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- EMDB-77393: HIV-1 reverse transcriptase (F227C) in complex with DNAddG Aptame... -

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Basic information

Entry
Database: EMDB / ID: EMD-77393
TitleHIV-1 reverse transcriptase (F227C) in complex with DNAddG Aptamer and unincorporated ISL-triphosphate
Map data
Sample
  • Complex: HIV-1 reverse transcriptase (F227C) in complex with DNAddG Aptamer and unincorporated ISL-triphosphate
    • Protein or peptide: Reverse transcriptase/ribonuclease H
    • Protein or peptide: p51 RT
    • DNA: DNAddG (38-MER)
  • Ligand: 2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(tetrahydrogen triphosphate)
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsReverse Transcriptase / DNA Polymerase Activity / Nucleoside Reverse Transcriptase Inhibitor / HIV-1 / VIRAL PROTEIN
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / viral genome integration into host DNA / Budding and maturation of HIV virion / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / 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 / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / identical protein binding
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 DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retrovirus capsid, C-terminal / Retroviral matrix protein / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / 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. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsHecksel CW / Walker SN / Klein DJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Infect Dis. / Year: 2026
Title: Allosteric Crosstalk
Authors: Hecksel CW / Walker SN / Raheem I / Asante-Appiah E / Calero G / Diamond TL / Gabelli SB / Gomez-Llorente Y / Hayes RP / Tummala S / Vergara S / Klein DJ
History
DepositionJun 1, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77393.png

Downloads & links

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Map

FileDownload / File: emd_77393.map.gz / Format: CCP4 / Size: 27.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 236 pix.
= 134.756 Å		0.57 Å/pix.
x 198 pix.
= 113.058 Å		0.57 Å/pix.
x 154 pix.
= 87.934 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.571 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.094
Minimum - Maximum-0.22608548 - 0.55261976
Average (Standard dev.)0.0021508958 (±0.028340735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin202219178
Dimensions198154236
Spacing154198236
CellA: 87.934 Å / B: 113.058 Å / C: 134.756 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: EMReady Filtered Map

Fileemd_77393_additional_1.map
AnnotationEMReady Filtered Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77393_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77393_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 reverse transcriptase (F227C) in complex with DNAddG Aptame...

EntireName: HIV-1 reverse transcriptase (F227C) in complex with DNAddG Aptamer and unincorporated ISL-triphosphate
Components
  • Complex: HIV-1 reverse transcriptase (F227C) in complex with DNAddG Aptamer and unincorporated ISL-triphosphate
    • Protein or peptide: Reverse transcriptase/ribonuclease H
    • Protein or peptide: p51 RT
    • DNA: DNAddG (38-MER)
  • Ligand: 2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(tetrahydrogen triphosphate)
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: HIV-1 reverse transcriptase (F227C) in complex with DNAddG Aptame...

SupramoleculeName: HIV-1 reverse transcriptase (F227C) in complex with DNAddG Aptamer and unincorporated ISL-triphosphate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 117.792 KDa

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Macromolecule #1: Reverse transcriptase/ribonuclease H

MacromoleculeName: Reverse transcriptase/ribonuclease H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 64.708191 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVPISPIETV PVKLKPGMDG PKVKQWPLTE EKIKALVEIC TEMEKEGKIS KIGPENPYNT PVFAIKKKDS TKWRKLVDFR ELNKRTQDF WEVQLGIPHP AGLKKKKSVT VLDVGDAYFS VPLDEDFRKY TAFTIPSINN ETPGIRYQYN VLPQGWKGSP A IFQSSMTK ...String:
MVPISPIETV PVKLKPGMDG PKVKQWPLTE EKIKALVEIC TEMEKEGKIS KIGPENPYNT PVFAIKKKDS TKWRKLVDFR ELNKRTQDF WEVQLGIPHP AGLKKKKSVT VLDVGDAYFS VPLDEDFRKY TAFTIPSINN ETPGIRYQYN VLPQGWKGSP A IFQSSMTK ILEPFRKQNP DIVIYQYMDD LYVGSDLEIG QHRTKIEELR QHLLRWGLTT PDKKHQKEPP CLWMGYELHP DK WTVQPIV LPEKDSWTVN DICKLVGKLN WASQIYPGIK VRQLSKLLRG TKALTEVIPL TEEAELELAE NREILKEPVH GVY YDPSKD LIAEIQKQGQ GQWTYQIYQE PFKNLKTGKY ARMRGAHTND VKQLTEAVQK ITTESIVIWG KTPKFKLPIQ KETW ETWWT EYWQATWIPE WEFVNTPPLV KLWYQLEKEP IVGAETFYVD GAANRETKLG KAGYVTNRGR QKVVTLTDTT NQKTE LQAI YLALQDSGLE VNIVTDSQYA LGIIQAQPDQ SESELVNQII EQLIKKEKVY LAWVPAHKGI GGNEQVDKLV SAGIRK VL

UniProtKB: Gag-Pol polyprotein

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Macromolecule #2: p51 RT

MacromoleculeName: p51 RT / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.201043 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHLE VLFQGPISPI ETVPVKLKPG MDGPKVKQWP LTEEKIKALV EICTEMEKEG KISKIGPENP YNTPVFAIKK KDSTKWRKL VDFRELNKRT QDFWEVQLGI PHPAGLKKKK SVTVLDVGDA YFSVPLDEDF RKYTAFTIPS INNETPGIRY Q YNVLPQGW ...String:
MAHHHHHHLE VLFQGPISPI ETVPVKLKPG MDGPKVKQWP LTEEKIKALV EICTEMEKEG KISKIGPENP YNTPVFAIKK KDSTKWRKL VDFRELNKRT QDFWEVQLGI PHPAGLKKKK SVTVLDVGDA YFSVPLDEDF RKYTAFTIPS INNETPGIRY Q YNVLPQGW KGSPAIFQSS MTKILEPFRK QNPDIVIYQY MDDLYVGSDL EIGQHRTKIE ELRQHLLRWG LTTPDKKHQK EP PFLWMGY ELHPDKWTVQ PIVLPEKDSW TVNDIQKLVG KLNWASQIYP GIKVRQLSKL LRGTKALTEV IPLTEEAELE LAE NREILK EPVHGVYYDP SKDLIAEIQK QGQGQWTYQI YQEPFKNLKT GKYARMRGAH TNDVKQLTEA VQKITTESIV IWGK TPKFK LPIQKETWET WWTEYWQATW IPEWEFVNTP PLVKLWYQLE KEPIVGAETF

UniProtKB: Gag-Pol polyprotein

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Macromolecule #3: DNAddG (38-MER)

MacromoleculeName: DNAddG (38-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.732527 KDa
SequenceString:
(DT)(DA)(DA)(DA)(DT)(DC)(OMC)(DC)(OMC)(DC) (DC)(DC)(DT)(DT)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DT)(DT)(DG)(DC)(DA)(DC)(DC)(DG) (DA)(DA)(DG)(DG)(DG)(DG)(DG)(DG)(DDG)

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Macromolecule #4: 2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(tetrahydrogen triphosphate)

MacromoleculeName: 2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(tetrahydrogen triphosphate)
type: ligand / ID: 4 / Number of copies: 1 / Formula: 6FN
Molecular weightTheoretical: 533.193 Da
Chemical component information

ChemComp-6FN:
2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(tetrahydrogen triphosphate)

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 80 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.157 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMTRIS
100.0 mMSodium ChlorideNaCl
10.0 mMMagnesium ChlorideMgCl2
0.05 %Lauryl Maltose Neopentyl Glycol (LMNG)
GridModel: HexAuFoil / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 38.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 21752 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 215000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3028564
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 1514482
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)

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