7SR6

Human Endogenous Retrovirus (HERV-K) reverse transcriptase ternary complex with dsDNA template Primer and dNTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.168 

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Ligand Structure Quality Assessment 


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Literature

Human endogenous retrovirus-K (HERV-K) reverse transcriptase (RT) structure and biochemistry reveals remarkable similarities to HIV-1 RT and opportunities for HERV-K-specific inhibition.

Baldwin, E.T.Gotte, M.Tchesnokov, E.P.Arnold, E.Hagel, M.Nichols, C.Dossang, P.Lamers, M.Wan, P.Steinbacher, S.Romero, D.L.

(2022) Proc Natl Acad Sci U S A 119: e2200260119-e2200260119

  • DOI: https://doi.org/10.1073/pnas.2200260119
  • Primary Citation of Related Structures:  
    7SR6

  • PubMed Abstract: 

    Human endogenous retroviruses (HERVs) comprise nearly 8% of the human genome and are derived from ancient integrations of retroviruses into the germline. The biology of HERVs is poorly defined, but there is accumulating evidence supporting pathological roles in diverse diseases, such as cancer, autoimmune, and neurodegenerative diseases. Functional proteins are produced by HERV-encoded genes, including reverse transcriptases (RTs), which could be a contributor to the pathology attributed to aberrant HERV-K expression. To facilitate the discovery and development of HERV-K RT potent and selective inhibitors, we expressed active HERV-K RT and determined the crystal structure of a ternary complex of this enzyme with a double-stranded DNA substrate. We demonstrate a range of RT inhibition with antiretroviral nucleotide analogs, while classic nonnucleoside analogs do not inhibit HERV-K RT. Detailed comparisons of HERV-K RT with other known RTs demonstrate similarities to diverse RT families and a striking similarity to the HIV-1 RT asymmetric heterodimer. Our analysis further reveals opportunities for selective HERV-K RT inhibition.


  • Organizational Affiliation

    ROME Therapeutics, Boston, MA 02215.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PolymeraseA,
B,
E [auth F],
F [auth G]
618Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q9UQG0 (Homo sapiens)
Explore Q9UQG0 
Go to UniProtKB:  Q9UQG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQG0
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*GP*GP*AP*CP*CP*TP*GP*AP*AP*AP*GP*CP*GP*AP*AP*AP*GP*GP*GP*AP*AP*A)-3')C [auth D],
G [auth H]
24Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*CP*CP*CP*TP*TP*TP*CP*GP*CP*TP*TP*TP*CP*AP*GP*GP*T)-3')D [auth E],
H [auth I]
21Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TTP (Subject of Investigation/LOI)
Query on TTP

Download Ideal Coordinates CCD File 
QA [auth F]THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
DCP
Query on DCP

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J [auth A]2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
PG6
Query on PG6

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JB [auth G],
Y [auth B]
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
DIO
Query on DIO

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AA [auth B]
BA [auth B]
BB [auth F]
CA [auth B]
CB [auth F]
AA [auth B],
BA [auth B],
BB [auth F],
CA [auth B],
CB [auth F],
DA [auth B],
DB [auth F],
EA [auth B],
EB [auth F],
FA [auth B],
IB [auth G],
K [auth A],
KB [auth G],
L [auth A],
LB [auth G],
M [auth A],
MA [auth F],
MB [auth G],
N [auth A],
NB [auth G],
O [auth A],
OA [auth F],
PA [auth F],
U [auth B],
UA [auth F],
V [auth B],
VA [auth F],
W [auth B],
WA [auth F],
X [auth B],
XA [auth F],
YA [auth F],
Z [auth B],
ZA [auth F]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
EDO
Query on EDO

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AB [auth F]
GA [auth B]
OB [auth G]
P [auth A]
RA [auth F]
AB [auth F],
GA [auth B],
OB [auth G],
P [auth A],
RA [auth F],
SA [auth F],
TA [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

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GB [auth F]
HA [auth B]
HB [auth F]
IA [auth B]
JA [auth D]
GB [auth F],
HA [auth B],
HB [auth F],
IA [auth B],
JA [auth D],
KA [auth D],
Q [auth A],
QB [auth G],
R [auth A],
RB [auth G],
S [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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FB [auth F],
PB [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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I [auth A],
LA [auth D],
NA [auth F],
SB [auth G],
T [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.168 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.697α = 90
b = 177.697β = 90
c = 117.414γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release