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- EMDB-35093: Cryo-EM structure of the SIN3L complex from S. pombe -

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Basic information

Entry
Database: EMDB / ID: EMD-35093
TitleCryo-EM structure of the SIN3L complex from S. pombe
Map data
Sample
  • Complex: The SIN3S complex
    • Protein or peptide: x 5 types
  • Protein or peptide: x 4 types
  • Ligand: x 2 types
Function / homology
Function and homology information


: / : / Regulation of TP53 Activity through Acetylation / PI5P Regulates TP53 Acetylation / : / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / SUMOylation of transcription cofactors / histone H3K9 deacetylase activity, hydrolytic mechanism ...: / : / Regulation of TP53 Activity through Acetylation / PI5P Regulates TP53 Acetylation / : / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / SUMOylation of transcription cofactors / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / HDACs deacetylate histones / histone H4K12 deacetylase activity, hydrolytic mechanism / SUMOylation of chromatin organization proteins / H3-H4 histone complex chaperone activity / cell cycle / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / pericentric heterochromatin formation / histone deacetylase / protein lysine deacetylase activity / histone deacetylase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / histone deacetylase complex / pericentric heterochromatin / methylated histone binding / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / heterochromatin formation / histone deacetylase binding / double-strand break repair via nonhomologous end joining / transcription corepressor activity / chromatin organization / histone binding / chromatin remodeling / cell division / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
LCCL domain superfamily / Transcriptional regulatory protein RXT2, N-terminal / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / Histone deacetylation protein Rxt3 / Sds3-like / Sds3-like / Sds3-like / Inhibitor of growth protein, N-terminal histone-binding ...LCCL domain superfamily / Transcriptional regulatory protein RXT2, N-terminal / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / Histone deacetylation protein Rxt3 / Sds3-like / Sds3-like / Sds3-like / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / Paired amphipathic helix superfamily / Paired amphipathic helix repeat / PAH domain profile. / Histone-binding protein RBBP4, N-terminal / : / Histone-binding protein RBBP4 or subunit C of CAF1 complex / Histone deacetylase / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / G-protein beta WD-40 repeat / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
RbAp48-related WD40 repeat-containing protein prw1 / Histone deacetylase clr6 / Chromatin modification-related protein png2 / Paired amphipathic helix protein pst3 / Transcriptional regulatory protein rxt2 / Transcriptional regulatory protein rxt3 / Paired amphipathic helix protein pst1 / Transcriptional regulatory protein dep1 / Transcriptional regulatory protein sds3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast) / fission yeast (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang C / Guo Z / Zhan X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2023
Title: Two assembly modes for SIN3 histone deacetylase complexes.
Authors: Chengcheng Wang / Zhouyan Guo / Chen Chu / Yichen Lu / Xiaofeng Zhang / Xiechao Zhan /
Abstract: The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes ...The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes (named SIN3L and SIN3S) targeting different chromatin regions. Here we present the cryo-electron microscopy structures of the SIN3L and SIN3S complexes from Schizosaccharomyces pombe (S. pombe), revealing two distinct assembly modes. In the structure of SIN3L, each Sin3 isoform (Pst1 and Pst3) interacts with one histone deacetylase Clr6, and one WD40-containing protein Prw1, forming two lobes. These two lobes are bridged by two vertical coiled-coil domains from Sds3/Dep1 and Rxt2/Png2, respectively. In the structure of SIN3S, there is only one lobe organized by another Sin3 isoform Pst2; each of the Cph1 and Cph2 binds to an Eaf3 molecule, providing two modules for histone recognition and binding. Notably, the Pst1 Lobe in SIN3L and the Pst2 Lobe in SIN3S adopt similar conformation with their deacetylase active sites exposed to the space; however, the Pst3 Lobe in SIN3L is in a compact state with its active center buried inside and blocked. Our work reveals two classical organization mechanisms for the SIN3/HDAC complexes to achieve specific targeting and provides a framework for studying the histone deacetylase complexes.
History
DepositionJan 10, 2023-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35093.png

Downloads & links

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Map

FileDownload / File: emd_35093.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.065061845 - 0.124308966
Average (Standard dev.)0.00014828116 (±0.0026157575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 391.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35093_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35093_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : The SIN3S complex

EntireName: The SIN3S complex
Components
  • Complex: The SIN3S complex
    • Protein or peptide: Paired amphipathic helix protein pst1
    • Protein or peptide: Paired amphipathic helix protein pst3
    • Protein or peptide: Histone deacetylase clr6
    • Protein or peptide: Transcriptional regulatory protein dep1
    • Protein or peptide: Transcriptional regulatory protein rxt2
  • Protein or peptide: Transcriptional regulatory protein sds3
  • Protein or peptide: Chromatin modification-related protein png2
  • Protein or peptide: Transcriptional regulatory protein rxt3
  • Protein or peptide: RbAp48-related WD40 repeat-containing protein prw1
  • Ligand: ZINC ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: The SIN3S complex

SupramoleculeName: The SIN3S complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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Macromolecule #1: Paired amphipathic helix protein pst1

MacromoleculeName: Paired amphipathic helix protein pst1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 171.667125 KDa
SequenceString: MAKDWQDARL GQCHRLEDYS NVAINYTGPY LTPSGTMAYH PGNAPLFTQA PPHTNPQGPP PFPLFNSISP VYDPATGRLL YRNVNTQVS HTAIPNPANG YAAVYGGPPS QLPPPPQPQS HPNVTVISAS PARAIEQQPT ILSSTDSNIP RPGTVKSSAS P FVPNQNPS ...String:
MAKDWQDARL GQCHRLEDYS NVAINYTGPY LTPSGTMAYH PGNAPLFTQA PPHTNPQGPP PFPLFNSISP VYDPATGRLL YRNVNTQVS HTAIPNPANG YAAVYGGPPS QLPPPPQPQS HPNVTVISAS PARAIEQQPT ILSSTDSNIP RPGTVKSSAS P FVPNQNPS APPPPPQEYR QLNVTDALSY LDLVKLQFHQ EPEIYNEFLD IMKEFKSQAI ETPEVITRVS KLFAGYPNLI QG FNTFLPP GYSIEISSAD PGSLAGIHIT TPQGPLMIND LGKTTAPPPP HGSTTPLPAA ASYTSMNMKQ SSASHPVLQP PAP STLQFN PSPSPAAPSY PPVDASVKQA ADLDQAINFV NNVKNRFSHK PEAYNSFLDI LKSYQHDQRP IQLVYFQVSQ LFAE APDLL EEFKRFLPDV SVNAPAETQD KSTVVPQESA TATPKRSPSA TPTSALPPIG KFAPPTTAKA QPAPEKRRGE PAVQT RNHS KRTRTATSSV EETTPRAFNV PIAQNKNPSE LEFLEHARQY LANESKYNEF IKLLELYSQE VFDKNALVER CYVFFG SNE HLMNWLKDLV KYNPANPIPV PRPRVDLTQC KSCGPSYRLL PKIELLLPCS GRDDLCWTIL NDAWVSFPTL ASEDSGF IA HRKNQFEENL HKLEEERYEY DRHIGANMRF IELLQIHADK MLKMSEVEKA NWTLPSNLGG KSVSIYHKVI KKVYGKEH A QQIIENLQKN PSVTIPIVLE RLKKKDREWR SLQNHWNELW HDIEEKNFYR SLDHQGVSFK SVDKKSTTPK FLISELRNL AQQQKVELSE GKVTPSHQFL FSYKDPNIIT DIARLFGVFL IHGSTHSAED NEKMSNFLRS FLSLFFDVPY DSFIPYLPTH FNEEESDID SLSSSLIEKP RASSSPIHHA NNNGLRLLKD VLKKTYRGAR ENRSSVKEDY VSESTERTPD ASEIDEHISE H EENDDESS SVFSTGEVWV NCKFTDTDGS LLDDGTKLSD RSVYNLFGNM SLYCFFRLFH TLYSRLEEIK NLEQMAYSKQ HD VKSNPVA VELGLVRHPS ERLGFALPTA DTVYEQAIQL CERLMEGEID QNGFEDALRC LYGIHAFRLY TVEKLVTSII KQL HSVTTN RRLAQVFMYY EKDRVQRRTS PRQQIMYRIQ TETAFGPDEN LCCIDWNSQT RQSAIRLMGR EDLTMGTLKS DAEK WCYYI GSYIMSSPTE GILPEHVRIP FLRKCLPSDE GNEDDESSSV VKSANAIITS FLESGLALTI PINTVKIRYE NGTED VFAR NSEQVYNGPY DKIRDYRQSK WREWLNSDEG WTQGLSKDKV RRIKPCTIES LFNESTLRSG KAERFSENAG VESIGK KGK NLLNESGNGK KLDKGLPPKV NGKSSVTRGN KTNLKARNGR NNDDSSNKIN LSEKEKEKES IEDEEKNREG SMSPVAK HA SDVEDDHDVA KSTAPDFETS SHRPERSSEK KSPSPVFTSV KQTAENDADN EDDKTDMDDQ TEETLDADNT MEEEPSKD D L

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Macromolecule #2: Paired amphipathic helix protein pst3

MacromoleculeName: Paired amphipathic helix protein pst3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 133.049766 KDa
SequenceString: MDVMNVPVDS ERDNPGDKVE TQSDKNHLPK ASPSQSQSPV NTSLHNGDGK DNGVATEPVE NKQILSERSV TRDDYEKGKT IVSSLALSS ISGKDGSISS QNAEGLSSSS NRPLDVNDAL SYLELVKYYF SERREIYNRF LEIMRDFKSQ ALDTLGVINR V SELFNGYP ...String:
MDVMNVPVDS ERDNPGDKVE TQSDKNHLPK ASPSQSQSPV NTSLHNGDGK DNGVATEPVE NKQILSERSV TRDDYEKGKT IVSSLALSS ISGKDGSISS QNAEGLSSSS NRPLDVNDAL SYLELVKYYF SERREIYNRF LEIMRDFKSQ ALDTLGVINR V SELFNGYP QLIEGFNTFL PSGYKIEVQL DSSNTSVVRV GTPMHPLPQQ GVQSTLPVAP SNEDQRTMES TSPTDSQPQP SA PNLVSST ENEKPRVDFN YAIAYMNKVK ARYPPNSDTY MEFLGVLRTY QKAQKSIFEV RARVAEIFKD SPDLLEEFKL FLP DNVDST EPSTPNVQKS PNRLPPVGNF SLPPSAPVRE KRNRPAHSAQ ISRSISKTSR MYRQTAEEPL NSYSLHVYPQ KITA PTSPY AATQEELLAF TTIRQHLPDT LAFHKFLELL HLYREKLLDK TELLNSFSKL VRNDNLTLWF SEFIRWSDNP ILVKN EPVD ERVYLPETFE CISLTYRKLP DSWKQDKCSG RDDLDNSVLN DDYISVAPKP SHVKNIMHHE NQYLQALQLV EDERYD YDR VLNTTESAIK ILANFCEPTI HEHLETALQE LERSKRIIKN ALIIVYGKEH ANLALDTLFK KLPTAAPVLL KRIKTKD QE WRRSKREWSK IWRQIEKKNA QAAFDDRYCR IEGRDRRGLS YSRILRDIDD IYQRQKHRID GAKLGFQFTQ VLCDSLIF L NILRLSDAQL TNSSFYSYAD KGRISAVLKA LLSQFFGIPL PREALETNLA SENIESVKKH RDGLSKIFIR PESADNSNN TNVSFQTDET QTEDETMSDI HPDDVENHSK SKFLGEESKN IIGYNFFGNA TMYVLFRLIC VCYSRLEHIK LFVESSTIYA SSTGGYENI LNICEKYLKG SCSRLEFRKY LQKFNNETCY MICSIERLLK VIFYRIHEIL LDPKLGQLLL LFESDGANSV T TPREQMVY RNHVESILAP ESKIFNMRWY PLEKRLCIQQ LLPADLTMHD FENPAKAFMY YVDSYAISHI TEGVDLMQVK MP FLRRSLQ RISQQGYLAG RGSGRLHSLF NEHFCKSNLQ LFFSTDTYVI FFEPNTENVY INSYNLWVDQ SSQSKKQNRT TNW RRWLES DEGWRKSKAN TDIKFFSETT LDQCIEAM

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Macromolecule #3: Histone deacetylase clr6

MacromoleculeName: Histone deacetylase clr6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 46.165844 KDa
SequenceString: MGFGKKKVSY FYDEDVGNYH YGPQHPMKPH RVRMVHNLVV NYNLYEKLNV ITPVRATRND MTRCHTDEYI EFLWRVTPDT MEKFQPHQL KFNVGDDCPV FDGLYEFCSI SAGGSIGAAQ ELNSGNAEIA INWAGGLHHA KKREASGFCY VNDIALAALE L LKYHQRVL ...String:
MGFGKKKVSY FYDEDVGNYH YGPQHPMKPH RVRMVHNLVV NYNLYEKLNV ITPVRATRND MTRCHTDEYI EFLWRVTPDT MEKFQPHQL KFNVGDDCPV FDGLYEFCSI SAGGSIGAAQ ELNSGNAEIA INWAGGLHHA KKREASGFCY VNDIALAALE L LKYHQRVL YIDIDVHHGD GVEEFFYTTD RVMTCSFHKF GEYFPGTGHI KDTGIGTGKN YAVNVPLRDG IDDESYESVF KP VISHIMQ WFRPEAVILQ CGTDSLAGDR LGCFNLSMKG HSMCVDFVKS FNLPMICVGG GGYTVRNVAR VWTYETGLLA GEE LDENLP YNDYLQYYGP DYKLNVLSNN MENHNTRQYL DSITSEIIEN LRNLSFAPSV QMHKTPGDFT FENAEKQNIA KEEI MDERV

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Macromolecule #4: Transcriptional regulatory protein dep1

MacromoleculeName: Transcriptional regulatory protein dep1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 55.701512 KDa
SequenceString: MTENLQSESI PHEILPKEPF DLPMNNLKSS PKNKDSEKRI NNSIAESEQV VDSALSNPET NANEDIIAPQ LPSQNSEIIE KNSPVNKLN SSTSLTTHQL ASLPKLEVTD HDNVSEAETV VLNEDEEKET SLVGSVSVTE DLGDSSAIGR TILVNNSVEP Q MENTANIT ...String:
MTENLQSESI PHEILPKEPF DLPMNNLKSS PKNKDSEKRI NNSIAESEQV VDSALSNPET NANEDIIAPQ LPSQNSEIIE KNSPVNKLN SSTSLTTHQL ASLPKLEVTD HDNVSEAETV VLNEDEEKET SLVGSVSVTE DLGDSSAIGR TILVNNSVEP Q MENTANIT IVSPSLKESD FESEEKATND NNGLIETNHN SKLEESSEHE EEEDEESNIE RTEDSDHQIP QRGGTLEAPR KG GPRSGVG SRKRKRATVS RKWSTNSESK IKRVALETSQ EESDREIADR RSASEQAHEA DDEKAIKRKE AFDALLNIET EFT FLRNRL YGKKLLKLNE HEEMIQNETH ERFNACIDLI TERRDDRVRL ATENLMKQLG NIKNVMDYVT KQRKYQLLFD KRRI RQALL TKIATKCFQL LNKQKSVHDP TYITQKTMSY RQSALLQKQR IEYEAAVLCE LNSFAGFPTA PIIETASFDD IRNDL LEMG CLSENQD

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Macromolecule #5: Transcriptional regulatory protein rxt2

MacromoleculeName: Transcriptional regulatory protein rxt2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 27.42926 KDa
SequenceString: MKQFEEQIER FKQALFED(SEP)D A(SEP)D(SEP)DS(SEP)IGE ALTNRGLKRK KGSKNVYYGC VGNSSGSSID IDYY NIGNT KRGVVSHFRR RIDPEWLDHD NPYNDINIAE IMSPLTKPQD LLTHPAISSI FEQNYLSILA SSALEIISAE HKYTA HLEQ LMVALLGDDP ...String:
MKQFEEQIER FKQALFED(SEP)D A(SEP)D(SEP)DS(SEP)IGE ALTNRGLKRK KGSKNVYYGC VGNSSGSSID IDYY NIGNT KRGVVSHFRR RIDPEWLDHD NPYNDINIAE IMSPLTKPQD LLTHPAISSI FEQNYLSILA SSALEIISAE HKYTA HLEQ LMVALLGDDP SLPGPPHEVF GISPEQCREL TITVQEALEK SKEFIRCWTN VRMDLLRAIR FKNKVIAYCQ GEDYNG NTQ VLSKNESDGK PNS

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Macromolecule #6: Transcriptional regulatory protein sds3

MacromoleculeName: Transcriptional regulatory protein sds3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 30.800586 KDa
SequenceString: MDVLSRVFDN EKEELDPLLN NPLTASEFRA KKAELEAELE SIRNGTCKTL LDLADELRRS RDEELEIAER WRTFLVNRAQ EEYEVEMKA AKEEYEYRCK TLKEMVLSHL NEKKRKIYEA KDMFDIGSES STLLLHDASS QFIDRRKLRH RRNAGNQQNT Q QLPSLNFF ...String:
MDVLSRVFDN EKEELDPLLN NPLTASEFRA KKAELEAELE SIRNGTCKTL LDLADELRRS RDEELEIAER WRTFLVNRAQ EEYEVEMKA AKEEYEYRCK TLKEMVLSHL NEKKRKIYEA KDMFDIGSES STLLLHDASS QFIDRRKLRH RRNAGNQQNT Q QLPSLNFF DDYLLFPTDE TAVIPQSVKN AVRNSVNSVK PTSAEASLFS PLLSMANANP TNGRERDPRA SERAERDREK AV EKGLSGA TEEDIQSDLQ LLKKELAKKK

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Macromolecule #7: Chromatin modification-related protein png2

MacromoleculeName: Chromatin modification-related protein png2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 34.925855 KDa
SequenceString: MGTSGIEIFA ALNDFTDAIV SVPESVCGKF TSLKEIDAQV RDIRQNVIQE IGVVLKNEKN DELSGEERCE RLQKTLKEIL PYSDSKICL ATDAMNNIKS CIDRLDAGFE YVELEIPQQL RLGYPDDRAL MNYHSTVTPQ TSERRRETRR HQNNQHSQQY S SQERSSSY ...String:
MGTSGIEIFA ALNDFTDAIV SVPESVCGKF TSLKEIDAQV RDIRQNVIQE IGVVLKNEKN DELSGEERCE RLQKTLKEIL PYSDSKICL ATDAMNNIKS CIDRLDAGFE YVELEIPQQL RLGYPDDRAL MNYHSTVTPQ TSERRRETRR HQNNQHSQQY S SQERSSSY NNFEDASSPQ SSYHTPTKRR KNAVPRKSSS PPLSSTKHAP QSTERRPVRR SESRLKQTNG EPLVKHDTLD SS DISREGE QLYCYCQQVS YGQMIGCDNE NCKREWFHLP CVGLVEPPKG IWYCKECEEL AKSSESRQ

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Macromolecule #8: Transcriptional regulatory protein rxt3

MacromoleculeName: Transcriptional regulatory protein rxt3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 39.464164 KDa
SequenceString: MEEKTPENEQ SKKTFDPKDS MKIEETSTNG SSQPSQPSNI KLSIGSILES SNDNGDPEYS ENGMGNMNMN TLPMATSTPM SYTKQPSEA KYPNSVWERK GVSDQEENTS SVKRQKTLPT QSSGEEEAKY SHPGAPTATS ADSISMESRP SNLSTSLSKT T SYPQFQVR ...String:
MEEKTPENEQ SKKTFDPKDS MKIEETSTNG SSQPSQPSNI KLSIGSILES SNDNGDPEYS ENGMGNMNMN TLPMATSTPM SYTKQPSEA KYPNSVWERK GVSDQEENTS SVKRQKTLPT QSSGEEEAKY SHPGAPTATS ADSISMESRP SNLSTSLSKT T SYPQFQVR QFVSPIISID NSALEPFLNR YPASESLFPV TEYEYTPWLE FPLLYSSIGK FVRVTIDIKW LNAAINPRLC RR EIWGTDV YTDDSDIATI LAHCGCFSLL KPVRKIAVVD LYILPPLVHY KGTRKNQIES RSWSSRQDGI SLKIKEVTWK PAC ASIFEN SIHTLTLEER LQARLELSRS STFKI

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Macromolecule #9: RbAp48-related WD40 repeat-containing protein prw1

MacromoleculeName: RbAp48-related WD40 repeat-containing protein prw1 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast)
Molecular weightTheoretical: 48.528926 KDa
SequenceString: MAVSAVPHPS KQAQASEEGI NQEKCINEEY KIWKKNSPFL YDLIITRALE WPCMSLQWYP EQQIFAEHGY TEQKMFLGVR ADVGKYLLA VASIQLPYLN QTVPPTTMEG ASAGDESSLR VNISNLYSHP ESVCSAKLMP QDDSCVATVG NYHNDVLVFD K ESFESYSS ...String:
MAVSAVPHPS KQAQASEEGI NQEKCINEEY KIWKKNSPFL YDLIITRALE WPCMSLQWYP EQQIFAEHGY TEQKMFLGVR ADVGKYLLA VASIQLPYLN QTVPPTTMEG ASAGDESSLR VNISNLYSHP ESVCSAKLMP QDDSCVATVG NYHNDVLVFD K ESFESYSS ASESPLKPKY RLTKHTQPCT SVCWNFLSKG TLVSGSQDAT LSCWDLNAYN ESDSASVLKV HISSHEKQVS DV RFHYKHQ DLLASVSYDQ YLHVHDIRRP DASTKPARSV HAHSGPIHSV AFNPHNDFIL ATCSTDKTIA LWDLRNLNQR LHT LEGHED IVTKISFSPH EEPILASTSA DRRTLVWDLS RIGEDQPAEE AQDGPPELLF MHGGHTSCTI DMDWCPNYNW TMAT AAEDN ILQIWTPSRS IWGNEQLEED ATAYLS

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #11: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 11 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.3000000000000003 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 389222
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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