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- EMDB-52977: CryoEM structure of the human LRP2 receptor ectodomain in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-52977
TitleCryoEM structure of the human LRP2 receptor ectodomain in complex with LRPAP1
Map data
Sample
  • Complex: Human LRP2 ectodomain in complex with unidentified endogenous ligands and LRPAP1
    • Complex: LRPAP1
      • Protein or peptide: x 1 types
    • Complex: Human LRP2 ectodomain in complex with unidentified endogenous ligands
      • Protein or peptide: x 5 types
    • Protein or peptide: x 1 types
  • Ligand: x 5 types
KeywordsMegalin / LRP2 / LDL receptor / ENDOCYTOSIS
Function / homology
Function and homology information


extracellular negative regulation of signal transduction / regulation of receptor-mediated endocytosis / Transport of RCbl within the body / negative regulation of very-low-density lipoprotein particle clearance / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / rough endoplasmic reticulum lumen / lipase binding ...extracellular negative regulation of signal transduction / regulation of receptor-mediated endocytosis / Transport of RCbl within the body / negative regulation of very-low-density lipoprotein particle clearance / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / rough endoplasmic reticulum lumen / lipase binding / positive regulation of lysosomal protein catabolic process / folate import across plasma membrane / cobalamin transport / receptor antagonist activity / amyloid-beta clearance by transcytosis / negative regulation of amyloid-beta clearance / ventricular compact myocardium morphogenesis / response to leptin / protein transporter activity / Vitamin D (calciferol) metabolism / low-density lipoprotein particle receptor activity / metal ion transport / transcytosis / vitamin D metabolic process / very-low-density lipoprotein particle receptor binding / cranial skeletal system development / positive regulation of amyloid-beta clearance / neuron projection arborization / coronary artery morphogenesis / cis-Golgi network / insulin-like growth factor I binding / negative regulation of receptor internalization / outflow tract septum morphogenesis / cargo receptor activity / positive regulation of neurogenesis / ventricular septum development / aorta development / low-density lipoprotein particle receptor binding / endoplasmic reticulum-Golgi intermediate compartment / forebrain development / vagina development / hormone binding / amyloid-beta clearance / negative regulation of BMP signaling pathway / negative regulation of protein binding / retinoid metabolic process / transport across blood-brain barrier / Retinoid metabolism and transport / endomembrane system / clathrin-coated pit / receptor-mediated endocytosis / endosome lumen / lipid metabolic process / kidney development / neural tube closure / phosphatidylinositol 3-kinase/protein kinase B signal transduction / brush border membrane / clathrin-coated endocytic vesicle membrane / sensory perception of sound / SH3 domain binding / Golgi lumen / cellular response to growth factor stimulus / male gonad development / endocytosis / Cargo recognition for clathrin-mediated endocytosis / heparin binding / protein transport / amyloid-beta binding / Clathrin-mediated endocytosis / protein-folding chaperone binding / gene expression / lysosome / cell population proliferation / signaling receptor complex / endosome / apical plasma membrane / receptor ligand activity / signaling receptor binding / external side of plasma membrane / axon / lysosomal membrane / calcium ion binding / dendrite / negative regulation of apoptotic process / cell surface / endoplasmic reticulum / Golgi apparatus / signal transduction / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Alpha-2-macroglobulin receptor-associated protein, domain 1 / Alpha-2-macroglobulin RAP, C-terminal / RAP domain superfamily / Alpha-2-macroglobulin RAP, domain 3 / Alpha-2-macroglobulin RAP, domain 2 / Alpha-2-macroglobulin receptor-associated protein / Alpha-2-macroglobulin RAP, N-terminal domain / Alpha-2-macroglobulin RAP, C-terminal domain / : / LRP2-like, EGF-like domain ...Alpha-2-macroglobulin receptor-associated protein, domain 1 / Alpha-2-macroglobulin RAP, C-terminal / RAP domain superfamily / Alpha-2-macroglobulin RAP, domain 3 / Alpha-2-macroglobulin RAP, domain 2 / Alpha-2-macroglobulin receptor-associated protein / Alpha-2-macroglobulin RAP, N-terminal domain / Alpha-2-macroglobulin RAP, C-terminal domain / : / LRP2-like, EGF-like domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Endoplasmic reticulum targeting sequence. / Low-density lipoprotein receptor domain class A / Legume lectin, beta chain, Mn/Ca-binding site / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Alpha-2-macroglobulin receptor-associated protein / Low-density lipoprotein receptor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsRamanadane K / Coscia F
Funding supportEuropean Union, Switzerland, France, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)101041298European Union
Swiss National Science FoundationP500PB_217862 Switzerland
Human Frontier Science Program (HFSP)LT0024/2024-L France
CitationJournal: To Be Published
Title: CryoEM structure of the human LRP2 receptor ectodomain in complex with LRPAP1
Authors: Ramanadane K / Coscia F
History
DepositionFeb 28, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52977.png

Downloads & links

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Map

FileDownload / File: emd_52977.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 560 pix.
= 534.8 Å		0.96 Å/pix.
x 560 pix.
= 534.8 Å		0.96 Å/pix.
x 560 pix.
= 534.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.955 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.015636453 - 0.9424161
Average (Standard dev.)0.009213428 (±0.021321679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 534.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_52977_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human LRP2 ectodomain in complex with unidentified endogenous lig...

EntireName: Human LRP2 ectodomain in complex with unidentified endogenous ligands and LRPAP1
Components
  • Complex: Human LRP2 ectodomain in complex with unidentified endogenous ligands and LRPAP1
    • Complex: LRPAP1
      • Protein or peptide: Alpha-2-macroglobulin receptor-associated protein
    • Complex: Human LRP2 ectodomain in complex with unidentified endogenous ligands
      • Protein or peptide: Low-density lipoprotein receptor-related protein 2
      • Protein or peptide: Unidentified peptide 1
      • Protein or peptide: Unidentified peptide 2
      • Protein or peptide: Unidentified peptide 3
      • Protein or peptide: Unidentified peptide 4
    • Protein or peptide: Unidentified peptide 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-galactopyranose
  • Ligand: CALCIUM ION
  • Ligand: NICKEL (II) ION

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Supramolecule #1: Human LRP2 ectodomain in complex with unidentified endogenous lig...

SupramoleculeName: Human LRP2 ectodomain in complex with unidentified endogenous ligands and LRPAP1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: LRPAP1

SupramoleculeName: LRPAP1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Human LRP2 ectodomain in complex with unidentified endogenous ligands

SupramoleculeName: Human LRP2 ectodomain in complex with unidentified endogenous ligands
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Alpha-2-macroglobulin receptor-associated protein

MacromoleculeName: Alpha-2-macroglobulin receptor-associated protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.404426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSYSREKNQP KPSPKRESGE EFRMEKLNQL WEKAQRLHLP PVRLAELHAD LKIQERDELA WKKLKLDGLD EDGEKEARLI RNLNVILAK YGLDGKKDAR QVTSNSLSGT QEDGLDDPRL EKLWHKAKTS GKFSGEELDK LWREFLHHKE KVHEYNVLLE T LSRTEEIH ...String:
MSYSREKNQP KPSPKRESGE EFRMEKLNQL WEKAQRLHLP PVRLAELHAD LKIQERDELA WKKLKLDGLD EDGEKEARLI RNLNVILAK YGLDGKKDAR QVTSNSLSGT QEDGLDDPRL EKLWHKAKTS GKFSGEELDK LWREFLHHKE KVHEYNVLLE T LSRTEEIH ENVISPSDLS DIKGSVLHSR HTELKEKLRS INQGLDRLRR VSHQGYSTEA EFEEPRVIDL WDLAQSANLT DK ELEAFRE ELKHFEAKIE KHNHYQKQLE IAHEKLRHAE SVGDGERVSR SREKHALLEG RTKELGYTVK KHLQDLSGRI SRA RHNELA LEVLFQGPHH HHHHHHHH

UniProtKB: Alpha-2-macroglobulin receptor-associated protein

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Macromolecule #2: Low-density lipoprotein receptor-related protein 2

MacromoleculeName: Low-density lipoprotein receptor-related protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 502.222469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDRGPAAVAC TLLLALVACL APASGQECDS AHFRCGSGHC IPADWRCDGT KDCSDDADEI GCAVVTCQQG YFKCQSEGQC IPNSWVCDQ DQDCDDGSDE RQDCSQSTCS SHQITCSNGQ CIPSEYRCDH VRDCPDGADE NDCQYPTCEQ LTCDNGACYN T SQKCDWKV ...String:
MDRGPAAVAC TLLLALVACL APASGQECDS AHFRCGSGHC IPADWRCDGT KDCSDDADEI GCAVVTCQQG YFKCQSEGQC IPNSWVCDQ DQDCDDGSDE RQDCSQSTCS SHQITCSNGQ CIPSEYRCDH VRDCPDGADE NDCQYPTCEQ LTCDNGACYN T SQKCDWKV DCRDSSDEIN CTEICLHNEF SCGNGECIPR AYVCDHDNDC QDGSDEHACN YPTCGGYQFT CPSGRCIYQN WV CDGEDDC KDNGDEDGCE SGPHDVHKCS PREWSCPESG RCISIYKVCD GILDCPGRED ENNTSTGKYC SMTLCSALNC QYQ CHETPY GGACFCPPGY IINHNDSRTC VEFDDCQIWG ICDQKCESRP GRHLCHCEEG YILERGQYCK ANDSFGEASI IFSN GRDLL IGDIHGRSFR ILVESQNRGV AVGVAFHYHL QRVFWTDTVQ NKVFSVDING LNIQEVLNVS VETPENLAVD WVNNK IYLV ETKVNRIDMV NLDGSYRVTL ITENLGHPRG IAVDPTVGYL FFSDWESLSG EPKLERAFMD GSNRKDLVKT KLGWPA GVT LDMISKRVYW VDSRFDYIET VTYDGIQRKT VVHGGSLIPH PFGVSLFEGQ VFFTDWTKMA VLKANKFTET NPQVYYQ AS LRPYGVTVYH SLRQPYATNP CKDNNGGCEQ VCVLSHRTDN DGLGFRCKCT FGFQLDTDER HCIAVQNFLI FSSQVAIR G IPFTLSTQED VMVPVSGNPS FFVGIDFDAQ DSTIFFSDMS KHMIFKQKID GTGREILAAN RVENVESLAF DWISKNLYW TDSHYKSISV MRLADKTRRT VVQYLNNPRS VVVHPFAGYL FFTDWFRPAK IMRAWSDGSH LLPVINTTLG WPNGLAIDWA ASRLYWVDA YFDKIEHSTF DGLDRRRLGH IEQMTHPFGL AIFGEHLFFT DWRLGAIIRV RKADGGEMTV IRSGIAYILH L KSYDVNIQ TGSNACNQPT HPNGDCSHFC FPVPNFQRVC GCPYGMRLAS NHLTCEGDPT NEPPTEQCGL FSFPCKNGRC VP NYYLCDG VDDCHDNSDE QLCGTLNNTC SSSAFTCGHG ECIPAHWRCD KRNDCVDGSD EHNCPTHAPA SCLDTQYTCD NHQ CISKNW VCDTDNDCGD GSDEKNCNST ETCQPSQFNC PNHRCIDLSF VCDGDKDCVD GSDEVGCVLN CTASQFKCAS GDKC IGVTN RCDGVFDCSD NSDEAGCPTR PPGMCHSDEF QCQEDGICIP NFWECDGHPD CLYGSDEHNA CVPKTCPSSY FHCDN GNCI HRAWLCDRDN DCGDMSDEKD CPTQPFRCPS WQWQCLGHNI CVNLSVVCDG IFDCPNGTDE SPLCNGNSCS DFNGGC THE CVQEPFGAKC LCPLGFLLAN DSKTCEDIDE CDILGSCSQH CYNMRGSFRC SCDTGYMLES DGRTCKVTAS ESLLLLV AS QNKIIADSVT SQVHNIYSLV ENGSYIVAVD FDSISGRIFW SDATQGKTWS AFQNGTDRRV VFDSSIILTE TIAIDWVG R NLYWTDYALE TIEVSKIDGS HRTVLISKNL TNPRGLALDP RMNEHLLFWS DWGHHPRIER ASMDGSMRTV IVQDKIFWP CGLTIDYPNR LLYFMDSYLD YMDFCDYNGH HRRQVIASDL IIRHPYALTL FEDSVYWTDR ATRRVMRANK WHGGNQSVVM YNIQWPLGI VAVHPSKQPN SVNPCAFSRC SHLCLLSSQG PHFYSCVCPS GWSLSPDLLN CLRDDQPFLI TVRQHIIFGI S LNPEVKSN DAMVPIAGIQ NGLDVEFDDA EQYIYWVENP GEIHRVKTDG TNRTVFASIS MVGPSMNLAL DWISRNLYST NP RTQSIEV LTLHGDIRYR KTLIANDGTA LGVGFPIGIT VDPARGKLYW SDQGTDSGVP AKIASANMDG TSVKTLFTGN LEH LECVTL DIEEQKLYWA VTGRGVIERG NVDGTDRMIL VHQLSHPWGI AVHDSFLYYT DEQYEVIERV DKATGANKIV LRDN VPNLR GLQVYHRRNA AESSNGCSNN MNACQQICLP VPGGLFSCAC ATGFKLNPDN RSCSPYNSFI VVSMLSAIRG FSLEL SDHS ETMVPVAGQG RNALHVDVDV SSGFIYWCDF SSSVASDNAI RRIKPDGSSL MNIVTHGIGE NGVRGIAVDW VAGNLY FTN AFVSETLIEV LRINTTYRRV LLKVTVDMPR HIVVDPKNRY LFWADYGQRP KIERSFLDCT NRTVLVSEGI VTPRGLA VD RSDGYVYWVD DSLDIIARIR INGENSEVIR YGSRYPTPYG ITVFENSIIW VDRNLKKIFQ ASKEPENTEP PTVIRDNI N WLRDVTIFDK QVQPRSPAEV NNNPCLENNG GCSHLCFALP GLHTPKCDCA FGTLQSDGKN CAISTENFLI FALSNSLRS LHLDPENHSP PFQTINVERT VMSLDYDSVS DRIYFTQNLA SGVGQISYAT LSSGIHTPTV IASGIGTADG IAFDWITRRI YYSDYLNQM INSMAEDGSN RTVIARVPKP RAIVLDPCQG YLYWADWDTH AKIERATLGG NFRVPIVNSS LVMPSGLTLD Y EEDLLYWV DASLQRIERS TLTGVDREVI VNAAVHAFGL TLYGQYIYWT DLYTQRIYRA NKYDGSGQIA MTTNLLSQPR GI NTVVKNQ KQQCNNPCEQ FNGGCSHICA PGPNGAECQC PHEGNWYLAN NRKHCIVDNG ERCGASSFTC SNGRCISEEW KCD NDNDCG DGSDEMESVC ALHTCSPTAF TCANGRCVQY SYRCDYYNDC GDGSDEAGCL FRDCNATTEF MCNNRRCIPR EFIC NGVDN CHDNNTSDEK NCPDRTCQSG YTKCHNSNIC IPRVYLCDGD NDCGDNSDEN PTYCTTHTCS SSEFQCASGR CIPQH WYCD QETDCFDASD EPASCGHSER TCLADEFKCD GGRCIPSEWI CDGDNDCGDM SDEDKRHQCQ NQNCSDSEFL CVNDRP PDR RCIPQSWVCD GDVDCTDGYD ENQNCTRRTC SENEFTCGYG LCIPKIFRCD RHNDCGDYSD ERGCLYQTCQ QNQFTCQ NG RCISKTFVCD EDNDCGDGSD ELMHLCHTPE PTCPPHEFKC DNGRCIEMMK LCNHLDDCLD NSDEKGCGIN ECHDPSIS G CDHNCTDTLT SFYCSCRPGY KLMSDKRTCV DIDECTEMPF VCSQKCENVI GSYICKCAPG YLREPDGKTC RQNSNIEPY LIFSNRYYLR NLTIDGYFYS LILEGLDNVV ALDFDRVEKR LYWIDTQRQV IERMFLNKTN KETIINHRLP AAESLAVDWV SRKLYWLDA RLDGLFVSDL NGGHRRMLAQ HCVDANNTFC FDNPRGLALH PQYGYLYWAD WGHRAYIGRV GMDGTNKSVI I STKLEWPN GITIDYTNDL LYWADAHLGY IEYSDLEGHH RHTVYDGALP HPFAITIFED TIYWTDWNTR TVEKGNKYDG SN RQTLVNT THRPFDIHVY HPYRQPIVSN PCGTNNGGCS HLCLIKPGGK GFTCECPDDF RTLQLSGSTY CMPMCSSTQF LCA NNEKCI PIWWKCDGQK DCSDGSDELA LCPQRFCRLG QFQCSDGNCT SPQTLCNAHQ NCPDGSDEDR LLCENHHCDS NEWQ CANKR CIPESWQCDT FNDCEDNSDE DSSHCASRTC RPGQFRCANG RCIPQAWKCD VDNDCGDHSD EPIEECMSSA HLCDN FTEF SCKTNYRCIP KWAVCNGVDD CRDNSDEQGC EERTCHPVGD FRCKNHHCIP LRWQCDGQND CGDNSDEENC APRECT ESE FRCVNQQCIP SRWICDHYND CGDNSDERDC EMRTCHPEYF QCTSGHCVHS ELKCDGSADC LDASDEADCP TRFPDGA YC QATMFECKNH VCIPPYWKCD GDDDCGDGSD EELHLCLDVP CNSPNRFRCD NNRCIYSHEV CNGVDDCGDG TDETEEHC R KPTPKPCTEY EYKCGNGHCI PHDNVCDDAD DCGDWSDELG CNKGKERTCA ENICEQNCTQ LNEGGFICSC TAGFETNVF DRTSCLDINE CEQFGTCPQH CRNTKGSYEC VCADGFTSMS DRPGKRCAAE GSSPLLLLPD NVRIRKYNLS SERFSEYLQD EEYIQAVDY DWDPKDIGLS VVYYTVRGEG SRFGAIKRAY IPNFESGRNN LVQEVDLKLK YVMQPDGIAV DWVGRHIYWS D VKNKRIEV AKLDGRYRKW LISTDLDQPA AIAVNPKLGL MFWTDWGKEP KIESAWMNGE DRNILVFEDL GWPTGLSIDY LN NDRIYWS DFKEDVIETI KYDGTDRRVI AKEAMNPYSL DIFEDQLYWI SKEKGEVWKQ NKFGQGKKEK TLVVNPWLTQ VRI FHQLRY NKSVPNLCKQ ICSHLCLLRP GGYSCACPQG SSFIEGSTTE CDAAIELPIN LPPPCRCMHG GNCYFDETDL PKCK CPSGY TGKYCEMAFS KGISPGTTGW SHPQFEKAGG GSGGGSGGGS WSHPQFEKGG GSGGGSGGGS WSHPQFEK

UniProtKB: Low-density lipoprotein receptor-related protein 2

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Macromolecule #3: Unidentified peptide 1

MacromoleculeName: Unidentified peptide 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 869.063 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #4: Unidentified peptide 2

MacromoleculeName: Unidentified peptide 2 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 613.749 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: Unidentified peptide 3

MacromoleculeName: Unidentified peptide 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.039273 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #6: Unidentified peptide 4

MacromoleculeName: Unidentified peptide 4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 698.854 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #7: Unidentified peptide 5

MacromoleculeName: Unidentified peptide 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.124378 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 19 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #11: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 11 / Number of copies: 2 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-galactopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-galactopyranose / type: ligand / ID: 12 / Number of copies: 7 / Formula: NGA
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NGA:
2-acetamido-2-deoxy-beta-D-galactopyranose

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Macromolecule #13: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 13 / Number of copies: 25 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #14: NICKEL (II) ION

MacromoleculeName: NICKEL (II) ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: NI
Molecular weightTheoretical: 58.693 Da
Chemical component information

ChemComp-NI:
NICKEL (II) ION

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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 mg/mL
BufferpH: 7.9
Component:
ConcentrationFormulaName
40.0 mMNaClsodium chloride
20.0 mMHEPESHEPES
0.2 %OGOG
0.0075 %Tween-20Tween-20
3.0 mMCaCl2calcium chloride
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (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: 0.75 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Composite map (please refer to related focused map and initial consensus map)
Number images used: 318131
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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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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