945 ---
obs0.1963 144235 98.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7810 0 134 236 8180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078145
X-RAY DIFFRACTIONf_angle_d1.01911050
X-RAY DIFFRACTIONf_dihedral_angle_d15.0283061
X-RAY DIFFRACTIONf_chiral_restr0.0471184
X-RAY DIFFRACTIONf_plane_restr0.0061385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0958-2.11960.31582220.26694234X-RAY DIFFRACTION91
2.1196-2.14460.28332190.23894448X-RAY DIFFRACTION97
2.1446-2.17070.26412730.24264526X-RAY DIFFRACTION97
2.1707-2.19820.28362350.23564504X-RAY DIFFRACTION97
2.1982-2.22710.28562440.23314545X-RAY DIFFRACTION98
2.2271-2.25760.2852400.23084407X-RAY DIFFRACTION97
2.2576-2.28990.30482560.22534637X-RAY DIFFRACTION98
2.2899-2.32410.26412510.22014464X-RAY DIFFRACTION98
2.3241-2.36040.24352810.22114570X-RAY DIFFRACTION98
2.3604-2.39910.25152570.21254478X-RAY DIFFRACTION98
2.3991-2.44040.25042510.20924576X-RAY DIFFRACTION98
2.4404-2.48480.25672710.20694541X-RAY DIFFRACTION98
2.4848-2.53260.32092440.20944552X-RAY DIFFRACTION98
2.5326-2.58430.24982000.20534591X-RAY DIFFRACTION99
2.5843-2.64050.27432420.21694614X-RAY DIFFRACTION99
2.6405-2.70190.2752410.23174544X-RAY DIFFRACTION99
2.7019-2.76940.25712500.22644538X-RAY DIFFRACTION99
2.7694-2.84430.28122860.2174530X-RAY DIFFRACTION99
2.8443-2.9280.282330.21784681X-RAY DIFFRACTION99
2.928-3.02250.23652360.2244557X-RAY DIFFRACTION99
3.0225-3.13050.24392630.22034634X-RAY DIFFRACTION99
3.1305-3.25580.24862340.22124601X-RAY DIFFRACTION99
3.2558-3.40390.23622230.20764652X-RAY DIFFRACTION100
3.4039-3.58330.23812700.19974603X-RAY DIFFRACTION100
3.5833-3.80760.19552210.18334653X-RAY DIFFRACTION100
3.8076-4.10140.21612010.16984681X-RAY DIFFRACTION100
4.1014-4.51380.17472330.15394639X-RAY DIFFRACTION100
4.5138-5.1660.17272030.15274668X-RAY DIFFRACTION100
5.166-6.5050.20352930.1824615X-RAY DIFFRACTION100
6.505-43.17720.21172610.18634618X-RAY DIFFRACTION100
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)
10.99280.1136-0.70690.98880.55972.77770.1637-0.2963-0.09040.35090.03570.13970.1815-0.0766-0.17120.55450.0242-0.02070.43650.07170.377148.1074-17.907860.3285
26.16930.37192.38921.7480.02192.77860.3378-0.4645-0.46360.37750.02320.39450.2365-0.4862-0.33710.568-0.04080.04040.38520.1120.463936.7652-26.971338.2655
31.0351-0.70260.84852.8503-1.03652.64480.0576-0.1161-0.19370.0250.16960.37720.0919-0.3254-0.1980.34570.0137-0.01610.3873-0.02260.432835.1805-15.683117.3479
44.1146-1.671.55432.4276-0.23311.0662-0.2025-0.4892-0.27010.23090.21120.10240.045-0.05540.02920.23280.01270.06380.41460.02880.339912.9417.10626.5625
55.14523.0607-0.89952.8455-1.75361.58780.074-0.39310.67170.1422-0.10581.0541-0.569-0.1368-0.01420.34520.0583-0.00570.5484-0.07710.517714.453916.94144.0356
64.9574-0.94721.11675.2090.32595.8342-0.10510.0420.15490.3961-0.0435-0.08-0.41450.17470.05170.3884-0.0527-0.04120.27870.0520.288456.23461.60936.8764
71.6982-0.25480.60714.7288-1.70981.4453-0.24970.43740.66230.2015-0.1776-0.9066-0.54980.5910.30880.6641-0.2473-0.15430.60340.16390.709963.728415.089330.6178
82.9640.22944.30223.8123-0.09287.4862-0.1139-0.08620.1830.2983-0.146-0.17310.23130.10770.22860.3573-0.0090.01510.4793-0.0110.382831.07625.70292.9648
93.1376-0.1632.77972.0035-1.26793.5714-0.3190.10650.39990.3633-0.1387-0.049-0.49620.0870.48870.4095-0.03630.03710.3451-0.01570.357636.326823.206711.0725
107.3999-0.80752.83577.25660.84073.4639-0.03110.00860.39950.1978-0.30630.5193-0.3327-0.20450.31570.4187-0.02610.05850.3134-0.02870.272941.10628.916620.9859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 194 )
2X-RAY DIFFRACTION2chain 'A' and (resid 195 through 296 )
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 421 )
4X-RAY DIFFRACTION4chain 'A' and (resid 422 through 527 )
5X-RAY DIFFRACTION5chain 'A' and (resid 528 through 554 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 83 )
7X-RAY DIFFRACTION7chain 'B' and (resid 84 through 238 )
8X-RAY DIFFRACTION8chain 'B' and (resid 239 through 269 )
9X-RAY DIFFRACTION9chain 'B' and (resid 270 through 383 )
10X-RAY DIFFRACTION10chain 'B' and (resid 384 through 428 )

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