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- EMDB-72118: Class I (T1D0+) of Human telomerase catalytic core with shelterin... -

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Entry
Database: EMDB / ID: EMD-72118
TitleClass I (T1D0+) of Human telomerase catalytic core with shelterin protein TPP1, BIBR1532, dGpNHpp and DNA primer ending in TTAG
Map data
Sample
  • Complex: Class I (T1D0+) of Human telomerase catalytic core with shelterin protein TPP1, BIBR1532, dGpNHpp and DNA primer ending in TTAG
    • Complex: Telomerase RNA
      • RNA: Telomerase RNA
    • Complex: Telomerase reverse transcriptase
      • Protein or peptide: Telomerase reverse transcriptase
    • Complex: Adrenocortical dysplasia protein homolog
      • Protein or peptide: Adrenocortical dysplasia protein homolog
    • Complex: DNA primer
      • DNA: Telomeric repeat substrate
    • Complex: Histones H2A and H2B
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
      • Protein or peptide: Histone H2A.J
  • Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
  • Ligand: 2-{[(2E)-3-(naphthalen-2-yl)but-2-enoyl]amino}benzoic acid
KeywordsDNA polymerase / Reverse Transcriptase / Ribonucleoprotein / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


telomere assembly / positive regulation of hair cycle / template-free RNA nucleotidyltransferase activity / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex ...telomere assembly / positive regulation of hair cycle / template-free RNA nucleotidyltransferase activity / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / regulation of establishment of protein localization to telomere / telomerase activity / telomerase inhibitor activity / shelterin complex / Telomere C-strand synthesis initiation / siRNA processing / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Telomere C-strand (Lagging Strand) Synthesis / positive regulation of stem cell proliferation / nuclear telomere cap complex / telomere capping / telomere maintenance via recombination / Polymerase switching on the C-strand of the telomere / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / telomerase RNA binding / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / protein localization to chromosome, telomeric region / DNA biosynthetic process / telomeric repeat DNA binding / RNA-templated transcription / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / replicative senescence / positive regulation of telomere maintenance / mitochondrial nucleoid / Telomere Extension By Telomerase / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of endothelial cell apoptotic process / response to cadmium ion / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of Wnt signaling pathway / telomere maintenance via telomerase / positive regulation of vascular associated smooth muscle cell proliferation / Replacement of protamines by nucleosomes in the male pronucleus / DNA polymerase binding / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere maintenance / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Regulation of PD-L1(CD274) transcription / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / mitochondrion organization / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / regulation of protein stability / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / innate immune response in mucosa / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / protein import into nucleus / Formation of the beta-catenin:TCF transactivating complex / intracellular protein transport / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PML body / Negative Regulation of CDH1 Gene Transcription / RNA-directed DNA polymerase / positive regulation of miRNA transcription / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Dengue Virus-Host Interactions / Meiotic recombination / Pre-NOTCH Transcription and Translation / RNA-directed DNA polymerase activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription coactivator binding / Transcriptional regulation of granulopoiesis
Similarity search - Function
Adrenocortical dysplasia protein / : / Telomerase reverse transcriptase, C-terminal extension / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / : ...Adrenocortical dysplasia protein / : / Telomerase reverse transcriptase, C-terminal extension / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Telomerase reverse transcriptase / Histone H2B type 1-C/E/F/G/I / Adrenocortical dysplasia protein homolog / Histone H2A.J
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang Y / Liu B / He Y / Feigon J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131901 United States
National Science Foundation (NSF, United States)MCB2016540 United States
CitationJournal: Nat Chem Biol / Year: 2026
Title: Structures of human telomerase with BIBR1532 reveal novel mechanism of inhibition.
Authors: Yuqing Wang / Baocheng Liu / Yao He / Juli Feigon /
Abstract: Human telomerase processively adds telomeric repeats (dGGTTAG) to chromosome 3'-ends to maintain telomere length. While mostly absent in somatic cells, telomerase is aberrantly upregulated in most ...Human telomerase processively adds telomeric repeats (dGGTTAG) to chromosome 3'-ends to maintain telomere length. While mostly absent in somatic cells, telomerase is aberrantly upregulated in most tumor cells to sustain cellular immortality, making it a promising oncology target. However, to date there are no reported structures of human telomerase with inhibitor, impeding structure-based drug design and optimization. We report nine cryo-electron microscopy structures of human telomerase with and without BIBR1532, a highly selective small-molecule telomerase inhibitor. Unexpectedly, BIBR1532 binds a previously unknown pocket between TERT finger and palm. BIBR1532 inhibits each step but disproportionately affects the rate-limiting first step of telomere repeat nucleotide addition. The structures reveal a rigid finger that explains telomerase's slow rate and low fidelity. Our study provides insights into telomerase catalytic mechanism and its inhibition by BIBR1532, explains why prior BIBR derivatives did not improve potency and suggests a rational approach for design of small-molecule telomerase inhibitors.
History
DepositionAug 13, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72118.png

Downloads & links

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Map

FileDownload / File: emd_72118.map.gz / Format: CCP4 / Size: 222.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 388 pix.
= 426.8 Å		1.1 Å/pix.
x 388 pix.
= 426.8 Å		1.1 Å/pix.
x 388 pix.
= 426.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.44121802 - 1.0458491
Average (Standard dev.)0.000066203065 (±0.013420687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions388388388
Spacing388388388
CellA=B=C: 426.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72118_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_72118_additional_1.map
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Half map: #1

Fileemd_72118_half_map_1.map
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Half map: #2

Fileemd_72118_half_map_2.map
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Sample components

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Entire : Class I (T1D0+) of Human telomerase catalytic core with shelterin...

EntireName: Class I (T1D0+) of Human telomerase catalytic core with shelterin protein TPP1, BIBR1532, dGpNHpp and DNA primer ending in TTAG
Components
  • Complex: Class I (T1D0+) of Human telomerase catalytic core with shelterin protein TPP1, BIBR1532, dGpNHpp and DNA primer ending in TTAG
    • Complex: Telomerase RNA
      • RNA: Telomerase RNA
    • Complex: Telomerase reverse transcriptase
      • Protein or peptide: Telomerase reverse transcriptase
    • Complex: Adrenocortical dysplasia protein homolog
      • Protein or peptide: Adrenocortical dysplasia protein homolog
    • Complex: DNA primer
      • DNA: Telomeric repeat substrate
    • Complex: Histones H2A and H2B
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
      • Protein or peptide: Histone H2A.J
  • Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
  • Ligand: 2-{[(2E)-3-(naphthalen-2-yl)but-2-enoyl]amino}benzoic acid

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Supramolecule #1: Class I (T1D0+) of Human telomerase catalytic core with shelterin...

SupramoleculeName: Class I (T1D0+) of Human telomerase catalytic core with shelterin protein TPP1, BIBR1532, dGpNHpp and DNA primer ending in TTAG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: Telomerase RNA

SupramoleculeName: Telomerase RNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Telomerase reverse transcriptase

SupramoleculeName: Telomerase reverse transcriptase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Adrenocortical dysplasia protein homolog

SupramoleculeName: Adrenocortical dysplasia protein homolog / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: DNA primer

SupramoleculeName: DNA primer / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

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Supramolecule #6: Histones H2A and H2B

SupramoleculeName: Histones H2A and H2B / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Telomerase reverse transcriptase

MacromoleculeName: Telomerase reverse transcriptase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 130.711492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GHMSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKSAMPRAP RCRAVRSLLR SHYREVLPLA TFVRRLGPQG WRLVQRGDPA AFRALVAQC LVCVPWDARP PPAAPSFRQV SCLKELVARV LQRLCERGAK NVLAFGFALL DGARGGPPEA FTTSVRSYLP N TVTDALRG ...String:
GHMSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKSAMPRAP RCRAVRSLLR SHYREVLPLA TFVRRLGPQG WRLVQRGDPA AFRALVAQC LVCVPWDARP PPAAPSFRQV SCLKELVARV LQRLCERGAK NVLAFGFALL DGARGGPPEA FTTSVRSYLP N TVTDALRG SGAWGLLLRR VGDDVLVHLL ARCALFVLVA PSCAYQVCGP PLYQLGAATQ ARPPPHASGP RRRLGCERAW NH SVREAGV PLGLPAPGAR RRGGSASRSL PLPKRPRRGA APEPERTPVG QGSWAHPGRT RGPSDRGFCV VSPARPAEEA TSL EGALSG TRHSHPSVGR QHHAGPPSTS RPPRPWDTPC PPVYAETKHF LYSSGDKEQL RPSFLLSSLR PSLTGARRLV ETIF LGSRP WMPGTPRRLP RLPQRYWQMR PLFLELLGNH AQCPYGVLLK THCPLRAAVT PAAGVCAREK PQGSVAAPEE EDTDP RRLV QLLRQHSSPW QVYGFVRACL RRLVPPGLWG SRHNERRFLR NTKKFISLGK HAKLSLQELT WKMSVRDCAW LRRSPG VGC VPAAEHRLRE EILAKFLHWL MSVYVVELLR SFFYVTETTF QKNRLFFYRK SVWSKLQSIG IRQHLKRVQL RELSEAE VR QHREARPALL TSRLRFIPKP DGLRPIVNMD YVVGARTFRR EKRAERLTSR VKALFSVLNY ERARRPGLLG ASVLGLDD I HRAWRTFVLR VRAQDPPPEL YFVKVDVTGA YDTIPQDRLT EVIASIIKPQ NTYCVRRYAV VQKAAHGHVR KAFKSHVST LTDLQPYMRQ FVAHLQETSP LRDAVVIEQS SSLNEASSGL FDVFLRFMCH HAVRIRGKSY VQCQGIPQGS ILSTLLCSLC YGDMENKLF AGIRRDGLLL RLVDDFLLVT PHLTHAKTFL RTLVRGVPEY GCVVNLRKTV VNFPVEDEAL GGTAFVQMPA H GLFPWCGL LLDTRTLEVQ SDYSSYARTS IRASLTFNRG FKAGRNMRRK LFGVLRLKCH SLFLDLQVNS LQTVCTNIYK IL LLQAYRF HACVLQLPFH QQVWKNPTFF LRVISDTASL CYSILKAKNA GMSLGAKGAA GPLPSEAVQW LCHQAFLLKL TRH RVTYVP LLGSLRTAQT QLSRKLPGTT LTALEAAANP ALPSDFKTIL D

UniProtKB: Telomerase reverse transcriptase

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Macromolecule #3: Adrenocortical dysplasia protein homolog

MacromoleculeName: Adrenocortical dysplasia protein homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.672637 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAGSGRLVLR PWIRELILGS ETPSSPRAGQ LLEVLQDAEA AVAGPSHAPD TSDVGATLLV SDGTHSVRCL VTREALDTSD WEEKEFGFR GTEGRLLLLQ DCGVHVQVAE GGAPAEFYLQ VDRFSLLPTE QPRLRVPGCN QDLDVQKKLY DCLEEHLSES T SSN

UniProtKB: Adrenocortical dysplasia protein homolog

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Macromolecule #5: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.937213 KDa
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #6: Histone H2A.J

MacromoleculeName: Histone H2A.J / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.047451 KDa
SequenceString:
MSGRGKQGGK VRAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESQKTKSK

UniProtKB: Histone H2A.J

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Macromolecule #2: Telomerase RNA

MacromoleculeName: Telomerase RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 145.477797 KDa
SequenceString: GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCU UUUGCUCCC CGCGCGCUGU UUUUCUCGCU GACUUUCAGC GGGCGGAAAA GCCUCGGCCU GCCGCCUUCC ACCGUUCAUU C UAGAGCAA ...String:
GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG AAGGGCGUAG GCGCCGUGCU UUUGCUCCC CGCGCGCUGU UUUUCUCGCU GACUUUCAGC GGGCGGAAAA GCCUCGGCCU GCCGCCUUCC ACCGUUCAUU C UAGAGCAA ACAAAAAAUG UCAGCUGCUG GCCCGUUCGC CCCUCCCGGG GACCUGCGGC GGGUCGCCUG CCCAGCCCCC GA ACCCCGC CUGGAGGCCG CGGUCGGCCC GGGGCUUCUC CGGAGGCACC CACUGCCACC GCGAAGAGUU GGGCUCUGUC AGC CGCGGG UCUCUCGGGG GCGAGGGCGA GGUUCAGGCC UUUCAGGCCG CAGGAAGAGG AACGGAGCGA GUCCCCGCGC GCGG CGCGA UUCCCUGAGC UGUGGGACGU GCACCCAGGA CUCGGCUCAC ACAUGC

GENBANK: GENBANK: U85256.1

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Macromolecule #4: Telomeric repeat substrate

MacromoleculeName: Telomeric repeat substrate / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.682672 KDa
SequenceString:
(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)

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Macromolecule #7: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]a...

MacromoleculeName: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
type: ligand / ID: 7 / Number of copies: 1 / Formula: XG4
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-XG4:
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine

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Macromolecule #8: 2-{[(2E)-3-(naphthalen-2-yl)but-2-enoyl]amino}benzoic acid

MacromoleculeName: 2-{[(2E)-3-(naphthalen-2-yl)but-2-enoyl]amino}benzoic acid
type: ligand / ID: 8 / Number of copies: 1 / Formula: 55C
Molecular weightTheoretical: 331.365 Da
Chemical component information

ChemComp-55C:
2-{[(2E)-3-(naphthalen-2-yl)but-2-enoyl]amino}benzoic acid

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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

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

26086

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 588132
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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