[English] 日本語
Yorodumi
- EMDB-72362: Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiq... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72362
TitleCryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (substrate structure)
Map dataFull map
Sample
  • Complex: Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork
    • Complex: Heterotetrameric SCF-FBH1 protein complex
      • Protein or peptide: F-box DNA helicase 1
    • Complex: 3-way DNA fork
      • DNA: DNA (45-MER)
      • DNA: DNA (5'-D(*TP*CP*GP*CP*TP*AP*CP*CP*TP*TP*CP*GP*CP*AP*GP*TP*C)-3')
      • DNA: DNA (45-MER)
      • DNA: DNA (5'-D(*CP*TP*GP*AP*CP*GP*CP*TP*TP*CP*CP*AP*TP*CP*GP*CP*TP*GP*TP*CP*TP*AP*G)-3')
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsHelicase / Translocase / Fork remodeler / Fork reversal / Replication fork / DNA binding / ISOMERASE-DNA complex
Function / homology
Function and homology information


response to intra-S DNA damage checkpoint signaling / DNA translocase activity / DNA catabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / SCF ubiquitin ligase complex / DNA 3'-5' helicase / 3'-5' DNA helicase activity / replication fork processing / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity ...response to intra-S DNA damage checkpoint signaling / DNA translocase activity / DNA catabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / SCF ubiquitin ligase complex / DNA 3'-5' helicase / 3'-5' DNA helicase activity / replication fork processing / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity / double-strand break repair via homologous recombination / positive regulation of protein phosphorylation / single-stranded DNA binding / double-stranded DNA binding / protein ubiquitination / DNA repair / DNA damage response / chromatin / ATP hydrolysis activity / ATP binding / nucleus
Similarity search - Function
UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
F-box DNA helicase 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.27 Å
AuthorsMullins EA / Schiltz CJ / Eichman BF
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136401 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: To Be Published
Title: F-box helicase 1 reverses replication forks through assembly on the lagging strand template at the fork junction
Authors: Greer BH / Mendia Garcia J / Mullins EA / Peacock EM / Haigh S / Schiltz CJ / Tsai M-S / Cortez D / Moreno-Herrero F / Eichman BF
History
DepositionAug 27, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72362.png

Downloads & links

-
Map

FileDownload / File: emd_72362.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 540 pix.
= 441.72 Å		0.82 Å/pix.
x 540 pix.
= 441.72 Å		0.82 Å/pix.
x 540 pix.
= 441.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.818 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00137
Minimum - Maximum-0.0014832234 - 0.0060543367
Average (Standard dev.)0.0000044226326 (±0.00017501213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 441.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_72362_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map

Fileemd_72362_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_72362_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_72362_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork

EntireName: Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork
Components
  • Complex: Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork
    • Complex: Heterotetrameric SCF-FBH1 protein complex
      • Protein or peptide: F-box DNA helicase 1
    • Complex: 3-way DNA fork
      • DNA: DNA (45-MER)
      • DNA: DNA (5'-D(*TP*CP*GP*CP*TP*AP*CP*CP*TP*TP*CP*GP*CP*AP*GP*TP*C)-3')
      • DNA: DNA (45-MER)
      • DNA: DNA (5'-D(*CP*TP*GP*AP*CP*GP*CP*TP*TP*CP*CP*AP*TP*CP*GP*CP*TP*GP*TP*CP*TP*AP*G)-3')
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

+
Supramolecule #1: Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork

SupramoleculeName: Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

+
Supramolecule #2: Heterotetrameric SCF-FBH1 protein complex

SupramoleculeName: Heterotetrameric SCF-FBH1 protein complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: 3-way DNA fork

SupramoleculeName: 3-way DNA fork / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: synthetic construct (others)

+
Macromolecule #1: DNA (45-MER)

MacromoleculeName: DNA (45-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.921935 KDa
SequenceString:
(DG)(DA)(DC)(DT)(DG)(DC)(DG)(DA)(DA)(DG) (DG)(DT)(DA)(DG)(DC)(DG)(DA)(DC)(DA)(DG) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DG)(DA) (DC)(DG)(DA)(DA)(DC)(DT)(DG)(DA)(DG)(DT) (DC) (DC)(DT)(DG)(DA)(DG)

+
Macromolecule #2: DNA (5'-D(*TP*CP*GP*CP*TP*AP*CP*CP*TP*TP*CP*GP*CP*AP*GP*TP*C)-3')

MacromoleculeName: DNA (5'-D(*TP*CP*GP*CP*TP*AP*CP*CP*TP*TP*CP*GP*CP*AP*GP*TP*C)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.11431 KDa
SequenceString:
(DT)(DC)(DG)(DC)(DT)(DA)(DC)(DC)(DT)(DT) (DC)(DG)(DC)(DA)(DG)(DT)(DC)

+
Macromolecule #3: DNA (45-MER)

MacromoleculeName: DNA (45-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.872895 KDa
SequenceString:
(DC)(DT)(DC)(DA)(DG)(DG)(DA)(DC)(DT)(DC) (DA)(DG)(DT)(DT)(DC)(DG)(DT)(DC)(DA)(DG) (DC)(DC)(DC)(DT)(DA)(DG)(DA)(DC)(DA) (DG)(DC)(DG)(DA)(DT)(DG)(DG)(DA)(DA)(DG) (DC) (DG)(DT)(DC)(DA)(DG)

+
Macromolecule #4: DNA (5'-D(*CP*TP*GP*AP*CP*GP*CP*TP*TP*CP*CP*AP*TP*CP*GP*CP*TP*GP*...

MacromoleculeName: DNA (5'-D(*CP*TP*GP*AP*CP*GP*CP*TP*TP*CP*CP*AP*TP*CP*GP*CP*TP*GP*TP*CP*TP*AP*G)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.983496 KDa
SequenceString:
(DC)(DT)(DG)(DA)(DC)(DG)(DC)(DT)(DT)(DC) (DC)(DA)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DG)

+
Macromolecule #5: F-box DNA helicase 1

MacromoleculeName: F-box DNA helicase 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA 3'-5' helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.518734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SNAMAKSNSV GQDSCQDSEG DMIFPAESSC ALPQEGSAGP GSPGSAPPSR KRSWSSEEES NQATGTSRWD GVSKKAPRHH LSVPCTRPR EARQEAEDST SRLSAESGET DQDAGDVGPD PIPDSYYGLL GTLPCQEALS HICSLPSEVL RHVFAFLPVE D LYWNLSLV ...String:
SNAMAKSNSV GQDSCQDSEG DMIFPAESSC ALPQEGSAGP GSPGSAPPSR KRSWSSEEES NQATGTSRWD GVSKKAPRHH LSVPCTRPR EARQEAEDST SRLSAESGET DQDAGDVGPD PIPDSYYGLL GTLPCQEALS HICSLPSEVL RHVFAFLPVE D LYWNLSLV CHLWREIISD PLFIPWKKLY HRYLMNEEQA VSKVDGILSN CGIEKESDLC VLNLIRYTAT TKCSPSVDPE RV LWSLRDH PLLPEAEACV RQHLPDLYAA AGGVNIWALV AAVVLLSSSV NDIQRLLFCL RRPSSTVTMP DVTETLYCIA VLL YAMREK GINISNRIHY NIFYCLYLQE NSCTQATKVK EEPSVWPGKK TIQLTHEQQL ILNHKMEPLQ VVKIMAFAGT GKTS TLVKY AEKWSQSRFL YVTFNKSIAK QAERVFPSNV ICKTFHSMAY GHIGRKYQSK KKLNLFKLTP FMVNSVLAEG KGGFI RAKL VCKTLENFFA SADEELTIDH VPIWCKNSQG QRVMVEQSEK LNGVLEASRL WDNMRKLGEC TEEAHQMTHD GYLKLW QLS KPSLASFDAI FVDEAQDCTP AIMNIVLSQP CGKIFVGDPH QQIYTFRGAV NALFTVPHTH VFYLTQSFRF GVEIAYV GA TILDVCKRVR KKTLVGGNHQ SGIRGDAKGQ VALLSRTNAN VFDEAVRVTE GEFPSRIHLI GGIKSFGLDR IIDIWILL Q PEEERRKQNL VIKDKFIRRW VHKEGFSGFK RYVTAAEDKE LEAKIAVVEK YNIRIPELVQ RIEKCHIEDL DFAEYILGT VHKAKGLEFD TVHVLDDFVK VPCARHNLPQ LPHFRVESFS EDEWNLLYVA VTRAKKRLIM TKSLENILTL AGEYFLQAEL TSNVLKTGV VRCCVGQCNN AIPVDTVLTM KKLPITYSNR KENKGGYLCH SCAEQRIGPL AFLTASPEQV RAMERTVENI V LPRHEALL FLVF

UniProtKB: F-box DNA helicase 1

+
Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

+
Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Average electron dose: 51.8 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Image recording ID1
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 7718
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChainDetails

9443

source_name: Other, initial_model_type: experimental modelPartial model from focused refinement
source_name: Other, initial_model_type: in silico modelIdeal B-form DNA generated by Coot
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9xzm:
Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (substrate structure)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more