[English] 日本語
Yorodumi
- EMDB-0974: Structure of nucleosome-bound human BAF complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0974
TitleStructure of nucleosome-bound human BAF complex
Map dataStructure of nucleosome-bound human BAF complex in the apo state
Sample
  • Complex: Structure of nucleosome-bound human BAF complex
    • Complex: Nucleosome
      • Protein or peptide: x 4 types
      • DNA: x 2 types
    • Complex: BAF
      • Protein or peptide: x 9 types
  • Ligand: x 1 types
KeywordsChromatin remodeler / Complex / GENE REGULATION
Function / homology
Function and homology information


negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / Positive Regulation of CDH1 Gene Transcription / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / Formation of the embryonic stem cell BAF (esBAF) complex ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / Positive Regulation of CDH1 Gene Transcription / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / Formation of the embryonic stem cell BAF (esBAF) complex / cellular response to cytochalasin B / neural retina development / npBAF complex / brahma complex / nBAF complex / blastocyst hatching / Formation of the canonical BAF (cBAF) complex / negative regulation of androgen receptor signaling pathway / N-acetyltransferase activity / hepatocyte differentiation / regulation of transepithelial transport / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / morphogenesis of a polarized epithelium / Formation of the polybromo-BAF (pBAF) complex / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Gap junction degradation / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex / protein localization to adherens junction / regulation of G0 to G1 transition / Cell-extracellular matrix interactions / dense body / Folding of actin by CCT/TriC / Tat protein binding / nucleosome array spacer activity / histone H3K14ac reader activity / RNA polymerase I preinitiation complex assembly / postsynaptic actin cytoskeleton / Ino80 complex / RSC-type complex / cellular response to fatty acid / blastocyst formation / Regulation of CDH1 Function / XY body / host-mediated activation of viral transcription / regulation of double-strand break repair / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / germ cell nucleus / RHOF GTPase cycle / adherens junction assembly / nucleosome disassembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / ATP-dependent chromatin remodeler activity / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / tight junction / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / nuclear androgen receptor binding / apical junction complex / positive regulation of double-strand break repair / nuclear chromosome / spinal cord development / regulation of chromosome organization / maintenance of blood-brain barrier / regulation of norepinephrine uptake / transporter regulator activity / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / establishment or maintenance of cell polarity / Recycling pathway of L1 / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of DNA replication / nitric-oxide synthase binding / regulation of embryonic development / brush border / regulation of G1/S transition of mitotic cell cycle / EPH-ephrin mediated repulsion of cells / histone H4K16ac reader activity / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / positive regulation of signal transduction by p53 class mediator / kinesin binding / ATP-dependent activity, acting on DNA / regulation of DNA repair / positive regulation of Wnt signaling pathway / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination
Similarity search - Function
SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : ...SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / DPF1-3, N-terminal domain / DPF1-3, N-terminal / : / SWI/SNF Subunit INI1, DNA binding domain / Chromatin-remodeling complex component Sfh1/SNF5 / SWI/SNF complex subunit BRG1 / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / SWIRM domain / Helicase/SANT-associated domain / SWIRM domain / SWIRM domain profile. / HSA domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / SANT domain profile. / HMG (high mobility group) box / Chromo/chromo shadow domain / Chromatin organization modifier domain / SANT domain / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / PHD-finger / BRCT domain superfamily / Actins signature 1. / Zinc finger C2H2 type domain profile. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Actin / Actin family / Actin / Zinc finger PHD-type profile. / Zinc finger C2H2-type / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 1A / Actin-like protein 6A / Histone H2B 1.1 / Histone H2A type 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Actin, cytoplasmic 1 / Histone H4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / Histone H3.3 / SWI/SNF complex subunit SMARCC2 ...AT-rich interactive domain-containing protein 1A / Actin-like protein 6A / Histone H2B 1.1 / Histone H2A type 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Actin, cytoplasmic 1 / Histone H4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / Histone H3.3 / SWI/SNF complex subunit SMARCC2 / Histone H2B / Zinc finger protein ubi-d4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Similarity search - Component
Biological speciesXenopus calcaratus (Biafran clawed frog) / Homo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShuang H / Zihan W
CitationJournal: Science / Year: 2020
Title: Structure of nucleosome-bound human BAF complex.
Authors: Shuang He / Zihan Wu / Yuan Tian / Zishuo Yu / Jiali Yu / Xinxin Wang / Jie Li / Bijun Liu / Yanhui Xu /
Abstract: Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to ...Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to cancers. The 3.7-angstrom-resolution cryo-electron microscopy structure of human BAF bound to the nucleosome reveals that the nucleosome is sandwiched by the base and the adenosine triphosphatase (ATPase) modules, which are bridged by the actin-related protein (ARP) module. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, engages with and pumps DNA along the nucleosome. The C-terminal α helix of SMARCB1, enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of the nucleosome. AT-rich interactive domain-containing protein 1A (ARID1A) and the SWI/SNF complex subunit SMARCC serve as a structural core and scaffold in the base module organization, respectively. Our study provides structural insights into subunit organization and nucleosome recognition of human BAF complex.
History
DepositionJan 22, 2020-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ltj
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0974.png

Downloads & links

-
Map

FileDownload / File: emd_0974.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of nucleosome-bound human BAF complex in the apo state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 512 pix.
= 532.48 Å		1.04 Å/pix.
x 512 pix.
= 532.48 Å		1.04 Å/pix.
x 512 pix.
= 532.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.48 / Movie #1: 0.6
Minimum - Maximum-1.2884388 - 3.305587
Average (Standard dev.)-0.00006621686 (±0.107257016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 532.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z532.480532.480532.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.2883.306-0.000

-
Supplemental data

-
Sample components

+
Entire : Structure of nucleosome-bound human BAF complex

EntireName: Structure of nucleosome-bound human BAF complex
Components
  • Complex: Structure of nucleosome-bound human BAF complex
    • Complex: Nucleosome
      • Protein or peptide: Histone H3.3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B
      • DNA: DNA (119-MER)
      • DNA: DNA (119-MER)
    • Complex: BAF
      • Protein or peptide: Transcription activator BRG1
      • Protein or peptide: Actin-like protein 6A
      • Protein or peptide: Actin, cytoplasmic 1
      • Protein or peptide: AT-rich interactive domain-containing protein 1A
      • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
      • Protein or peptide: SWI/SNF complex subunit SMARCC2
      • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
      • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
      • Protein or peptide: Zinc finger protein ubi-d4
  • Ligand: ZINC ION

+
Supramolecule #1: Structure of nucleosome-bound human BAF complex

SupramoleculeName: Structure of nucleosome-bound human BAF complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15

+
Supramolecule #2: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #14-#15
Source (natural)Organism: Xenopus calcaratus (Biafran clawed frog)

+
Supramolecule #3: BAF

SupramoleculeName: BAF / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#13
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.360983 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAA IGALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.3

+
Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

+
Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.993295 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG GVTIAQGGVL PNIQSVLLPK KTESAKSAKS K

UniProtKB: Histone H2A type 1

+
Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.873086 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSDPAKSAPA AKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAG RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B

+
Macromolecule #5: Transcription activator BRG1

MacromoleculeName: Transcription activator BRG1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 184.923828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTPDPPLGG TPRPGPSPGP GPSPGAMLGP SPGPSPGSAH SMMGPSPGPP SAGHPIPTQG PGGYPQDNMH QMHKPMESMH EKGMSDDPR YNQMKGMGMR SGGHAGMGPP PSPMDQHSQG YPSPLGGSEH ASSPVPASGP SSGPQMSSGP GGAPLDGADP Q ALGQQNRG ...String:
MSTPDPPLGG TPRPGPSPGP GPSPGAMLGP SPGPSPGSAH SMMGPSPGPP SAGHPIPTQG PGGYPQDNMH QMHKPMESMH EKGMSDDPR YNQMKGMGMR SGGHAGMGPP PSPMDQHSQG YPSPLGGSEH ASSPVPASGP SSGPQMSSGP GGAPLDGADP Q ALGQQNRG PTPFNQNQLH QLRAQIMAYK MLARGQPLPD HLQMAVQGKR PMPGMQQQMP TLPPPSVSAT GPGPGPGPGP GP GPGPAPP NYSRPHGMGG PNMPPPGPSG VPPGMPGQPP GGPPKPWPEG PMANAAAPTS TPQKLIPPQP TGRPSPAPPA VPP AASPVM PPQTQSPGQP AQPAPMVPLH QKQSRITPIQ KPRGLDPVEI LQEREYRLQA RIAHRIQELE NLPGSLAGDL RTKA TIELK ALRLLNFQRQ LRQEVVVCMR RDTALETALN AKAYKRSKRQ SLREARITEK LEKQQKIEQE RKRRQKHQEY LNSIL QHAK DFKEYHRSVT GKIQKLTKAV ATYHANTERE QKKENERIEK ERMRRLMAED EEGYRKLIDQ KKDKRLAYLL QQTDEY VAN LTELVRQHKA AQVAKEKKKK KKKKKAENAE GQTPAIGPDG EPLDETSQMS DLPVKVIHVE SGKILTGTDA PKAGQLE AW LEMNPGYEVA PRSDSEESGS EEEEEEEEEE QPQAAQPPTL PVEEKKKIPD PDSDDVSEVD ARHIIENAKQ DVDDEYGV S QALARGLQSY YAVAHAVTER VDKQSALMVN GVLKQYQIKG LEWLVSLYNN NLNGILADEM GLGKTIQTIA LITYLMEHK RINGPFLIIV PLSTLSNWAY EFDKWAPSVV KVSYKGSPAA RRAFVPQLRS GKFNVLLTTY EYIIKDKHIL AKIRWKYMIV DEGHRMKNH HCKLTQVLNT HYVAPRRLLL TGTPLQNKLP ELWALLNFLL PTIFKSCSTF EQWFNAPFAM TGEKVDLNEE E TILIIRRL HKVLRPFLLR RLKKEVEAQL PEKVEYVIKC DMSALQRVLY RHMQAKGVLL TDGSEKDKKG KGGTKTLMNT IM QLRKICN HPYMFQHIEE SFSEHLGFTG GIVQGLDLYR ASGKFELLDR ILPKLRATNH KVLLFCQMTS LMTIMEDYFA YRG FKYLRL DGTTKAEDRG MLLKTFNEPG SEYFIFLLST RAGGLGLNLQ SADTVIIFDS DWNPHQDLQA QDRAHRIGQQ NEVR VLRLC TVNSVEEKIL AAAKYKLNVD QKVIQAGMFD QKSSSHERRA FLQAILEHEE QDESRHCSTG SGSASFAHTA PPPAG VNPD LEEPPLKEED EVPDDETVNQ MIARHEEEFD LFMRMDLDRR REEARNPKRK PRLMEEDELP SWIIKDDAEV ERLTCE EEE EKMFGRGSRH RKEVDYSDSL TEKQWLKAIE EGTLEEIEEE VRQKKSSRKR KRDSDAGSST PTTSTRSRDK DDESKKQ KK RGRPPAEKLS PNPPNLTKKM KKIVDAVIKY KDSSSGRQLS EVFIQLPSRK ELPEYYELIR KPVDFKKIKE RIRNHKYR S LNDLEKDVML LCQNAQTFNL EGSLIYEDSI VLQSVFTSVR QKIEKEDDSE GEESEEEEEG EEEGSESESR SVKVKIKLG RKEKAQDRLK GGRRRPSRGS RAKPVVSDDD SEEEQEEDRS GSGSEED

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4

+
Macromolecule #6: Actin-like protein 6A

MacromoleculeName: Actin-like protein 6A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.236273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GALVFDIGSY TVRAGYAGED CPKVDFPTAI GMVVERDDGS TLMEIDGDKG KQGGPTYYID TNALRVPREN MEAISPLKNG MVEDWDSFQ AILDHTYKMH VKSEASLHPV LMSEAPWNTR AKREKLTELM FEHYNIPAFF LCKTAVLTAF ANGRSTGLIL D SGATHTTA ...String:
GALVFDIGSY TVRAGYAGED CPKVDFPTAI GMVVERDDGS TLMEIDGDKG KQGGPTYYID TNALRVPREN MEAISPLKNG MVEDWDSFQ AILDHTYKMH VKSEASLHPV LMSEAPWNTR AKREKLTELM FEHYNIPAFF LCKTAVLTAF ANGRSTGLIL D SGATHTTA IPVHDGYVLQ QGIVKSPLAG DFITMQCREL FQEMNIELVP PYMIASKEAV REGSPANWKR KEKLPQVTRS WH NYMCNCV IQDFQASVLQ VSDSTYDEQV AAQMPTVHYE FPNGYNCDFG AERLKIPEGL FDPSNVKGLS GNTMLGVSHV VTT SVGMCD IDIRPGLYGS VIVAGGNTLI QSFTDRLNRE LSQKTPPSMR LKLIANNTTV ERRFSSWIGG SILASLGTFQ QMWI SKQEY EP

UniProtKB: Actin-like protein 6A

+
Macromolecule #7: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.78266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

+
Macromolecule #8: AT-rich interactive domain-containing protein 1A

MacromoleculeName: AT-rich interactive domain-containing protein 1A / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 142.316531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TESKSKKSSS STTTNEKITK LYELGGEPER KMWVDRYLAF TEEKAMGMTN LPAVGRKPLD LYRLYVSVKE IGGLTQVNKN KKWRELATN LNVGTSSSAA SSLKKQYIQC LYAFECKIER GEDPPPDIFA AADSKKSQPK IQPPSPAGSG SMQGPQTPQS T SSSMAEGG ...String:
TESKSKKSSS STTTNEKITK LYELGGEPER KMWVDRYLAF TEEKAMGMTN LPAVGRKPLD LYRLYVSVKE IGGLTQVNKN KKWRELATN LNVGTSSSAA SSLKKQYIQC LYAFECKIER GEDPPPDIFA AADSKKSQPK IQPPSPAGSG SMQGPQTPQS T SSSMAEGG DLKPPTPAST PHSQIPPLPG MSRSNSVGIQ DAFNDGSDST FQKRNSMTPN PGYQPSMNTS DMMGRMSYEP NK DPYGSMR KAPGSDPFMS SGQGPNGGMG DPYSRAAGPG LGNVAMGPRQ HYPYGGPYDR VRTEPGIGPE GNMSTGAPQP NLM PSNPDS GMYSPSRYPP QQQQQQQQRH DSYGNQFSTQ GTPSGSPFPS QQTTMYQQQQ QNYKRPMDGT YGPPAKRHEG EMYS VPYST GQGQPQQQQL PPAQPQPASQ QQAAQPSPQQ DVYNQYGNAY PATATAATER RPAGGPQNQF PFQFGRDRVS APPGT NAQQ NMPPQMMGGP IQASAEVAQQ GTMWQGRNDM TYNYANRQST GSAPQGPAYH GVNRTDEMLH TDQRANHEGS WPSHGT RQP PYGPSAPVPP MTRPPPSNYQ PPPSMQNHIP QVSSPAPLPR PMENRTSPSK SPFLHSGMKM QKAGPPVPAS HIAPAPV QP PMIRRDITFP PGSVEATQPV LKQRRRLTMK DIGTPEAWRV MMSLKSGLLA ESTWALDTIN ILLYDDNSIM TFNLSQLP G LLELLVEYFR RCLIEIFGIL KEYEVGDPGQ RTLLDPGRFS KVSSPAPMEG GEEEEELLGP KLEEEEEEEV VENDEEIAF SGKDKPASEN SEEKLISKFD KLPVKIVQKN DPFVVDCSDK LGRVQEFDSG LLHWRIGGGD TTEHIQTHFE SKTELLPSRP HAPCPPAPR KHVTTAEGTP GTTDQEGPPP DGPPEKRITA TMDDMLSTRS STLTEDGAKS SEAIKESSKF PFGISPAQSH R NIKILEDE PHSKDETPLC TLLDWQDSLA KRCVCVSNTI RSLSFVPGND FEMSKHPGLL LILGKLILLH HKHPERKQAP LT YEKEEEQ DQGVSCNKVE WWWDCLEMLR ENTLVTLANI SGQLDLSPYP ESICLPVLDG LLHWAVCPSA EAQDPFSTLG PNA VLSPQR LVLETLSKLS IQDNNVDLIL ATPPFSRLEK LYSTMVRFLS DRKNPVCREM AVVLLANLAQ GDSLAARAIA VQKG SIGNL LGFLEDSLAA TQFQQSQASL LHMQNPPFEP TSVDMMRRAA RALLALAKVD ENHSEFTLYE SRLLDISVSP LMNSL VSQV ICDVLFLIGQ S

UniProtKB: AT-rich interactive domain-containing protein 1A

+
Macromolecule #9: SWI/SNF-related matrix-associated actin-dependent regulator of ch...

MacromoleculeName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.015094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMMMALSKTF GQKPVKFQLE DDGEFYMIGS EVGNYLRMFR GSLYKRYPSL WRRLATVEER KKIVASSHGK KTKPNTKDHG YTTLATSVT LLKASEVEEI LDGNDEKYKA VSISGGSGGS GGSDPAVIHE NASQPEVLVP IRLDMEIDGQ KLRDAFTWNM N EKLMTPEM ...String:
MMMMALSKTF GQKPVKFQLE DDGEFYMIGS EVGNYLRMFR GSLYKRYPSL WRRLATVEER KKIVASSHGK KTKPNTKDHG YTTLATSVT LLKASEVEEI LDGNDEKYKA VSISGGSGGS GGSDPAVIHE NASQPEVLVP IRLDMEIDGQ KLRDAFTWNM N EKLMTPEM FSEILCDDLD LNPLTFVPAI ASAIRQQIES YPTDSILEDQ SDQRVIIKLN IHVGNISLVD QFEWDMSEKE NS PEKFALK LCSELGLGGE FVTTIAYSIR GQLSWHQKTY AFSENPLPTV EIAIRNTGDA DQWCPLLETL TDAEMEKKIR DQD RNTRRM RRLANTAPAW

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

+
Macromolecule #10: SWI/SNF complex subunit SMARCC2

MacromoleculeName: SWI/SNF complex subunit SMARCC2 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 133.048109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVRKKDGGP NVKYYEAADT VTQFDNVRLW LGKNYKKYIQ AEPPTNKSLS SLVVQLLQFQ EEVFGKHVSN APLTKLPIKC FLDFKAGGS LCHILAAAYK FKSDQGWRRY DFQNPSRMDR NVEMFMTIEK SLVQNNCLSR PNIFLCPEIE PKLLGKLKDI I KRHQGTVT ...String:
MAVRKKDGGP NVKYYEAADT VTQFDNVRLW LGKNYKKYIQ AEPPTNKSLS SLVVQLLQFQ EEVFGKHVSN APLTKLPIKC FLDFKAGGS LCHILAAAYK FKSDQGWRRY DFQNPSRMDR NVEMFMTIEK SLVQNNCLSR PNIFLCPEIE PKLLGKLKDI I KRHQGTVT EDKNNASHVV YPVPGNLEEE EWVRPVMKRD KQVLLHWGYY PDSYDTWIPA SEIEASVEDA PTPEKPRKVH AK WILDTDT FNEWMNEEDY EVNDDKNPVS RRKKISAKTL TDEVNSPDSD RRDKKGGNYK KRKRSPSPSP TPEAKKKNAK KGP STPYTK SKRGHREEEQ EDLTKDMDEP SPVPNVEEVT LPKTVNTKKD SESAPVKGGT MTDLDEQEDE SMETTGKDED ENST GNKGE QTKNPDLHED NVTEQTHHII IPSYAAWFDY NSVHAIERRA LPEFFNGKNK SKTPEIYLAY RNFMIDTYRL NPQEY LTST ACRRNLAGDV CAIMRVHAFL EQWGLINYQV DAESRPTPMG PPPTSHFHVL ADTPSGLVPL QPKTPQQTSA SQQMLN FPD KGKEKPTDMQ NFGLRTDMYT KKNVPSKSKA AASATREWTE QETLLLLEAL EMYKDDWNKV SEHVGSRTQD ECILHFL RL PIEDPYLEDS EASLGPLAYQ PIPFSQSGNP VMSTVAFLAS VVDPRVASAA AKSALEEFSK MKEEVPTALV EAHVRKVE E AAKVTGKADP AFGLESSGIA GTTSDEPERI EESGNDEARV EGQATDEKKE PKEPREGGGA IEEEAKEKTS EAPKKDEEK GKEGDSEKES EKSDGDPIVD PEKEKEPKEG QEEVLKEVVE SEGERKTKVE RDIGEGNLST AAAAALAAAA VKAKHLAAVE ERKIKSLVA LLVETQMKKL EIKLRHFEEL ETIMDREREA LEYQRQQLLA DRQAFHMEQL KYAEMRARQQ HFQQMHQQQQ Q PPPALPPG SQPIPPTGAA GPPAVHGLAV APASVVPAPA GSGAPPGSLG PSEQIGQAGS TAGPQQQQPA GAPQPGAVPP GV PPPGPHG PSPFPNQQTP PSMMPGAVPG SGHPGVAGNA PLGLPFGMPP PPPPPAPSII PFGSLADSIS INLPAPPNLH GHH HHLPFA PGTLPPPNLP VSMANPLHPN LPATTTMPSS LPLGPGLGSA AAQSPAIVAA VQGNLLPSAS PLPDPGTPLP PDPT APSPG TVTPVPPPQ

UniProtKB: SWI/SNF complex subunit SMARCC2

+
Macromolecule #11: SWI/SNF-related matrix-associated actin-dependent regulator of ch...

MacromoleculeName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.311391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAARAGFQSV APSGGAGASG GAGAAAALGP GGTPGPPVRM GPAPGQGLYR SPMPGAAYPR PGMLPGSRMT PQGPSMGPPG YGGNPSVRP GLAQSGMDQS RKRPAPQQIQ QVQQQAVQNR NHNAKKKKMA DKILPQRIRE LVPESQAYMD LLAFERKLDQ T IMRKRLDI ...String:
MAARAGFQSV APSGGAGASG GAGAAAALGP GGTPGPPVRM GPAPGQGLYR SPMPGAAYPR PGMLPGSRMT PQGPSMGPPG YGGNPSVRP GLAQSGMDQS RKRPAPQQIQ QVQQQAVQNR NHNAKKKKMA DKILPQRIRE LVPESQAYMD LLAFERKLDQ T IMRKRLDI QEALKRPIKQ KRKLRIFISN TFNPAKSDAE DGEGTVASWE LRVEGRLLED SALSKYDATK QKRKFSSFFK SL VIELDKD LYGPDNHLVE WHRTATTQET DGFQVKRPGD VNVRCTVLLM LDYQPPQFKL DPRLARLLGI HTQTRPVIIQ ALW QYIKTH KLQDPHEREF VICDKYLQQI FESQRMKFSE IPQRLHALLM PPEPIIINHV ISVDPNDQKK TACYDIDVEV DDTL KTQMN SFLLSTASQQ EIATLDNKIH ETIETINQLK TQREFMLSFA RDPQGFINDW LQSQCRDLKT MTDVVGNPEE ERRAE FYFQ PWAQEAVCRY FYSKVQQRRQ ELEQALGIRN T

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

+
Macromolecule #12: SWI/SNF-related matrix-associated actin-dependent regulator of ch...

MacromoleculeName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.710371 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKRPSYAPP PTPAPATQMP STPGFVGYNP YSHLAYNNYR LGGNPGTNSR VTASSGITIP KPPKPPDKPL MPYMRYSRKV WDQVKASNP DLKLWEIGKI IGGMWRDLTD EEKQEYLNEY EAEKIEYNES MKAYHNSPAY LAYINAKSRA EAALEEESRQ R QSRMEKGE ...String:
MSKRPSYAPP PTPAPATQMP STPGFVGYNP YSHLAYNNYR LGGNPGTNSR VTASSGITIP KPPKPPDKPL MPYMRYSRKV WDQVKASNP DLKLWEIGKI IGGMWRDLTD EEKQEYLNEY EAEKIEYNES MKAYHNSPAY LAYINAKSRA EAALEEESRQ R QSRMEKGE PYMSIQPAED PDDYDDGFSM KHTATARFQR NHRLISEILS ESVVPDVRSV VTTARMQVLK RQVQSLMVHQ RK LEAELLQ IEERHQEKKR KFLESTDSFN NELKRLCGLK VEVDMEKIAA EIAQAEEQAR KRQEEREKEA AEQAERSQSS IVP EEEQAA NKGEEKKDDE NIPMETEETH LEETTESQQN GEEGTSTPED KESGQEGVDS MAEEGTSDSN TGSESNSATV EEPP TDPIP EDEKKE

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1

+
Macromolecule #13: Zinc finger protein ubi-d4

MacromoleculeName: Zinc finger protein ubi-d4 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.781926 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAVVENVVK LLGEQYYKDA MEQCHNYNAR LCAERSVRLP FLDSQTGVAQ SNCYIWMEKR HRGPGLASGQ LYSYPARRWR KKRRAHPPE DPRLSFPSIK PGGSGGSGGS YACDICGKRY KNRPGLSYHY AHSHLAEEEG EDKEDSQPPT PVSQRSEEQK S KKGPDGLA ...String:
MAAVVENVVK LLGEQYYKDA MEQCHNYNAR LCAERSVRLP FLDSQTGVAQ SNCYIWMEKR HRGPGLASGQ LYSYPARRWR KKRRAHPPE DPRLSFPSIK PGGSGGSGGS YACDICGKRY KNRPGLSYHY AHSHLAEEEG EDKEDSQPPT PVSQRSEEQK S KKGPDGLA LPNNYCDFCL GDSKINKKTG QPEELVSCSD CGRSGHPSCL QFTPVMMAAV KTYRWQCIEC KCCNICGTSE ND DQLLFCD DCDRGYHMYC LTPSMSEPPE GSWSCHLCLD LLKEKASIYQ NQNSS

UniProtKB: Zinc finger protein ubi-d4, Zinc finger protein ubi-d4

+
Macromolecule #14: DNA (119-MER)

MacromoleculeName: DNA (119-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.520266 KDa
SequenceString: (DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG) (DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA) (DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC) (DC) (DG)(DC)(DT)(DT)(DA)(DA) ...String:
(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG) (DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA) (DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC) (DC) (DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC) (DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC) (DG)(DC) (DT)(DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA) (DC)(DC)(DG) (DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DC) (DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT) (DC)(DA)(DG)(DA)

+
Macromolecule #15: DNA (119-MER)

MacromoleculeName: DNA (119-MER) / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.92952 KDa
SequenceString: (DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG) (DC) (DG)(DG)(DT)(DT)(DA)(DA) ...String:
(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG) (DC) (DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA) (DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC) (DA)(DG) (DC)(DG)(DC)(DG)(DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA) (DG)(DC)(DG) (DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC) (DG)(DG)(DC)(DA)

+
Macromolecule #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 320658
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more