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- EMDB-57179: Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition lig... -

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Basic information

Entry
Database: EMDB / ID: EMD-57179
TitleCryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2, UNC10088 and Bach1
Map data
Sample
  • Complex: SCF FBXO22, NSD2, UNC10088
    • Protein or peptide: F-box only protein 22
    • Protein or peptide: Histone-lysine N-methyltransferase NSD2
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: Cullin-1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Transcription regulator protein BACH1
  • Ligand: ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide
KeywordsUbiquitin Ligase / Targeted protein degradation / cullin-RING ligase / SKP1 CUL1 F box SCF / Nuclear receptor binding SET domain-containing 2 NSD2 / LIGASE
Function / homology
Function and homology information


atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / regulation of skeletal muscle fiber development / Regulation of HMOX1 expression and activity / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / Parkin-FBXW7-Cul1 ubiquitin ligase complex / positive regulation of isotype switching to IgA isotypes ...atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / regulation of skeletal muscle fiber development / Regulation of HMOX1 expression and activity / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / Parkin-FBXW7-Cul1 ubiquitin ligase complex / positive regulation of isotype switching to IgA isotypes / atrial septum primum morphogenesis / membranous septum morphogenesis / F-box domain binding / regulation of establishment of protein localization / ligand-modulated transcription factor activity / PcG protein complex / histone H3K36 methyltransferase activity / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / ubiquitin ligase activator activity / NEDD8 ligase activity / protein K27-linked ubiquitination / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of response to oxidative stress / nucleocytoplasmic transport / histone H3 methyltransferase activity / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Prolactin receptor signaling / negative regulation of mitophagy / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / cullin family protein binding / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / site of DNA damage / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / transcription-coupled nucleotide-excision repair / negative regulation of insulin receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / post-translational protein modification / intrinsic apoptotic signaling pathway / molecular function activator activity / animal organ morphogenesis / T cell activation / cellular response to starvation / protein modification process / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / negative regulation of canonical NF-kappaB signal transduction / Heme signaling / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Nonhomologous End-Joining (NHEJ) / cellular response to amino acid stimulus / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of CRY and PER proteins / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / Activation of NF-kappaB in B cells / Iron uptake and transport / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of NOTCH4 signaling / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / bone development / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / PKMTs methylate histone lysines / beta-catenin binding / DNA-binding transcription repressor activity, RNA polymerase II-specific
Similarity search - Function
FIST, C-domain / FIST C domain / FIST_C / BACH, basic leucine zipper (bZIP) domain / : / : / : / : / : / : ...FIST, C-domain / FIST C domain / FIST_C / BACH, basic leucine zipper (bZIP) domain / : / : / : / : / : / : / : / : / F-box domain / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / NSD, Cys-His rich domain / : / : / : / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cysteine-rich motif following a subset of SET domains / Cullin, N-terminal / Cullin protein neddylation domain / : / Basic-leucine zipper (bZIP) domain signature. / Cullin, conserved site / Cullin alpha solenoid domain / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Basic-leucine zipper (bZIP) domain profile. / Cullin protein neddylation domain / Post-SET domain / Post-SET domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Cullin / HMG (high mobility group) box / Basic-leucine zipper domain superfamily / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / BTB/POZ domain / BTB domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / SKP1/BTB/POZ domain superfamily / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcription regulator protein BACH1 / Histone-lysine N-methyltransferase NSD2 / E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / Cullin-1 / F-box only protein 22
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsAmann SJ / Robertson KC / Grishkovskaya I / Liu T / James LI / Brown NB / Haselbach D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA242305 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35GM128855 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 11, 2026-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57179.png

Downloads & links

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Map

FileDownload / File: emd_57179.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 240 pix.
= 228.24 Å		0.95 Å/pix.
x 240 pix.
= 228.24 Å		0.95 Å/pix.
x 240 pix.
= 228.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.951 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.00044654662 - 3.7330108
Average (Standard dev.)0.005358304 (±0.0585396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 228.23999 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SCF FBXO22, NSD2, UNC10088

EntireName: SCF FBXO22, NSD2, UNC10088
Components
  • Complex: SCF FBXO22, NSD2, UNC10088
    • Protein or peptide: F-box only protein 22
    • Protein or peptide: Histone-lysine N-methyltransferase NSD2
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: Cullin-1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Transcription regulator protein BACH1
  • Ligand: ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide

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Supramolecule #1: SCF FBXO22, NSD2, UNC10088

SupramoleculeName: SCF FBXO22, NSD2, UNC10088 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: F-box only protein 22

MacromoleculeName: F-box only protein 22 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.56227 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEPVGCCGEC RGSSVDPRST FVLSNLAEVV ERVLTFLPAK ALLRVACVCR LWRECVRRVL RTHRSVTWIS AGLAEAGHLE GHCLVRVVA EELENVRILP HTVLYMADSE TFISLEECRG HKRARKRTSM ETALALEKLF PKQCQVLGIV TPGIVVTPMG S GSNRPQEI ...String:
MEPVGCCGEC RGSSVDPRST FVLSNLAEVV ERVLTFLPAK ALLRVACVCR LWRECVRRVL RTHRSVTWIS AGLAEAGHLE GHCLVRVVA EELENVRILP HTVLYMADSE TFISLEECRG HKRARKRTSM ETALALEKLF PKQCQVLGIV TPGIVVTPMG S GSNRPQEI EIGESGFALL FPQIEGIKIQ PFHFIKDPKN LTLERHQLTE VGLLDNPELR VVLVFGYNCC KVGASNYLQQ VV STFSDMN IILAGGQVDN LSSLTSEKNP LDIDASGVVG LSFSGHRIQS ATVLLNEDVS DEKTAEAAMQ RLKAANIPEH NTI GFMFAC VGRGFQYYRA KGNVEADAFR KFFPSVPLFG FFGNGEIGCD RIVTGNFILR KCNEVKDDDL FHSYTTIMAL IHLG SSK

UniProtKB: F-box only protein 22

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Macromolecule #2: Histone-lysine N-methyltransferase NSD2

MacromoleculeName: Histone-lysine N-methyltransferase NSD2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine36 N-dimethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 152.515469 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEFSIKQSPL SVQSVVKCIK MKQAPEILGS ANGKTPSCEV NRECSVFLSK AQLSSSLQEG VMQKFNGHDA LPFIPADKLK DLTSRVFNG EPGAHDAKLR FESQEMKGIG TPPNTTPIKN GSPEIKLKIT KTYMNGKPLF ESSICGDSAA DVSQSEENGQ K PENKARRN ...String:
MEFSIKQSPL SVQSVVKCIK MKQAPEILGS ANGKTPSCEV NRECSVFLSK AQLSSSLQEG VMQKFNGHDA LPFIPADKLK DLTSRVFNG EPGAHDAKLR FESQEMKGIG TPPNTTPIKN GSPEIKLKIT KTYMNGKPLF ESSICGDSAA DVSQSEENGQ K PENKARRN RKRSIKYDSL LEQGLVEAAL VSKISSPSDK KIPAKKESCP NTGRDKDHLL KYNVGDLVWS KVSGYPWWPC MV SADPLLH SYTKLKGQKK SARQYHVQFF GDAPERAWIF EKSLVAFEGE GQFEKLCQES AKQAPTKAEK IKLLKPISGK LRA QWEMGI VQAEEAASMS VEERKAKFTF LYVGDQLHLN PQVAKEAGIA AESLGEMAES SGVSEEAAEN PKSVREECIP MKRR RRAKL CSSAETLESH PDIGKSTPQK TAEADPRRGV GSPPGRKKTT VSMPRSRKGD AASQFLVFCQ KHRDEVVAEH PDASG EEIE ELLRSQWSLL SEKQRARYNT KFALVAPVQA EEDSGNVNGK KRNHTKRIQD PTEDAEAEDT PRKRLRTDKH SLRKRD TIT DKTARTSSYK AMEAASSLKS QAATKNLSDA CKPLKKRNRA STAASSALGF SKSSSPSASL TENEVSDSPG DEPSESP YE SADETQTEVS VSSKKSERGV TAKKEYVCQL CEKPGSLLLC EGPCCGAFHL ACLGLSRRPE GRFTCSECAS GIHSCFVC K ESKTDVKRCV VTQCGKFYHE ACVKKYPLTV FESRGFRCPL HSCVSCHASN PSNPRPSKGK MMRCVRCPVA YHSGDACLA AGCSVIASNS IICTAHFTAR KGKRHHAHVN VSWCFVCSKG GSLLCCESCP AAFHPDCLNI EMPDGSWFCN DCRAGKKLHF QDIIWVKLG NYRWWPAEVC HPKNVPPNIQ KMKHEIGEFP VFFFGSKDYY WTHQARVFPY MEGDRGSRYQ GVRGIGRVFK N ALQEAEAR FREIKLQREA RETQESERKP PPYKHIKVNK PYGKVQIYTA DISEIPKCNC KPTDENPCGF DSECLNRMLM FE CHPQVCP AGEFCQNQCF TKRQYPETKI IKTDGKGWGL VAKRDIRKGE FVNEYVGELI DEEECMARIK HAHENDITHF YML TIDKDR IIDAGPKGNY SRFMNHSCQP NCETLKWTVN GDTRVGLFAV CDIPAGTELT FNYNLDCLGN EKTVCRCGAS NCSG FLGDR PKTSTTLSSE EKGKKTKKKT RRRRAKGEGK RQSEDECFRC GDGGQLVLCD RKFCTKAYHL SCLGLGKRPF GKWEC PWHH CDVCGKPSTS FCHLCPNSFC KEHQDGTAFS CTPDGRSYCC EHDLGAASVR STKTEKPPPE PGKPKGKRRR RRGWRR VTE GK

UniProtKB: Histone-lysine N-methyltransferase NSD2

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Macromolecule #3: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #4: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.800367 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR ...String:
MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR DCLFRPLNKQ VTNAVLKLIE KERNGETINT RLISGVVQSY VELGLNEDDA FAKGPTLTVY KESFESQFLA DT ERFYTRE STEFLQQNPV TEYMKKAEAR LLEEQRRVQV YLHESTQDEL ARKCEQVLIE KHLEIFHTEF QNLLDADKNE DLG RMYNLV SRIQDGLGEL KKLLETHIHN QGLAAIEKCG EAALNDPKMY VQTVLDVHKK YNALVMSAFN NDAGFVAALD KACG RFINN NAVTKMAQSS SKSPELLARY CDSLLKKSSK NPEEAELEDT LNQVMVVFKY IEDKDVFQKF YAKMLAKRLV HQNSA SDDA EASMISKLKQ ACGFEYTSKL QRMFQDIGVS KDLNEQFKKH LTNSEPLDLD FSIQVLSSGS WPFQQSCTFA LPSELE RSY QRFTAFYASR HSGRKLTWLY QLSKGELVTN CFKNRYTLQA STFQMAILLQ YNTEDAYTVQ QLTDSTQIKM DILAQVL QI LLKSKLLVLE DENANVDEVE LKPDTLIKLY LGYKNKKLRV NINVPMKTEQ KQEQETTHKN IEEDRKLLIQ AAIVRIMK M RKVLKHQQLL GEVLTQLSSR FKPRVPVIKK CIDILIEKEY LERVDGEKDT YSYLA

UniProtKB: Cullin-1

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Macromolecule #5: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #6: Transcription regulator protein BACH1

MacromoleculeName: Transcription regulator protein BACH1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.052586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLSENSVFA YESSVHSTNV LLSLNDQRKK DVLCDVTIFV EGQRFRAHRS VLAACSSYFH SRIVGQADGE LNITLPEEVT VKGFEPLIQ FAYTAKLILS KENVDEVCKC VEFLSVHNIE ESCFQFLKFK FLDSTADQQE CPRKKCFSSH CQKTDLKLSL L DQRDLETD ...String:
MSLSENSVFA YESSVHSTNV LLSLNDQRKK DVLCDVTIFV EGQRFRAHRS VLAACSSYFH SRIVGQADGE LNITLPEEVT VKGFEPLIQ FAYTAKLILS KENVDEVCKC VEFLSVHNIE ESCFQFLKFK FLDSTADQQE CPRKKCFSSH CQKTDLKLSL L DQRDLETD EVEEFLENKN VQTPQCKLRR YQGNAKASPP LQDSASQTYE SMCLEKDAAL ALPSLCPKYR KFQKAFGTDR VR TGESSVK DIHASVQPNE RSENECLGGV PECRDLQVML KCDESKLAME PEETKKDPAS QCPTEKSEVT PFPHNSSIDP HGL YSLSLL HTYDQYGDLN FAGMQNTTVL TEKPLSGTDV QEKTFGESQD LPLKSDLGTR EDSSVASSDR SSVEREVAEH LAKG FWSDI CSTDTPCQMQ LSPAVAKDGS EQISQKRSEC PWLGIRISES PEPGQRTFTT LSSVNCPFIS TLSTEGCSSN LEIGN DDYV SEPQQEPCPY ACVISLGDDS ETDTEGDSES CSAREQECEV KLPFNAQRII SLSRNDFQSL LKMHKLTPEQ LDCIHD IRR RSKNRIAAQR CRKRKLDCIQ NLESEIEKLQ SEKESLLKER DHILSTLGET KQNLTGLCQK VCKEAALSQE QIQILAK YS AADCPLSFLI SEKDKSTPDG ELALPSIFSL SDRPPAVLPP CARGNSEPGY ARGQESQQMS TATSEQAGPA EQCRQSGG I SDFCQQMTDK CTTDE

UniProtKB: Transcription regulator protein BACH1

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Macromolecule #7: ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquino...

MacromoleculeName: ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide
type: ligand / ID: 7 / Number of copies: 1 / Formula: A1J20
Molecular weightTheoretical: 608.684 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
Component:
ConcentrationNameFormula
20.0 mMHEPES
200.0 mMSodium ChlorideNaCl
1.0 mMDTT
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
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: OTHER
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 73358
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

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

PDB-29hh:
Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2, UNC10088 and Bach1

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