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- EMDB-9626: Cryo-EM structure of human Ribonuclease P -

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Basic information

Entry
Database: EMDB / ID: EMD-9626
TitleCryo-EM structure of human Ribonuclease P
Map data
Sample
  • Complex: RNase PRibonuclease P
    • RNA: x 1 types
    • Protein or peptide: x 10 types
  • Ligand: x 1 types
KeywordsRibonuclease P / RNA-protein complex / HYDROLASE-RNA complex
Function / homology
Function and homology information


multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / tRNA decay / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / tRNA processing ...multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / tRNA decay / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / tRNA processing / centriolar satellite / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / fibrillar center / rRNA processing / response to xenobiotic stimulus / intracellular membrane-bounded organelle / nucleolus / extracellular space / RNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ribonuclease P protein subunit Rpp38 / Ribonuclease P protein subunit Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit / Pop1, N-terminal / POPLD domain / Ribonuclease P/MRP protein subunit Pop5 / Ribonucleases P/MRP protein subunit Pop1 / Ribonucleases P/MRP protein subunit POP1, N-terminal / POPLD (NUC188) domain / Ribonucleases P/MRP protein subunit Rpp20/Pop7 ...Ribonuclease P protein subunit Rpp38 / Ribonuclease P protein subunit Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit / Pop1, N-terminal / POPLD domain / Ribonuclease P/MRP protein subunit Pop5 / Ribonucleases P/MRP protein subunit Pop1 / Ribonucleases P/MRP protein subunit POP1, N-terminal / POPLD (NUC188) domain / Ribonucleases P/MRP protein subunit Rpp20/Pop7 / Rpp20 subunit of nuclear RNase MRP and P / RNase P subunit Pop5/Rpp14/Rnp2-like / Ribonuclease P/MRP subunit Rpp29 / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / RNase P subunit p30 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 / RNase P subunit p30 / RNAse P Rpr2/Rpp21/SNM1 subunit domain / Ribonuclease P protein subunit Rpp29/RNP1 / Ribonuclease P/MRP subunit Rpp29 superfamily / Ribonuclease P/MRP, subunit p29 / A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins. / Rof/RNase P-like / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Polymerase/histidinol phosphatase-like / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
Ribonuclease P protein subunit p20 / Ribonuclease P protein subunit p40 / Ribonuclease P protein subunit p14 / Ribonuclease P protein subunit p29 / Ribonuclease P protein subunit p38 / Ribonuclease P protein subunit p30 / Ribonuclease P/MRP protein subunit POP5 / Ribonucleases P/MRP protein subunit POP1 / Ribonuclease P protein subunit p25 / Ribonuclease P protein subunit p21
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsWu J / Niu S
CitationJournal: Cell / Year: 2018
Title: Cryo-EM Structure of the Human Ribonuclease P Holoenzyme.
Authors: Jian Wu / Shuangshuang Niu / Ming Tan / Chenhui Huang / Mingyue Li / Yang Song / Qianmin Wang / Juan Chen / Shaohua Shi / Pengfei Lan / Ming Lei /
Abstract: Ribonuclease (RNase) P is a ubiquitous ribozyme that cleaves the 5' leader from precursor tRNAs. Here, we report cryo-electron microscopy structures of the human nuclear RNase P alone and in ...Ribonuclease (RNase) P is a ubiquitous ribozyme that cleaves the 5' leader from precursor tRNAs. Here, we report cryo-electron microscopy structures of the human nuclear RNase P alone and in complex with tRNA. Human RNase P is a large ribonucleoprotein complex that contains 10 protein components and one catalytic RNA. The protein components form an interlocked clamp that stabilizes the RNA in a conformation optimal for substrate binding. Human RNase P recognizes the tRNA using a double-anchor mechanism through both protein-RNA and RNA-RNA interactions. Structural comparison of the apo and tRNA-bound human RNase P reveals that binding of tRNA induces a local conformational change in the catalytic center, transforming the ribozyme into an active state. Our results also provide an evolutionary model depicting how auxiliary RNA elements in bacterial RNase P, essential for substrate binding, and catalysis, were replaced by the much more complex and multifunctional protein components in higher organisms.
History
DepositionAug 20, 2018-
Header (metadata) releaseDec 5, 2018-
Map releaseDec 5, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ahr
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9626.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.03
Minimum - Maximum-0.09011597 - 0.19876729
Average (Standard dev.)0.00018916799 (±0.006135494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0900.1990.000

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Supplemental data

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Sample components

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Entire : RNase P

EntireName: RNase PRibonuclease P
Components
  • Complex: RNase PRibonuclease P
    • RNA: H1 RNA
    • Protein or peptide: Ribonucleases P/MRP protein subunit POP1
    • Protein or peptide: Ribonuclease P protein subunit p38
    • Protein or peptide: Ribonuclease P protein subunit p29
    • Protein or peptide: Ribonuclease P/MRP protein subunit POP5
    • Protein or peptide: Ribonuclease P protein subunit p25
    • Protein or peptide: Ribonuclease P protein subunit p20
    • Protein or peptide: Ribonuclease P protein subunit p14
    • Protein or peptide: Ribonuclease P protein subunit p30
    • Protein or peptide: Ribonuclease P protein subunit p21
    • Protein or peptide: Ribonuclease P protein subunit p40
  • Ligand: ZINC ION

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Supramolecule #1: RNase P

SupramoleculeName: RNase P / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: H1 RNA

MacromoleculeName: H1 RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110.244172 KDa
SequenceString: AUAGGGCGGA GGGAAGCUCA UCAGUGGGGC CACGAGCUGA GUGCGUCCUG UCACUCCACU CCCAUGUCCC UUGGGAAGGU CUGAGACUA GGGCCAGAGG CGGCCCUAAC AGGGCUCUCC CUGAGCUUCG GGGAGGUGAG UUCCCAGAGA ACGGGGCUCC G CGCGAGGU ...String:
AUAGGGCGGA GGGAAGCUCA UCAGUGGGGC CACGAGCUGA GUGCGUCCUG UCACUCCACU CCCAUGUCCC UUGGGAAGGU CUGAGACUA GGGCCAGAGG CGGCCCUAAC AGGGCUCUCC CUGAGCUUCG GGGAGGUGAG UUCCCAGAGA ACGGGGCUCC G CGCGAGGU CAGACUGGGC AGGAGAUGCC GUGGACCCCG CCCUUCGGGG AGGGGCCCGG CGGAUGCCUC CUUUGCCGGA GC UUGGAAC AGACUCACGG CCAGCGAAGU GAGUUCAAUG GCUGAGGUGA GGUACCCCGC AGGGGACCUC AUAACCCAAU UCA GACUAC UCUCCUCCGC CCAUU

GENBANK: GENBANK: X16612.1

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Macromolecule #2: Ribonucleases P/MRP protein subunit POP1

MacromoleculeName: Ribonucleases P/MRP protein subunit POP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 114.896141 KDa
SequenceString: MSNAKERKHA KKMRNQPTNV TLSSGFVADR GVKHHSGGEK PFQAQKQEPH PGTSRQRQTR VNPHSLPDPE VNEQSSSKGM FRKKGGWKA GPEGTSQEIP KYITASTFAQ ARAAEISAML KAVTQKSSNS LVFQTLPRHM RRRAMSHNVK RLPRRLQEIA Q KEAEKAVH ...String:
MSNAKERKHA KKMRNQPTNV TLSSGFVADR GVKHHSGGEK PFQAQKQEPH PGTSRQRQTR VNPHSLPDPE VNEQSSSKGM FRKKGGWKA GPEGTSQEIP KYITASTFAQ ARAAEISAML KAVTQKSSNS LVFQTLPRHM RRRAMSHNVK RLPRRLQEIA Q KEAEKAVH QKKEHSKNKC HKARRCHMNR TLEFNRRQKK NIWLETHIWH AKRFHMVKKW GYCLGERPTV KSHRACYRAM TN RCLLQDL SYYCCLELKG KEEEILKALS GMCNIDTGLT FAAVHCLSGK RQGSLVLYRV NKYPREMLGP VTFIWKSQRT PGD PSESRQ LWIWLHPTLK QDILEEIKAA CQCVEPIKSA VCIADPLPTP SQEKSQTELP DEKIGKKRKR KDDGENAKPI KKII GDGTR DPCLPYSWIS PTTGIIISDL TMEMNRFRLI GPLSHSILTE AIKAASVHTV GEDTEETPHR WWIETCKKPD SVSLH CRQE AIFELLGGIT SPAEIPAGTI LGLTVGDPRI NLPQKKSKAL PNPEKCQDNE KVRQLLLEGV PVECTHSFIW NQDICK SVT ENKISDQDLN RMRSELLVPG SQLILGPHES KIPILLIQQP GKVTGEDRLG WGSGWDVLLP KGWGMAFWIP FIYRGVR VG GLKESAVHSQ YKRSPNVPGD FPDCPAGMLF AEEQAKNLLE KYKRRPPAKR PNYVKLGTLA PFCCPWEQLT QDWESRVQ A YEEPSVASSP NGKESDLRRS EVPCAPMPKK THQPSDEVGT SIEHPREAEE VMDAGCQESA GPERITDQEA SENHVAATG SHLCVLRSRK LLKQLSAWCG PSSEDSRGGR RAPGRGQQGL TREACLSILG HFPRALVWVS LSLLSKGSPE PHTMICVPAK EDFLQLHED WHYCGPQESK HSDPFRSKIL KQKEKKKREK RQKPGRASSD GPAGEEPVAG QEALTLGLWS GPLPRVTLHC S RTLLGFVT QGDFSMAVGC GEALGFVSLT GLLDMLSSQP AAQRGLVLLR PPASLQYRFA RIAIEV

UniProtKB: Ribonucleases P/MRP protein subunit POP1

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Macromolecule #3: Ribonuclease P protein subunit p38

MacromoleculeName: Ribonuclease P protein subunit p38 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.891443 KDa
SequenceString: MAAAPQAPGR GSLRKTRPLV VKTSLNNPYI IRWSALESED MHFILQTLED RLKAIGLQKI EDKKKKNKTP FLKKESREKC SIAVDISEN LKEKKTDAKQ QVSGWTPAHV RKQLAIGVNE VTRALERREL LLVLVCKSVK PAMITSHLIQ LSLSRSVPAC Q VPRLSERI ...String:
MAAAPQAPGR GSLRKTRPLV VKTSLNNPYI IRWSALESED MHFILQTLED RLKAIGLQKI EDKKKKNKTP FLKKESREKC SIAVDISEN LKEKKTDAKQ QVSGWTPAHV RKQLAIGVNE VTRALERREL LLVLVCKSVK PAMITSHLIQ LSLSRSVPAC Q VPRLSERI APVIGLKCVL ALAFKKNTTD FVDEVRAIIP RVPSLSVPWL QDRIEDSGEN LETEPLESQD RELLDTSFED LS KPKRKLA DGRQASVTLQ PLKIKKLIPN PNKIRKPPKS KKATPK

UniProtKB: Ribonuclease P protein subunit p38

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Macromolecule #4: Ribonuclease P protein subunit p29

MacromoleculeName: Ribonuclease P protein subunit p29 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.474854 KDa
SequenceString: MKSVIYHALS QKEANDSDVQ PSGAQRAEAF VRAFLKRSTP RMSPQAREDQ LQRKAVVLEY FTRHKRKEKK KKAKGLSARQ RRELRLFDI KPEQQRYSLF LPLHELWKQY IRDLCSGLKP DTQPQMIQAK LLKADLHGAI ISVTKSKCPS YVGITGILLQ E TKHIFKII ...String:
MKSVIYHALS QKEANDSDVQ PSGAQRAEAF VRAFLKRSTP RMSPQAREDQ LQRKAVVLEY FTRHKRKEKK KKAKGLSARQ RRELRLFDI KPEQQRYSLF LPLHELWKQY IRDLCSGLKP DTQPQMIQAK LLKADLHGAI ISVTKSKCPS YVGITGILLQ E TKHIFKII TKEDRLKVIP KLNCVFTVET DGFISYIYGS KFQLRSSERS AKKFKAKGTI DL

UniProtKB: Ribonuclease P protein subunit p29

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Macromolecule #5: Ribonuclease P/MRP protein subunit POP5

MacromoleculeName: Ribonuclease P/MRP protein subunit POP5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.844672 KDa
SequenceString:
MVRFKHRYLL CELVSDDPRC RLSLDDRVLS SLVRDTIARV HGTFGAAACS IGFAVRYLNA YTGIVLLRCR KEFYQLVWSA LPFITYLEN KGHRYPCFFN TLHVGGTIRT CQKFLIQYNR RQLLILLQNC TDEGEREAIQ KSVTRSCLLE EEEESGEEAA E AME

UniProtKB: Ribonuclease P/MRP protein subunit POP5

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Macromolecule #6: Ribonuclease P protein subunit p25

MacromoleculeName: Ribonuclease P protein subunit p25 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.659406 KDa
SequenceString: MENFRKVRSE EAPAGCGAEG GGPGSGPFAD LAPGAVHMRV KEGSKIRNLM AFATASMAQP ATRAIVFSGC GRATTKTVTC AEILKRRLA GLHQVTRLRY RSVREVWQSL PPGPTQGQTP GEPAASLSVL KNVPGLAILL SKDALDPRQP GYQPPNPHPG P SSPPAAPA ...String:
MENFRKVRSE EAPAGCGAEG GGPGSGPFAD LAPGAVHMRV KEGSKIRNLM AFATASMAQP ATRAIVFSGC GRATTKTVTC AEILKRRLA GLHQVTRLRY RSVREVWQSL PPGPTQGQTP GEPAASLSVL KNVPGLAILL SKDALDPRQP GYQPPNPHPG P SSPPAAPA SKRSLGEPAA GEGSAKRSQP EPGVADEDQT A

UniProtKB: Ribonuclease P protein subunit p25

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Macromolecule #7: Ribonuclease P protein subunit p20

MacromoleculeName: Ribonuclease P protein subunit p20 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.672866 KDa
SequenceString:
MAENREPRGA VEAELDPVEY TLRKRLPSRL PRRPNDIYVN MKTDFKAQLA RCQKLLDGGA RGQNACSEIY IHGLGLAINR AINIALQLQ AGSFGSLQVA ANTSTVELVD ELEPETDTRE PLTRIRNNSA IHIRVFRVTP K

UniProtKB: Ribonuclease P protein subunit p20

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Macromolecule #8: Ribonuclease P protein subunit p14

MacromoleculeName: Ribonuclease P protein subunit p14 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.707014 KDa
SequenceString:
MPAPAATYER VVYKNPSEYH YMKVCLEFQD CGVGLNAAQF KQLLISAVKD LFGEVDAALP LDILTYEEKT LSAILRICSS GLVKLWSSL TLLGSYKGKK CAFRVIQVSP FLLALSGNSR ELVLD

UniProtKB: Ribonuclease P protein subunit p14

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Macromolecule #9: Ribonuclease P protein subunit p30

MacromoleculeName: Ribonuclease P protein subunit p30 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.364277 KDa
SequenceString: MAVFADLDLR AGSDLKALRG LVETAAHLGY SVVAINHIVD FKEKKQEIEK PVAVSELFTT LPIVQGKSRP IKILTRLTII VSDPSHCNV LRATSSRARL YDVVAVFPKT EKLFHIACTH LDVDLVCITV TEKLPFYFKR PPINVAIDRG LAFELVYSPA I KDSTMRRY ...String:
MAVFADLDLR AGSDLKALRG LVETAAHLGY SVVAINHIVD FKEKKQEIEK PVAVSELFTT LPIVQGKSRP IKILTRLTII VSDPSHCNV LRATSSRARL YDVVAVFPKT EKLFHIACTH LDVDLVCITV TEKLPFYFKR PPINVAIDRG LAFELVYSPA I KDSTMRRY TISSALNLMQ ICKGKNVIIS SAAERPLEIR GPYDVANLGL LFGLSESDAK AAVSTNCRAA LLHGETRKTA FG IISTVKK PRPSEGDEDC LPASKKAKCE G

UniProtKB: Ribonuclease P protein subunit p30

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Macromolecule #10: Ribonuclease P protein subunit p21

MacromoleculeName: Ribonuclease P protein subunit p21 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.596068 KDa
SequenceString:
MAGPVKDREA FQRLNFLYQA AHCVLAQDPE NQALARFYCY TERTIAKRLV LRRDPSVKRT LCRGCSSLLV PGLTCTQRQR RCRGQRWTV QTCLTCQRSQ RFLNDPGHLL WGDRPEAQLG SQADSKPLQP LPNTAHSISD RLPEEKMQTQ GSSNQ

UniProtKB: Ribonuclease P protein subunit p21

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Macromolecule #11: Ribonuclease P protein subunit p40

MacromoleculeName: Ribonuclease P protein subunit p40 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.884844 KDa
SequenceString: MATLRRLREA PRHLLVCEKS NFGNHKSRHR HLVQTHYYNY RVSFLIPECG ILSEELKNLV MNTGPYYFVK NLPLHELITP EFISTFIKK GSCYALTYNT HIDEDNTVAL LPNGKLILSL DKDTYEETGL QGHPSQFSGR KIMKFIVSID LMELSLNLDS K KYERISWS ...String:
MATLRRLREA PRHLLVCEKS NFGNHKSRHR HLVQTHYYNY RVSFLIPECG ILSEELKNLV MNTGPYYFVK NLPLHELITP EFISTFIKK GSCYALTYNT HIDEDNTVAL LPNGKLILSL DKDTYEETGL QGHPSQFSGR KIMKFIVSID LMELSLNLDS K KYERISWS FKEKKPLKFD FLLAWHKTGS EESTMMSYFS KYQIQEHQPK VALSTLRDLQ CPVLQSSELE GTPEVSCRAL EL FDWLGAV FSNVDLNNEP NNFISTYCCP EPSTVVAKAY LCTITGFILP EKICLLLEHL CHYFDEPKLA PWVTLSVQGF ADS PVSWEK NEHGFRKGGE HLYNFVIFNN QDYWLQMAVG ANDHCPP

UniProtKB: Ribonuclease P protein subunit p40

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 400198

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