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- EMDB-52226: Structure of Zincore (SEPHS1:QRICH1) binding to ZFP91 on DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-52226
TitleStructure of Zincore (SEPHS1:QRICH1) binding to ZFP91 on DNA
Map dataMain Map
Sample
  • Complex: Zincore
    • Protein or peptide: E3 ubiquitin-protein ligase ZFP91
    • Protein or peptide: Transcriptional regulator QRICH1
    • DNA: DNA (31-MER)
    • DNA: DNA (31-MER)
    • Protein or peptide: Selenide, water dikinase 1
  • Ligand: ZINC ION
KeywordsZincore Complex / Transcriptional regulator complex / SEPHS1 / Selenide / water dikinase 1 / selenophosphate synthetase 1 / QRICH1 / Zinc finger protein / ZFP91 / Transcription factor / STRUCTURAL PROTEIN
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
Selenide, water dikinase 1 / Transcriptional regulator QRICH1 / E3 ubiquitin-protein ligase ZFP91
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsBorza R / Perrakis A
Funding support Netherlands, 1 items
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, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52226.png

Downloads & links

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Map

FileDownload / File: emd_52226.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 440 pix.
= 288.64 Å		0.66 Å/pix.
x 440 pix.
= 288.64 Å		0.66 Å/pix.
x 440 pix.
= 288.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.09515174 - 0.2591774
Average (Standard dev.)-0.000020048836 (±0.0073188846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 288.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Map Half A

Fileemd_52226_half_map_1.map
AnnotationMap Half A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Map Half B

Fileemd_52226_half_map_2.map
AnnotationMap Half B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Zincore

EntireName: Zincore
Components
  • Complex: Zincore
    • Protein or peptide: E3 ubiquitin-protein ligase ZFP91
    • Protein or peptide: Transcriptional regulator QRICH1
    • DNA: DNA (31-MER)
    • DNA: DNA (31-MER)
    • Protein or peptide: Selenide, water dikinase 1
  • Ligand: ZINC ION

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Supramolecule #1: Zincore

SupramoleculeName: Zincore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#5, #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase ZFP91

MacromoleculeName: E3 ubiquitin-protein ligase ZFP91 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.557219 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPGETEEPRP PEQQDQEGGE AAKAAPEEPQ QRPPEAVAAA PAGTTSSRVL RGGRDRGRAA AAAAAAAVSR RRKAEYPRRR RSSPSARPP DVPGQQPQAA KSPSPVQGKK SPRLLCIEKV TTDKDPKEEK EEEDDSALPQ EVSIAASRPS RGWRSSRTSV S RHRDTENT ...String:
MPGETEEPRP PEQQDQEGGE AAKAAPEEPQ QRPPEAVAAA PAGTTSSRVL RGGRDRGRAA AAAAAAAVSR RRKAEYPRRR RSSPSARPP DVPGQQPQAA KSPSPVQGKK SPRLLCIEKV TTDKDPKEEK EEEDDSALPQ EVSIAASRPS RGWRSSRTSV S RHRDTENT RSSRSKTGSL QLICKSEPNT DQLDYDVGEE HQSPGGISSE EEEEEEEEML ISEEEIPFKD DPRDETYKPH LE RETPKPR RKSGKVKEEK EKKEIKVEVE VEVKEEENEI REDEEPPRKR GRRRKDDKSP RLPKRRKKPP IQYVRCEMEG CGT VLAHPR YLQHHIKYQH LLKKKYVCPH PSCGRLFRLQ KQLLRHAKHH TDQRDYICEY CARAFKSSHN LAVHRMIHTG EKPL QCEIC GFTCRQKASL NWHMKKHDAD SFYQFSCNIC GKKFEKKDSV VAHKAKSHPE VLIAEALAAN AGALITSTDI LGTNP ESLT QPSDGQGLPL LPEPLGNSTS GECLLLEAEG MSKSYCSGTE RVSLMADGKI FVGSGSSGGT EGLVMNSDIL GATTEV LIE DSDSAGP

UniProtKB: E3 ubiquitin-protein ligase ZFP91

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Macromolecule #2: Selenide, water dikinase 1

MacromoleculeName: Selenide, water dikinase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: selenide, water dikinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.953461 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTRESFNPE SYELDKSFRL TRFTELKGTG CKVPQDVLQK LLESLQENHF QEDEQFLGAV MPRLGIGMDT CVIPLRHGGL SLVQTTDYI YPIVDDPYMM GRIACANVLS DLYAMGVTEC DNMLMLLGVS NKMTDRERDK VMPLIIQGFK DAAEEAGTSV T GGQTVLNP ...String:
MSTRESFNPE SYELDKSFRL TRFTELKGTG CKVPQDVLQK LLESLQENHF QEDEQFLGAV MPRLGIGMDT CVIPLRHGGL SLVQTTDYI YPIVDDPYMM GRIACANVLS DLYAMGVTEC DNMLMLLGVS NKMTDRERDK VMPLIIQGFK DAAEEAGTSV T GGQTVLNP WIVLGGVATT VCQPNEFIMP DNAVPGDVLV LTKPLGTQVA VAVHQWLDIP EKWNKIKLVV TQEDVELAYQ EA MMNMARL NRTAAGLMHT FNAHAATDIT GFGILGHAQN LAKQQRNEVS FVIHNLPVLA KMAAVSKACG NMFGLMHGTC PET SGGLLI CLPREQAARF CAEIKSPKYG EGHQAWIIGI VEKGNRTARI IDKPRIIEVA PQVATQNVNP TPGATS

UniProtKB: Selenide, water dikinase 1

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Macromolecule #3: Transcriptional regulator QRICH1

MacromoleculeName: Transcriptional regulator QRICH1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.507156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNNSLENTIS FEEYIRVKAR SVPQHRMKEF LDSLASKGPE ALQEFQQTAT TTMVYQQGGN CIYTDSTEVA GSLLELACPV TTSVQPQTQ QEQQIQVQQP QQVQVQVQVQ QSPQQVSAQL SPQLTVHQPT EQPIQVQVQI QGQAPQSAAP SIQTPSLQSP S PSQLQAAQ ...String:
MNNSLENTIS FEEYIRVKAR SVPQHRMKEF LDSLASKGPE ALQEFQQTAT TTMVYQQGGN CIYTDSTEVA GSLLELACPV TTSVQPQTQ QEQQIQVQQP QQVQVQVQVQ QSPQQVSAQL SPQLTVHQPT EQPIQVQVQI QGQAPQSAAP SIQTPSLQSP S PSQLQAAQ IQVQHVQAAQ QIQAAEIPEE HIPHQQIQAQ LVAGQSLAGG QQIQIQTVGA LSPPPSQQGS PREGERRVGT AS VLQPVKK RKVDMPITVS YAISGQPVAT VLAIPQGQQQ SYVSLRPDLL TVDSAHLYSA TGTITSPTGE TWTIPVYSAQ PRG DPQQQS ITHIAIPQEA YNAVHVSGSP TALAAVKLED DKEKMVGTTS VVKNSHEEVV QTLANSLFPA QFMNGNIHIP VAVQ AVAGT YQNTAQTVHI WDPQQQPQQQ TPQEQTPPPQ QQQQQLQVTC SAQTVQVAEV EPQSQPQPSP ELLLPNSLKP EEGLE VWKN WAQTKNAELE KDAQNRLAPI GRRQLLRFQE DLISSAVAEL NYGLCLMTRE ARNGEGEPYD PDVLYYIFLC IQKYLF ENG RVDDIFSDLY YVRFTEWLHE VLKDVQPRVT PLGYVLPSHV TEEMLWECKQ LGAHSPSTLL TTLMFFNTKY FLLKTVD QH MKLAFSKVLR QTKKNPSNPK DKSTSIRYLK ALGIHQTGQK VTDDMYAEQT ENPENPLRCP IKLYDFYLFK CPQSVKGR N DTFYLTPEPV VAPNSPIWYS VQPISREQMG QMLTRILVIR EIQEAIAVAN ASTMH

UniProtKB: Transcriptional regulator QRICH1

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Macromolecule #4: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.314979 KDa
SequenceString:
(DG)(DC)(DG)(DA)(DC)(DC)(DT)(DG)(DC)(DC) (DC)(DC)(DT)(DT)(DT)(DA)(DA)(DG)(DA)(DG) (DC)(DA)(DC)(DC)(DC)(DC)(DC)(DC)(DT) (DC)(DC)

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Macromolecule #5: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.755242 KDa
SequenceString:
(DG)(DG)(DA)(DG)(DG)(DG)(DG)(DG)(DG)(DT) (DG)(DC)(DT)(DC)(DT)(DT)(DA)(DA)(DA)(DG) (DG)(DG)(DG)(DC)(DA)(DG)(DG)(DT)(DC) (DG)(DC)

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7542 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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 selectionDetails: Multiple particle selections
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 42621
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

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

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