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- EMDB-52488: Cryo-EM map of human UBR4/KCMF1/CALM1 in complex with UBE2A -

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Basic information

Entry
Database: EMDB / ID: EMD-52488
TitleCryo-EM map of human UBR4/KCMF1/CALM1 in complex with UBE2A
Map data
Sample
  • Complex: Complex of the ubiquitin ligase UBR4/KCMF1/CALM1 with the ubiquitin conjugating enzyme UBE2A
    • Protein or peptide: UBR4
    • Protein or peptide: KCMF1
    • Protein or peptide: CALM1
    • Protein or peptide: UBE2A
KeywordsUbiquitin ligase Protein quality control / LIGASE
Function / homology
Function and homology information


negative regulation of HRI-mediated signaling / HULC complex / synaptic signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / protein K27-linked ubiquitination / positive regulation of mitophagy / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization ...negative regulation of HRI-mediated signaling / HULC complex / synaptic signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / protein K27-linked ubiquitination / positive regulation of mitophagy / 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 / DNA damage tolerance / 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 / E2 ubiquitin-conjugating enzyme / CaMK IV-mediated phosphorylation of CREB / PKA activation / 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 ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / ubiquitin conjugating enzyme activity / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / tertiary granule membrane / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / ficolin-1-rich granule membrane / Regulation of MECP2 expression and activity / DARPP-32 events / protein K63-linked ubiquitination / catalytic complex / Smooth Muscle Contraction / 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 / protein K48-linked ubiquitination / response to UV / specific granule membrane / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / positive regulation of autophagy / FCERI mediated Ca+2 mobilization / substantia nigra development / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / ubiquitin binding / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / spindle microtubule / calcium channel regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis
Similarity search - Function
E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / : / E3 ubiquitin-protein ligase UBR4-like domain / 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 / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / UBR4 E3 catalytic module profile. / : / 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. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / 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 / Ubiquitin-conjugating enzyme E2 A / E3 ubiquitin-protein ligase UBR4 / E3 ubiquitin-protein ligase KCMF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsGrabarczyk DB / Clausen T
Funding support Austria, European Union, 2 items
OrganizationGrant numberCountry
Austrian Research Promotion Agency852936 Austria
H2020 Marie Curie Actions of the European Commission847548European Union
CitationJournal: Science / Year: 2025
Title: Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control.
Authors: Daniel B Grabarczyk / Julian F Ehrmann / Paul Murphy / Woo Seok Yang / Robert Kurzbauer / Lillie E Bell / Luiza Deszcz / Jana Neuhold / Alexander Schleiffer / Alexandra Shulkina / Juyeon Lee ...Authors: Daniel B Grabarczyk / Julian F Ehrmann / Paul Murphy / Woo Seok Yang / Robert Kurzbauer / Lillie E Bell / Luiza Deszcz / Jana Neuhold / Alexander Schleiffer / Alexandra Shulkina / Juyeon Lee / Jin Seok Shin / Anton Meinhart / Gijs A Versteeg / Eszter Zavodszky / Hyun Kyu Song / Ramanujan S Hegde / Tim Clausen /
Abstract: Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome ...Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome system, where UBR4 acts as an essential E4 ubiquitin ligase, amplifying degradation marks on defective proteins. Cryo-electron microscopy analysis of UBR4 in complex with its cofactors KCMF1 and CALM1 reveals a massive 1.3-megadalton ring structure, featuring a central substrate-binding arena and flexibly attached catalytic units. Our structure shows how UBR4 binds substrate and extends lysine-48-specific ubiquitin chains. Efficient substrate targeting depends on both preubiquitination and specific N-degrons, with KCMF1 acting as a key substrate filter. The architecture of the E4 megacomplex is conserved across eukaryotes, but species-specific adaptations allow UBR4 to perform its precisely tuned quality control function in diverse cellular environments.
History
DepositionJan 8, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52488.png

Downloads & links

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Map

FileDownload / File: emd_52488.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 384 pix.
= 486.912 Å		1.27 Å/pix.
x 384 pix.
= 486.912 Å		1.27 Å/pix.
x 384 pix.
= 486.912 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.268 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00228
Minimum - Maximum-0.0031856494 - 0.013650671
Average (Standard dev.)-0.00007724354 (±0.00042018318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 486.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52488_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52488_half_map_1.map
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Half map: #2

Fileemd_52488_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of the ubiquitin ligase UBR4/KCMF1/CALM1 with the ubiquit...

EntireName: Complex of the ubiquitin ligase UBR4/KCMF1/CALM1 with the ubiquitin conjugating enzyme UBE2A
Components
  • Complex: Complex of the ubiquitin ligase UBR4/KCMF1/CALM1 with the ubiquitin conjugating enzyme UBE2A
    • Protein or peptide: UBR4
    • Protein or peptide: KCMF1
    • Protein or peptide: CALM1
    • Protein or peptide: UBE2A

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Supramolecule #1: Complex of the ubiquitin ligase UBR4/KCMF1/CALM1 with the ubiquit...

SupramoleculeName: Complex of the ubiquitin ligase UBR4/KCMF1/CALM1 with the ubiquitin conjugating enzyme UBE2A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: UBR4

MacromoleculeName: UBR4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MATSGGEEAA AAAPAPGTPA TGADTTPGWE VAVRPLLSAS YSAFEMKELP QLVASVIESE SEILHHEKQY EPFYSSFVAL STHYITTVCS LIPRNQLQSV AAACKVLIEF SLLRLENPDE ACAVSQKHLI LLIKGLCTGC SRLDRTEIIT FTAMMKSAKL PQTVKTLSDV ...String:
MATSGGEEAA AAAPAPGTPA TGADTTPGWE VAVRPLLSAS YSAFEMKELP QLVASVIESE SEILHHEKQY EPFYSSFVAL STHYITTVCS LIPRNQLQSV AAACKVLIEF SLLRLENPDE ACAVSQKHLI LLIKGLCTGC SRLDRTEIIT FTAMMKSAKL PQTVKTLSDV EDQKELASPV SPELRQKEVQ MNFLNQLTSV FNPRTVASQP ISTQTLVEGE NDEQSSTDQA SAIKTKNVFI AQNVASLQEL GGSEKLLRVC LNLPYFLRYI NRFQDAVLAN SFFIMPATVA DATAVRNGFH SLVIDVTMAL DTLSLPVLEP LNPSRLQDVT VLSLSCLYAG VSVATCMAIL HVGSAQQVRT GSTSSKEDDY ESDAATIVQK CLEIYDMIGQ AISSSRRAGG EHYQNFQLLG AWCLLNSLFL ILNLSPTALA DKGKEKDPLA ALRVRDILSR TKEGVGSPKL GPGKGHQGFG VLSVILANHA IKLLTSLFQD LQVEALHKGW ETDGPPAALS IMAQSTSIQR IQRLIDSVPL MNLLLTLLST SYRKACVLQR QRKGSMSSDA SASTDSNTYY EDDFSSTEED SSQDDDSEPI LGQWFEETIS PSKEKAAPPP PPPPPPLESS PRVKSPSKQA PGEKGNILAS RKDPELFLGL ASNILNFITS SMLNSRNNFI RNYLSVSLSE HHMATLASII KEVDKDGLKG SSDEEFAAAL YHFNHSLVTS DLQSPNLQNT LLQQLGVAPF SEGPWPLYIH PQSLSVLSRL LLIWQHKASA QGDPDVPECL KVWDRFLSTM KQNALQGVVP SETEDLNVEH LQMLLLIFHN FTETGRRAIL SLFVQIIQEL SVNMDAQMRF VPLILARLLL IFDYLLHQYS KAPVYLFEQV QHNLLSPPFG WASGSQDSNS RRATTPLYHG FKEVEENWSK HFSSDAVPHP RFYCVLSPEA SEDDLNRLDS VACDVLFSKL VKYDELYAAL TALLAAGSQL DTVRRKENKN VTALEACALQ YYFLILWRIL GILPPSKTYI NQLSMNSPEM SECDILHTLR WSSRLRISSY VNWIKDHLIK QGMKAEHASS LLELASTTKC SSVKYDVEIV EEYFARQISS FCSIDCTTIL QLHEIPSLQS IYTLDAAISK VQVSLDEHFS KMAAETDPHK SSEITKNLLP ATLQLIDTYA SFTRAYLLQN FNEEGTTEKP SKEKLQGFAA VLAIGSSRCK ANTLGPTLVQ NLPSSVQTVC ESWNNINTNE FPNIGSWRNA FANDTIPSES YISAVQAAHL GTLCSQSLPL AASLKHTLLS LVRLTGDLIV WSDEMNPPQV IRTLLPLLLE SSTESVAEIS SNSLERILGP AESDEFLARV YEKLITGCYN ILANHADPNS GLDESILEEC LQYLEKQLES SQARKAMEEF FSDSGELVQI MMATANENLS AKFCNRVLKF FTKLFQLTEK SPNPSLLHLC GSLAQLACVE PVRLQAWLTR MTTSPPKDSD QLDVIQENRQ LLQLLTTYIV RENSQVGEGV CAVLLGTLTP MATEMLANGD GTGFPELMVV MATLASAGQG AGHLQLHNAA VDWLSRCKKY LSQKNVVEKL NANVMHGKHV MILECTCHIM SYLADVTNAL SQSNGQGPSH LSVDGEERAI EVDSDWVEEL AVEEEDSQAE DSDEDSLCNK LCTFTITQKE FMNQHWYHCH TCKMVDGVGV CTVCAKVCHK DHEISYAKYG SFFCDCGAKE DGSCLALVKR TPSSGMSSTM KESAFQSEPR ISESLVRHAS TSSPADKAKV TISDGKVADE EKPKKSSLCR TVEGCREELQ NQANFSFAPL VLDMLNFLMD AIQTNFQQAS AVGSSSRAQQ ALSELHTVEK AVEMTDQLMV PTLGSQEGAF ENVRMNYSGD QGQTIRQLIS AHVLRRVAMC VLSSPHGRRQ HLAVSHEKGK ITVLQLSALL KQADSSKRKL TLTRLASAPV PFTVLSLTGN PCKEDYLAVC GLKDCHVLTF SSSGSVSDHL VLHPQLATGN FIIKAVWLPG SQTELAIVTA DFVKIYDLCV DALSPTFYFL LPSSKIRDVT FLFNEEGKNI IVIMSSAGYI YTQLMEEASS AQQGPFYVTN VLEINHEDLK DSNSQVAGGG VSVYYSHVLQ MLFFSYCQGK SFAATISRTT LEVLQLFPIN IKSSNGGSKT SPALCQWSEV MNHPGLVCCV QQTTGVPLVV MVKPDTFLIQ EIKTLPAKAK IQDMVAIRHT ACNEQQRTTM ILLCEDGSLR IYMANVENTS YWLQPSLQPS SVISIMKPVR KRKTATITTR TSSQVTFPID FFEHNQQLTD VEFGGNDLLQ VYNAQQIKHR LNSTGMYVAN TKPGGFTIEI SNNNSTMVMT GMRIQIGTQA IERAPSYIEI FGRTMQLNLS RSRWFDFPFT REEALQADKK LNLFIGASVD PAGVTMIDAV KIYGKTKEQF GWPDEPPEEF PSASVSNICP SNLNQSNGTG DSDSAAPTTT SGTVLERLVV SSLEALESCF AVGPIIEKER NKNAAQELAT LLLSLPAPAS VQQQSKSLLA SLHTSRSAYH SHKDQALLSK AVQCLNTSSK EGKDLDPEVF QRLVITARSI AIMRPNNLVH FTESKLPQME TEGMDEGKEP QKQLEGDCCS FITQLVNHFW KLHASKPKNA FLAPACLPGL THIEATVNAL VDIIHGYCTC ELDCINTASK IYMQMLLCPD PAVSFSCKQA LIRVLRPRNK RRHVTLPSSP RSNTPMGDKD DDDDDDADEK MQSSGIPNGG HIRQESQEQS EVDHGDFEMV SESMVLETAE NVNNGNPSPL EALLAGAEGF PPMLDIPPDA DDETMVELAI ALSLQQDQQG SSSSALGLQS LGLSGQAPSS SSLDAGTLSD TTASAPASDD EGSTAATDGS TLRTSPADHG GSVGSESGGS AVDSVAGEHS VSGRSSAYGD ATAEGHPAGP GSVSSSTGAI STTTGHQEGD GSEGEGEGET EGDVHTSNRL HMVRLMLLER LLQTLPQLRN VGGVRAIPYM QVILMLTTDL DGEDEKDKGA LDNLLSQLIA ELGMDKKDVS KKNERSALNE VHLVVMRLLS VFMSRTKSGS KSSICESSSL ISSATAAALL SSGAVDYCLH VLKSLLEYWK SQQNDEEPVA TSQLLKPHTT SSPPDMSPFF LRQYVKGHAA DVFEAYTQLL TEMVLRLPYQ IKKITDTNSR IPPPVFDHSW FYFLSEYLMI QQTPFVRRQV RKLLLFICGS KEKYRQLRDL HTLDSHVRGI KKLLEEQGIF LRASVVTASS GSALQYDTLI SLMEHLKACA EIAAQRTINW QKFCIKDDSV LYFLLQVSFL VDEGVSPVLL QLLSCALCGS KVLAALAASS GSSSASSSSA PVAASSGQAT TQSKSSTKKS KKEEKEKEKD GETSGSQEDQ LCTALVNQLN KFADKETLIQ FLRCFLLESN SSSVRWQAHC LTLHIYRNSS KSQQELLLDL MWSIWPELPA YGRKAAQFVD LLGYFSLKTP QTEKKLKEYS QKAVEILRTQ NHILTNHPNS NIYNTLSGLV EFDGYYLESD PCLVCNNPEV PFCYIKLSSI KVDTRYTTTQ QVVKLIGSHT ISKVTVKIGD LKRTKMVRTI NLYYNNRTVQ AIVELKNKPA RWHKAKKVQL TPGQTEVKID LPLPIVASNL MIEFADFYEN YQASTETLQC PRCSASVPAN PGVCGNCGEN VYQCHKCRSI NYDEKDPFLC NACGFCKYAR FDFMLYAKPC CAVDPIENEE DRKKAVSNIN TLLDKADRVY HQLMGHRPQL ENLLCKVNEA APEKPQDDSG TAGGISSTSA SVNRYILQLA QEYCGDCKNS FDELSKIIQK VFASRKELLE YDLQQREAAT KSSRTSVQPT FTASQYRALS VLGCGHTSST KCYGCASAVT EHCITLLRAL ATNPALRHIL VSQGLIRELF DYNLRRGAAA MREEVRQLMC LLTRDNPEAT QQMNDLIIGK VSTALKGHWA NPDLASSLQY EMLLLTDSIS KEDSCWELRL RCALSLFLMA VNIKTPVVVE NITLMCLRIL QKLIKPPAPT SKKNKDVPVE ALTTVKPYCN EIHAQAQLWL KRDPKASYDA WKKCLPIRGI DGNGKAPSKS ELRHLYLTEK YVWRWKQFLS RRGKRTSPLD LKLGHNNWLR QVLFTPATQA ARQAACTIVE ALATIPSRKQ QVLDLLTSYL DELSIAGECA AEYLALYQKL ITSAHWKVYL AARGVLPYVG NLITKEIARL LALEEATLST DLQQGYALKS LTGLLSSFVE VESIKRHFKS RLVGTVLNGY LCLRKLVVQR TKLIDETQDM LLEMLEDMTT GTESETKAFM AVCIETAKRY NLDDYRTPVF IFERLCSIIY PEENEVTEFF VTLEKDPQQE DFLQGRMPGN PYSSNEPGIG PLMRDIKNKI CQDCDLVALL EDDSGMELLV NNKIISLDLP VAEVYKKVWC TTNEGEPMRI VYRMRGLLGD ATEEFIESLD STTDEEEDEE EVYKMAGVMA QCGGLECMLN RLAGIRDFKQ GRHLLTVLLK LFSYCVKVKV NRQQLVKLEM NTLNVMLGTL NLALVAEQES KDSGGAAVAE QVLSIMEIIL DESNAEPLSE DKGNLLLTGD KDQLVMLLDQ INSTFVRSNP SVLQGLLRII PYLSFGEVEK MQILVERFKP YCNFDKYDED HSGDDKVFLD CFCKIAAGIK NNSNGHQLKD LILQKGITQN ALDYMKKHIP SAKNLDADIW KKFLSRPALP FILRLLRGLA IQHPGTQVLI GTDSIPNLHK LEQVSSDEGI GTLAENLLEA LREHPDVNKK IDAARRETRA EKKRMAMAMR QKALGTLGMT TNEKGQVVTK TALLKQMEEL IEEPGLTCCI CREGYKFQPT KVLGIYTFTK RVALEEMENK PRKQQGYSTV SHFNIVHYDC HLAAVRLARG REEWESAALQ NANTKCNGLL PVWGPHVPES AFATCLARHN TYLQECTGQR EPTYQLNIHD IKLLFLRFAM EQSFSADTGG GGRESNIHLI PYIIHTVLYV LNTTRATSRE EKNLQGFLEQ PKEKWVESAF EVDGPYYFTV LALHILPPEQ WRATRVEILR RLLVTSQARA VAPGGATRLT DKAVKDYSAY RSSLLFWALV DLIYNMFKKV PTSNTEGGWS CSLAEYIRHN DMPIYEAADK ALKTFQEEFM PVETFSEFLD VAGLLSEITD PESFLKDLLN SVPHHHHHHH HHH

UniProtKB: E3 ubiquitin-protein ligase UBR4

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Macromolecule #2: KCMF1

MacromoleculeName: KCMF1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSRHEGVSCD ACLKGNFRGR RYKCLICYDY DLCASCYESG ATTTRHTTDH PMQCILTRVD FDLYYGGEAF SVEQPQSFTC PYCGKMGYTE TSLQEHVTSE HAETSTEVIC PICAALPGGD PNHVTDDFAA HLTLEHRAPR DLDESSGVRH VRRMFHPGRG LGGPRARRSN ...String:
MSRHEGVSCD ACLKGNFRGR RYKCLICYDY DLCASCYESG ATTTRHTTDH PMQCILTRVD FDLYYGGEAF SVEQPQSFTC PYCGKMGYTE TSLQEHVTSE HAETSTEVIC PICAALPGGD PNHVTDDFAA HLTLEHRAPR DLDESSGVRH VRRMFHPGRG LGGPRARRSN MHFTSSSTGG LSSSQSSYSP SNREAMDPIA ELLSQLSGVR RSAGGQLNSS GPSASQLQQL QMQLQLERQH AQAARQQLET ARNATRRTNT SSVTTTITQS TATTNIANTE SSQQTLQNSQ FLLTRLNDPK MSETERQSME SERADRSLFV QELLLSTLVR EESSSSDEDD RGEMADFGAM GCVDIMPLDV ALENLNLKES NKGNEPPPPP LSAWSHPQFE K

UniProtKB: E3 ubiquitin-protein ligase KCMF1

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Macromolecule #3: CALM1

MacromoleculeName: CALM1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MDYKDDDDKM ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

UniProtKB: Calmodulin-1

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Macromolecule #4: UBE2A

MacromoleculeName: UBE2A / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSYYHHHHHH DYDIPTTENL YFQGCAMSTP ARRRLMRDFK RLQEDPPAGV SGAPSENNIM VWNAVIFGPE GTPFEDGTFK LTIEFTEEYP NKPPTVRFVS KMFHPNVYAD GSICLDILQN RWSPTYDVSS ILTSIQSLLD EPNPNSPANS QAAQLYQENK REYEKRVSAI VEQSWRDC

UniProtKB: Ubiquitin-conjugating enzyme E2 A

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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: 7.5
VitrificationCryogen name: ETHANE

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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: 0.8 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Symmetry expanded / Number images used: 154691
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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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

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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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