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- PDB-9hju: Structure of 2x Zincore (SEPHS1:QRICH1) binding to ZFP91 on DNA -

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Basic information

Entry
Database: PDB / ID: 9hju
TitleStructure of 2x Zincore (SEPHS1:QRICH1) binding to ZFP91 on DNA
Components
  • (DNA (31-MER)) x 2
  • E3 ubiquitin-protein ligase ZFP91
  • Selenide, water dikinase 1
  • Transcriptional regulator QRICH1
KeywordsSTRUCTURAL PROTEIN / Zincore Complex / Transcriptional regulator complex / SEPHS1 / Selenide / water dikinase 1 / selenophosphate synthetase 1 / QRICH1 / Zinc finger protein / ZFP91 / Transcription factor
Function / homology
Function and homology information


selenide, water dikinase / selenide, water dikinase activity / integrated stress response signaling / selenocysteine biosynthetic process / PERK-mediated unfolded protein response / activation of NF-kappaB-inducing kinase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / protein K63-linked ubiquitination / endoplasmic reticulum unfolded protein response / response to endoplasmic reticulum stress ...selenide, water dikinase / selenide, water dikinase activity / integrated stress response signaling / selenocysteine biosynthetic process / PERK-mediated unfolded protein response / activation of NF-kappaB-inducing kinase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / protein K63-linked ubiquitination / endoplasmic reticulum unfolded protein response / response to endoplasmic reticulum stress / RING-type E3 ubiquitin transferase / protein modification process / ubiquitin-protein transferase activity / nuclear membrane / positive regulation of apoptotic process / protein heterodimerization activity / regulation of transcription by RNA polymerase II / GTP binding / positive regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein of unknown function DUF3504 / Domain of unknown function (DUF3504) / : / Selenophosphate synthetase / : / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily ...Protein of unknown function DUF3504 / Domain of unknown function (DUF3504) / : / Selenophosphate synthetase / : / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Selenide, water dikinase 1 / Transcriptional regulator QRICH1 / E3 ubiquitin-protein ligase ZFP91
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsBorza, R. / Perrakis, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Oncode Institute Netherlands
CitationJournal: Science / Year: 2025
Title: Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression.
Authors: Daniëlle Bianchi / Razvan Borza / Erica De Zan / Guizela Huelsz-Prince / Sebastian Gregoricchio / Marleen Dekker / Alex Fish / Abdelghani Mazouzi / Lona J Kroese / Simon Linder / Miguel ...Authors: Daniëlle Bianchi / Razvan Borza / Erica De Zan / Guizela Huelsz-Prince / Sebastian Gregoricchio / Marleen Dekker / Alex Fish / Abdelghani Mazouzi / Lona J Kroese / Simon Linder / Miguel Hernandez-Quiles / Michiel Vermeulen / Patrick H N Celie / Paul Krimpenfort / Ji-Ying Song / Wilbert Zwart / Lodewyk Wessels / Sebastian M B Nijman / Anastassis Perrakis / Thijn R Brummelkamp /
Abstract: Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting ...Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting of QRICH1 and SEPHS1, as a ZNF-specific coregulator essential for embryonic development in mice and associated with developmental syndromes in humans. We also identified ZFP91 as a representative Zincore client, binding the conserved promoter motif CTTTAAR. Cryo-electron microscopy of a Zincore-ZFP91-DNA complex revealed a SEPHS1 arginine clamp to recognize the DNA-bound zinc finger domains. This mode of binding explains recognition of different ZNFs and stabilizes ZFP91 onto its cognate DNA motif. Thus, our study identified Zincore as a ZNF-specific coregulator essential for development, involving a distinctive mechanism that locks ZNFs onto DNA and regulates transcription.
History
DepositionDec 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase ZFP91
B: Selenide, water dikinase 1
C: Selenide, water dikinase 1
D: Transcriptional regulator QRICH1
E: Transcriptional regulator QRICH1
F: Selenide, water dikinase 1
G: Selenide, water dikinase 1
H: Transcriptional regulator QRICH1
I: Transcriptional regulator QRICH1
K: DNA (31-MER)
L: DNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)600,79716
Polymers600,47011
Non-polymers3275
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 9 molecules ABCFGDEHI

#1: Protein E3 ubiquitin-protein ligase ZFP91 / RING-type E3 ubiquitin transferase ZFP91 / Zinc finger protein 757 / Zinc finger protein 91 homolog / Zfp-91


Mass: 63557.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZFP91, ZNF757, FKSG11 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q96JP5, RING-type E3 ubiquitin transferase
#2: Protein
Selenide, water dikinase 1 / Selenium donor protein 1 / Selenophosphate synthase 1


Mass: 42953.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPHS1, SELD, SPS, SPS1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P49903, selenide, water dikinase
#3: Protein
Transcriptional regulator QRICH1 / Glutamine-rich protein 1


Mass: 86507.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QRICH1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q2TAL8

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DNA chain , 2 types, 2 molecules KL

#4: DNA chain DNA (31-MER)


Mass: 9314.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (31-MER)


Mass: 9755.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 1 types, 5 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dual Zincore Complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7542

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Topazparticle selection
3EPUimage acquisition
5cryoSPARCCTF correction
8UCSF ChimeraXmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
14PHENIXdev_4788model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Multiple particle selection
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138830 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.16 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00324731
ELECTRON MICROSCOPYf_angle_d0.46833784
ELECTRON MICROSCOPYf_dihedral_angle_d13.3673719
ELECTRON MICROSCOPYf_chiral_restr0.0393781
ELECTRON MICROSCOPYf_plane_restr0.0044148

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