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- EMDB-49876: E3 ligase UBR4-KCMF1-calmodulin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49876
TitleE3 ligase UBR4-KCMF1-calmodulin complex
Map data
Sample
  • Complex: Human E3 ubiquitin ligase UBR4-KCMF1-calmodulin complex (Silencing Factor of ISR, SiFI)
    • Protein or peptide: E3 ubiquitin-protein ligase UBR4
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: E3 ubiquitin-protein ligase KCMF1
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
KeywordsE3 ligase / UBR4 / ISR / LIGASE
Function / homology
Function and homology information


negative regulation of HRI-mediated signaling / synaptic signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / protein K27-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization / cytoplasm protein quality control / protein K11-linked ubiquitination ...negative regulation of HRI-mediated signaling / synaptic signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / protein K27-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization / cytoplasm protein quality control / protein K11-linked ubiquitination / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / tertiary granule membrane / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / ficolin-1-rich granule membrane / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / protein K63-linked ubiquitination / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / protein K48-linked ubiquitination / cellular response to interferon-beta / specific granule membrane / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / positive regulation of autophagy / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / RAF activation / Transcriptional activation of mitochondrial biogenesis / RING-type E3 ubiquitin transferase / Stimuli-sensing channels / cellular response to type II interferon / long-term synaptic potentiation / response to calcium ion / RAS processing / spindle pole / Signaling by RAF1 mutants
Similarity search - Function
E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / UBR4 E3 catalytic module profile. / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / : ...E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / UBR4 E3 catalytic module profile. / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / : / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / zinc finger / : / Zinc finger C2H2 type domain profile. / Zinc finger C2H2-type / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Armadillo-type fold / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
Calmodulin-1 / E3 ubiquitin-protein ligase UBR4 / E3 ubiquitin-protein ligase KCMF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYang Z / Rape MP
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
The G. Harold and Leila Y. Mathers Foundation United States
Citation
Journal: Nature / Year: 2025
Title: Molecular basis of SIFI activity in the integrated stress response.
Authors: Zhi Yang / Diane L Haakonsen / Michael Heider / Samuel R Witus / Alex Zelter / Tobias Beschauner / Michael J MacCoss / Michael Rapé /
Abstract: Chronic stress response activation impairs cell survival and causes devastating degenerative diseases. Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase silencing factor ...Chronic stress response activation impairs cell survival and causes devastating degenerative diseases. Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase silencing factor of the integrated stress response (SIFI), to terminate stress response signalling and ensure cellular homeostasis. How a silencing factor can sense stress across cellular scales to elicit timely stress response inactivation is poorly understood. Here we combine cryo-electron microscopy analysis of endogenous SIFI with AlphaFold modelling and biochemical studies to report the structural and mechanistic basis of the silencing of the integrated stress response. SIFI detects both stress indicators and stress response components through flexible domains within an easily accessible scaffold, before building linkage-specific ubiquitin chains at separate, sterically restricted elongation modules. Ubiquitin handover by a ubiquitin-like domain couples versatile substrate modification to linkage-specific ubiquitin polymer formation. Stress response silencing therefore exploits a catalytic mechanism that is geared towards processing many diverse proteins and therefore allows a single enzyme to monitor and, if needed, modulate a complex cellular state.
#1: Journal: Biorxiv / Year: 2024
Title: The molecular basis of integrated stress response silencing
Authors: Yang Z / Haakonsen DL / Heider M / Witus SR / Zelter A / Beschauner T / MacCoss MJ / Rape M
History
DepositionMar 22, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49876.png

Downloads & links

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Map

FileDownload / File: emd_49876.map.gz / Format: CCP4 / Size: 244.1 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.)
1.05 Å/pix.
x 400 pix.
= 419.2 Å		1.05 Å/pix.
x 400 pix.
= 419.2 Å		1.05 Å/pix.
x 400 pix.
= 419.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.146
Minimum - Maximum-0.6976985 - 1.4928006
Average (Standard dev.)0.0010224823 (±0.026568636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49876_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_49876_half_map_1.map
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Half map: #1

Fileemd_49876_half_map_2.map
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Sample components

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Entire : Human E3 ubiquitin ligase UBR4-KCMF1-calmodulin complex (Silencin...

EntireName: Human E3 ubiquitin ligase UBR4-KCMF1-calmodulin complex (Silencing Factor of ISR, SiFI)
Components
  • Complex: Human E3 ubiquitin ligase UBR4-KCMF1-calmodulin complex (Silencing Factor of ISR, SiFI)
    • Protein or peptide: E3 ubiquitin-protein ligase UBR4
    • Protein or peptide: Calmodulin-1
    • Protein or peptide: E3 ubiquitin-protein ligase KCMF1
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Human E3 ubiquitin ligase UBR4-KCMF1-calmodulin complex (Silencin...

SupramoleculeName: Human E3 ubiquitin ligase UBR4-KCMF1-calmodulin complex (Silencing Factor of ISR, SiFI)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.27 MDa

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Macromolecule #1: E3 ubiquitin-protein ligase UBR4

MacromoleculeName: E3 ubiquitin-protein ligase UBR4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 577.180938 KDa
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKATSGGEE AAAAAPAPGT PATGADTTPG WEVAVRPLLS ASYSAFEMKE LPQLVASVIE SESEILHHE KQYEPFYSSF VALSTHYITT VCSLIPRNQL QSVAAACKVL IEFSLLRLEN PDEACAVSQK HLILLIKGLC T GCSRLDRT ...String:
MDYKDHDGDY KDHDIDYKDD DDKATSGGEE AAAAAPAPGT PATGADTTPG WEVAVRPLLS ASYSAFEMKE LPQLVASVIE SESEILHHE KQYEPFYSSF VALSTHYITT VCSLIPRNQL QSVAAACKVL IEFSLLRLEN PDEACAVSQK HLILLIKGLC T GCSRLDRT EIITFTAMMK SAKLPQTVKT LSDVEDQKEL ASPVSPELRQ KEVQMNFLNQ LTSVFNPRTV ASQPISTQTL VE GENDEQS STDQASAIKT KNVFIAQNVA SLQELGGSEK LLRVCLNLPY FLRYINRFQD AVLANSFFIM PATVADATAV RNG FHSLVI DVTMALDTLS LPVLEPLNPS RLQDVTVLSL SCLYAGVSVA TCMAILHVGS AQQVRTGSTS SKEDDYESDA ATIV QKCLE IYDMIGQAIS SSRRAGGEHY QNFQLLGAWC LLNSLFLILN LSPTALADKG KEKDPLAALR VRDILSRTKE GVGSP KLGP GKGHQGFGVL SVILANHAIK LLTSLFQDLQ VEALHKGWET DGPPAALSIM AQSTSIQRIQ RLIDSVPLMN LLLTLL STS YRKACVLQRQ RKGSMSSDAS ASTDSNTYYE DDFSSTEEDS SQDDDSEPIL GQWFEETISP SKEKAAPPPP PPPPPLE SS PRVKSPSKQA PGEKGNILAS RKDPELFLGL ASNILNFITS SMLNSRNNFI RNYLSVSLSE HHMATLASII KEVDKDGL K GSSDEEFAAA LYHFNHSLVT SDLQSPNLQN TLLQQLGVAP FSEGPWPLYI HPQSLSVLSR LLLIWQHKAS AQGDPDVPE CLKVWDRFLS TMKQNALQGV VPSETEDLNV EHLQMLLLIF HNFTETGRRA ILSLFVQIIQ ELSVNMDAQM RFVPLILARL LLIFDYLLH QYSKAPVYLF EQVQHNLLSP PFGWASGSQD SNSRRATTPL YHGFKEVEEN WSKHFSSDAV PHPRFYCVLS P EASEDDLN RLDSVACDVL FSKLVKYDEL YAALTALLAA GSQLDTVRRK ENKNVTALEA CALQYYFLIL WRILGILPPS KT YINQLSM NSPEMSECDI LHTLRWSSRL RISSYVNWIK DHLIKQGMKA EHASSLLELA STTKCSSVKY DVEIVEEYFA RQI SSFCSI DCTTILQLHE IPSLQSIYTL DAAISKVQVS LDEHFSKMAA ETDPHKSSEI TKNLLPATLQ LIDTYASFTR AYLL QNFNE EGTTEKPSKE KLQGFAAVLA IGSSRCKANT LGPTLVQNLP SSVQTVCESW NNINTNEFPN IGSWRNAFAN DTIPS ESYI SAVQAAHLGT LCSQSLPLAA SLKHTLLSLV RLTGDLIVWS DEMNPPQVIR TLLPLLLESS TESVAEISSN SLERIL GPA ESDEFLARVY EKLITGCYNI LANHADPNSG LDESILEECL QYLEKQLESS QARKAMEEFF SDSGELVQIM MATANEN LS AKFCNRVLKF FTKLFQLTEK SPNPSLLHLC GSLAQLACVE PVRLQAWLTR MTTSPPKDSD QLDVIQENRQ LLQLLTTY I VRENSQVGEG VCAVLLGTLT PMATEMLANG DGTGFPELMV VMATLASAGQ GAGHLQLHNA AVDWLSRCKK YLSQKNVVE KLNANVMHGK HVMILECTCH IMSYLADVTN ALSQSNGQGP SHLSVDGEER AIEVDSDWVE ELAVEEEDSQ AEDSDEDSLC NKLCTFTIT QKEFMNQHWY HCHTCKMVDG VGVCTVCAKV CHKDHEISYA KYGSFFCDCG AKEDGSCLAL VKRTPSSGMS S TMKESAFQ SEPRISESLV RHASTSSPAD KAKVTISDGK VADEEKPKKS SLCRTVEGCR EELQNQANFS FAPLVLDMLN FL MDAIQTN FQQASAVGSS SRAQQALSEL HTVEKAVEMT DQLMVPTLGS QEGAFENVRM NYSGDQGQTI RQLISAHVLR RVA MCVLSS PHGRRQHLAV SHEKGKITVL QLSALLKQAD SSKRKLTLTR LASAPVPFTV LSLTGNPCKE DYLAVCGLKD CHVL TFSSS GSVSDHLVLH PQLATGNFII KAVWLPGSQT ELAIVTADFV KIYDLCVDAL SPTFYFLLPS SKIRDVTFLF NEEGK NIIV IMSSAGYIYT QLMEEASSAQ QGPFYVTNVL EINHEDLKDS NSQVAGGGVS VYYSHVLQML FFSYCQGKSF AATISR TTL EVLQLFPINI KSSNGGSKTS PALCQWSEVM NHPGLVCCVQ QTTGVPLVVM VKPDTFLIQE IKTLPAKAKI QDMVAIR HT ACNEQQRTTM ILLCEDGSLR IYMANVENTS YWLQPSLQPS SVISIMKPVR KRKTATITTR TSSQVTFPID FFEHNQQL T DVEFGGNDLL QVYNAQQIKH RLNSTGMYVA NTKPGGFTIE ISNNNSTMVM TGMRIQIGTQ AIERAPSYIE IFGRTMQLN LSRSRWFDFP FTREEALQAD KKLNLFIGAS VDPAGVTMID AVKIYGKTKE QFGWPDEPPE EFPSASVSNI CPSNLNQSNG TGDSDSAAP TTTSGTVLER LVVSSLEALE SCFAVGPIIE KERNKNAAQE LATLLLSLPA PASVQQQSKS LLASLHTSRS A YHSHKDQA LLSKAVQCLN TSSKEGKDLD PEVFQRLVIT ARSIAIMRPN NLVHFTESKL PQMETEGMDE GKEPQKQLEG DC CSFITQL VNHFWKLHAS KPKNAFLAPA CLPGLTHIEA TVNALVDIIH GYCTCELDCI NTASKIYMQM LLCPDPAVSF SCK QALIRV LRPRNKRRHV TLPSSPRSNT PMGDKDDDDD DDADEKMQSS GIPNGGHIRQ ESQEQSEVDH GDFEMVSESM VLET AENVN NGNPSPLEAL LAGAEGFPPM LDIPPDADDE TMVELAIALS LQQDQQGSSS SALGLQSLGL SGQAPSSSSL DAGTL SDTT ASAPASDDEG STAATDGSTL RTSPADHGGS VGSESGGSAV DSVAGEHSVS GRSSAYGDAT AEGHPAGPGS VSSSTG AIS TTTGHQEGDG SEGEGEGETE GDVHTSNRLH MVRLMLLERL LQTLPQLRNV GGVRAIPYMQ VILMLTTDLD GEDEKDK GA LDNLLSQLIA ELGMDKKDVS KKNERSALNE VHLVVMRLLS VFMSRTKSGS KSSICESSSL ISSATAAALL SSGAVDYC L HVLKSLLEYW KSQQNDEEPV ATSQLLKPHT TSSPPDMSPF FLRQYVKGHA ADVFEAYTQL LTEMVLRLPY QIKKITDTN SRIPPPVFDH SWFYFLSEYL MIQQTPFVRR QVRKLLLFIC GSKEKYRQLR DLHTLDSHVR GIKKLLEEQG IFLRASVVTA SSGSALQYD TLISLMEHLK ACAEIAAQRT INWQKFCIKD DSVLYFLLQV SFLVDEGVSP VLLQLLSCAL CGSKVLAALA A SSGSSSAS SSSAPVAASS GQATTQSKSS TKKSKKEEKE KEKDGETSGS QEDQLCTALV NQLNKFADKE TLIQFLRCFL LE SNSSSVR WQAHCLTLHI YRNSSKSQQE LLLDLMWSIW PELPAYGRKA AQFVDLLGYF SLKTPQTEKK LKEYSQKAVE ILR TQNHIL TNHPNSNIYN TLSGLVEFDG YYLESDPCLV CNNPEVPFCY IKLSSIKVDT RYTTTQQVVK LIGSHTISKV TVKI GDLKR TKMVRTINLY YNNRTVQAIV ELKNKPARWH KAKKVQLTPG QTEVKIDLPL PIVASNLMIE FADFYENYQA STETL QCPR CSASVPANPG VCGNCGENVY QCHKCRSINY DEKDPFLCNA CGFCKYARFD FMLYAKPCCA VDPIENEEDR KKAVSN INT LLDKADRVYH QLMGHRPQLE NLLCKVNEAA PEKPQDDSGT AGGISSTSAS VNRYILQLAQ EYCGDCKNSF DELSKII QK VFASRKELLE YDLQQREAAT KSSRTSVQPT FTASQYRALS VLGCGHTSST KCYGCASAVT EHCITLLRAL ATNPALRH I LVSQGLIREL FDYNLRRGAA AMREEVRQLM CLLTRDNPEA TQQMNDLIIG KVSTALKGHW ANPDLASSLQ YEMLLLTDS ISKEDSCWEL RLRCALSLFL MAVNIKTPVV VENITLMCLR ILQKLIKPPA PTSKKNKDVP VEALTTVKPY CNEIHAQAQL WLKRDPKAS YDAWKKCLPI RGIDGNGKAP SKSELRHLYL TEKYVWRWKQ FLSRRGKRTS PLDLKLGHNN WLRQVLFTPA T QAARQAAC TIVEALATIP SRKQQVLDLL TSYLDELSIA GECAAEYLAL YQKLITSAHW KVYLAARGVL PYVGNLITKE IA RLLALEE ATLSTDLQQG YALKSLTGLL SSFVEVESIK RHFKSRLVGT VLNGYLCLRK LVVQRTKLID ETQDMLLEML EDM TTGTES ETKAFMAVCI ETAKRYNLDD YRTPVFIFER LCSIIYPEEN EVTEFFVTLE KDPQQEDFLQ GRMPGNPYSS NEPG IGPLM RDIKNKICQD CDLVALLEDD SGMELLVNNK IISLDLPVAE VYKKVWCTTN EGEPMRIVYR MRGLLGDATE EFIES LDST TDEEEDEEEV YKMAGVMAQC GGLECMLNRL AGIRDFKQGR HLLTVLLKLF SYCVKVKVNR QQLVKLEMNT LNVMLG TLN LALVAEQESK DSGGAAVAEQ VLSIMEIILD ESNAEPLSED KGNLLLTGDK DQLVMLLDQI NSTFVRSNPS VLQGLLR II PYLSFGEVEK MQILVERFKP YCNFDKYDED HSGDDKVFLD CFCKIAAGIK NNSNGHQLKD LILQKGITQN ALDYMKKH I PSAKNLDADI WKKFLSRPAL PFILRLLRGL AIQHPGTQVL IGTDSIPNLH KLEQVSSDEG IGTLAENLLE ALREHPDVN KKIDAARRET RAEKKRMAMA MRQKALGTLG MTTNEKGQVV TKTALLKQME ELIEEPGLTC CICREGYKFQ PTKVLGIYTF TKRVALEEM ENKPRKQQGY STVSHFNIVH YDCHLAAVRL ARGREEWESA ALQNANTKCN GLLPVWGPHV PESAFATCLA R HNTYLQEC TGQREPTYQL NIHDIKLLFL RFAMEQSFSA DTGGGGRESN IHLIPYIIHT VLYVLNTTRA TSREEKNLQG FL EQPKEKW VESAFEVDGP YYFTVLALHI LPPEQWRATR VEILRRLLVT SQARAVAPGG ATRLTDKAVK DYSAYRSSLL FWA LVDLIY NMFKKVPTSN TEGGWSCSLA EYIRHNDMPI YEAADKALKT FQEEFMPVET FSEFLDVAGL LSEITDPESF LKDL LNSVP

UniProtKB: E3 ubiquitin-protein ligase UBR4

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Macromolecule #2: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.852545 KDa
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

UniProtKB: Calmodulin-1

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Macromolecule #3: E3 ubiquitin-protein ligase KCMF1

MacromoleculeName: E3 ubiquitin-protein ligase KCMF1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.992348 KDa
SequenceString: MSRHEGVSCD ACLKGNFRGR RYKCLICYDY DLCASCYESG ATTTRHTTDH PMQCILTRVD FDLYYGGEAF SVEQPQSFTC PYCGKMGYT ETSLQEHVTS EHAETSTEVI CPICAALPGG DPNHVTDDFA AHLTLEHRAP RDLDESSGVR HVRRMFHPGR G LGGPRARR ...String:
MSRHEGVSCD ACLKGNFRGR RYKCLICYDY DLCASCYESG ATTTRHTTDH PMQCILTRVD FDLYYGGEAF SVEQPQSFTC PYCGKMGYT ETSLQEHVTS EHAETSTEVI CPICAALPGG DPNHVTDDFA AHLTLEHRAP RDLDESSGVR HVRRMFHPGR G LGGPRARR SNMHFTSSST GGLSSSQSSY SPSNREAMDP IAELLSQLSG VRRSAGGQLN SSGPSASQLQ QLQMQLQLER QH AQAARQQ LETARNATRR TNTSSVTTTI TQSTATTNIA NTESSQQTLQ NSQFLLTRLN DPKMSETERQ SMESERADRS LFV QELLLS TLVREESSSS DEDDRGEMAD FGAMGCVDIM PLDVALENLN LKESNKGNEP PPPPL

UniProtKB: E3 ubiquitin-protein ligase KCMF1

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 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

Concentration3.6 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9d9z

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87263
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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  • 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

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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

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