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- PDB-6c0r: Crystal structure of HIV-1 K103N/Y181C mutant reverse transcripta... -

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Basic information

Entry
Database: PDB / ID: 6c0r
TitleCrystal structure of HIV-1 K103N/Y181C mutant reverse transcriptase in complex with non-nucleoside inhibitor 25a
Components
  • Reverse transcriptase p51 subunit
  • Reverse transcriptase/ribonuclease H
KeywordsREPLICATION / non-nucleoside inhibitor
Function / homology
Function and homology information


: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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. / 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 / 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. / Ribonuclease H superfamily / Aspartic peptidase domain 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
Chem-K5C / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.049 Å
AuthorsYang, Y. / Nguyen, L.A. / Smithline, Z.B. / Steitz, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2018
Title: Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2-d]pyrimidine non-nucleoside inhibitors.
Authors: Yang, Y. / Kang, D. / Nguyen, L.A. / Smithline, Z.B. / Pannecouque, C. / Zhan, P. / Liu, X. / Steitz, T.A.
History
DepositionJan 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H
B: Reverse transcriptase p51 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,32344
Polymers113,9542
Non-polymers3,37042
Water11,512639
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13850 Å2
ΔGint-82 kcal/mol
Surface area46080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.823, 73.055, 109.077
Angle α, β, γ (deg.)90.00, 100.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Reverse transcriptase/ribonuclease H / Pr160Gag-Pol


Mass: 63914.129 Da / Num. of mol.: 1 / Mutation: K103N, K172A, K173A, Y181C, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein Reverse transcriptase p51 subunit / Pr160Gag-Pol


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
Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase

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Non-polymers , 6 types, 681 molecules

#3: Chemical ChemComp-K5C / 4-({4-[(4-{4-[(E)-2-cyanoethenyl]-2,6-dimethylphenoxy}thieno[3,2-d]pyrimidin-2-yl)amino]piperidin-1-yl}methyl)benzene-1-sulfonamide


Mass: 574.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H30N6O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 50 mM MES buffer (pH 6.0-6.6), 10% (v/v) polyethylene glycol (PEG) 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 10 mM spermine
PH range: 6.0-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.049→50 Å / Num. obs: 76614 / % possible obs: 96.7 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0351 / Rrim(I) all: 0.04138 / Net I/σ(I): 15.59
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.105 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 12054 / CC1/2: 0.44 / Rrim(I) all: 1.305 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSJune 1, 2017data reduction
XDSJune 1, 2017data scaling
PHENIX1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q


Resolution: 2.049→48.849 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 3834 5 %Random selection
Rwork0.1805 ---
obs0.1821 76614 96.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.049→48.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7921 0 209 639 8769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048463
X-RAY DIFFRACTIONf_angle_d0.57611463
X-RAY DIFFRACTIONf_dihedral_angle_d15.3895045
X-RAY DIFFRACTIONf_chiral_restr0.0451224
X-RAY DIFFRACTIONf_plane_restr0.0041433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0491-2.0750.35981220.33782261X-RAY DIFFRACTION81
2.075-2.10230.3531400.31442668X-RAY DIFFRACTION97
2.1023-2.13110.31371430.30392702X-RAY DIFFRACTION97
2.1311-2.16150.32641420.29262708X-RAY DIFFRACTION98
2.1615-2.19380.33371420.28712697X-RAY DIFFRACTION97
2.1938-2.22810.29331440.26752734X-RAY DIFFRACTION97
2.2281-2.26460.30561410.26742687X-RAY DIFFRACTION97
2.2646-2.30370.25631410.24762680X-RAY DIFFRACTION96
2.3037-2.34560.27851430.23772709X-RAY DIFFRACTION98
2.3456-2.39070.30861410.22562681X-RAY DIFFRACTION98
2.3907-2.43950.26631440.21642737X-RAY DIFFRACTION98
2.4395-2.49250.25681430.21362713X-RAY DIFFRACTION98
2.4925-2.55050.27321420.19892705X-RAY DIFFRACTION98
2.5505-2.61430.24421440.19232739X-RAY DIFFRACTION98
2.6143-2.68490.26471430.20142718X-RAY DIFFRACTION98
2.6849-2.76390.26211440.19932722X-RAY DIFFRACTION98
2.7639-2.85320.24611440.1992733X-RAY DIFFRACTION98
2.8532-2.95510.25821430.20062727X-RAY DIFFRACTION98
2.9551-3.07340.22871440.20022728X-RAY DIFFRACTION98
3.0734-3.21330.22361420.18732705X-RAY DIFFRACTION97
3.2133-3.38260.23081370.17992596X-RAY DIFFRACTION93
3.3826-3.59450.20061440.16912736X-RAY DIFFRACTION98
3.5945-3.87190.19411440.15962745X-RAY DIFFRACTION98
3.8719-4.26140.15631450.14562756X-RAY DIFFRACTION98
4.2614-4.87750.1751430.15112715X-RAY DIFFRACTION97
4.8775-6.14330.2221430.1762712X-RAY DIFFRACTION96
6.1433-48.86330.18511460.17432766X-RAY DIFFRACTION95
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)
12.57420.5673-1.29312.70380.10142.86840.5312-0.23160.27910.9691-0.29680.60210.0246-0.051-0.17531.4094-0.11190.22780.7494-0.01910.530246.7401-14.784770.4449
20.70110.4959-0.21111.071.98695.09380.0683-0.13720.11980.4441-0.05190.44960.6998-0.8588-0.26621.1499-0.01970.13180.93670.1290.782439.8554-17.310159.0432
30.47780.62-0.5911.38351.08084.0120.2186-0.1601-0.23090.51690.01030.0690.36390.0794-0.13180.89710.0345-0.07060.64280.06950.522253.8339-23.198153.3447
42.8184-0.66312.21683.3357-1.44414.09690.3128-1.3048-1.36260.49480.70071.37210.4609-1.2778-0.2110.7237-0.12380.01830.9160.41521.152730.5668-21.170626.6832
54.0644-1.88861.3241.3595-0.6590.94020.0477-0.023-0.15460.02870.13730.13530.1769-0.1578-0.14870.444-0.05520.02520.4718-0.03530.504624.01171.34767.2331
67.78830.89551.22764.49920.81665.102-0.2598-0.3413-0.19710.11370.21650.3999-0.258-0.3450.00870.2990.02350.07470.50490.06470.495414.29978.98536.6566
76.1312-0.47231.61816.2668-0.53375.4019-0.1128-0.14370.390.5366-0.0571-0.1859-0.31390.45940.0320.5119-0.0601-0.04670.43420.07270.305656.45432.044636.7796
82.87513.9413-3.58759.6777-8.22237.14230.4293-0.22480.96541.6107-0.25120.4731-1.84440.44830.13691.4798-0.2678-0.10040.90830.04241.166755.411127.073833.7229
92.4943-0.17190.24235.7575-2.90192.2413-0.0414-0.14590.4360.6181-0.1945-0.7369-0.35340.71070.16310.8489-0.1942-0.13440.6707-0.00320.575661.890313.244634.5229
106.8762-0.69245.8831-0.01860.37555.1124-0.01830.7813-0.8350.17520.3202-0.3065-0.2881.1492-0.25510.6833-0.1725-0.1161.2030.21291.014958.168122.368313.8196
112.6567-0.63621.79332.309-1.3383.0044-0.21850.14320.30940.4038-0.0151-0.0549-0.44130.03880.26410.5067-0.0440.07160.4255-0.02060.45936.425319.55813.1329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 226 )
4X-RAY DIFFRACTION4chain 'A' and (resid 227 through 383 )
5X-RAY DIFFRACTION5chain 'A' and (resid 384 through 473 )
6X-RAY DIFFRACTION6chain 'A' and (resid 474 through 554 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 83 )
8X-RAY DIFFRACTION8chain 'B' and (resid 84 through 104 )
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 194 )
10X-RAY DIFFRACTION10chain 'B' and (resid 195 through 253 )
11X-RAY DIFFRACTION11chain 'B' and (resid 254 through 428 )

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