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Yorodumi- EMDB-42685: Structure of Ran bound to RCC1 and the nucleosome core particle (... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42685 | |||||||||
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Title | Structure of Ran bound to RCC1 and the nucleosome core particle (composite map) | |||||||||
Map data | Composite map of the Ran-RCC1-NCP complex. The Ran-RCC1 portion was taken from a focus-refined Ran-RCC1 map. The NCP portion was taken from a 1-side bound Ran-RCC1-NCP map. Both local-sharpened. | |||||||||
Sample |
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Keywords | GTPase / Guanine nucleotide exchange factor / chromatin-binding / NUCLEAR PROTEIN | |||||||||
Function / homology | Function and homology information HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band ...HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Regulation of endogenous retroelements by KRAB-ZFP proteins / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / larval somatic muscle development / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / mitotic nuclear membrane reassembly / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / manchette / sulfate binding / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / regulation of mitotic nuclear division / dynein intermediate chain binding / nuclear chromosome / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / nucleosome binding / spindle assembly / ribosomal subunit export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / nucleosomal DNA binding / viral process / centriole / protein export from nucleus / mitotic spindle organization / guanyl-nucleotide exchange factor activity / G protein activity / condensed nuclear chromosome / male germ cell nucleus / chromosome segregation / hippocampus development / Transcriptional regulation by small RNAs / recycling endosome / heterochromatin formation / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / G1/S transition of mitotic cell cycle / structural constituent of chromatin / GDP binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / nucleosome / melanosome / positive regulation of protein binding / nucleosome assembly / nuclear envelope / chromatin organization / mitotic cell cycle / chromosome / histone binding / midbody / actin cytoskeleton organization / nucleic acid binding / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / GTP binding / protein-containing complex binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Drosophila melanogaster (fruit fly) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Huang SK / Rubinstein JL / Kay LE | |||||||||
Funding support | Canada, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle Authors: Huang SK / Rubinstein JL / Kay LE | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42685.map.gz | 14.9 MB | EMDB map data format | |
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Header (meta data) | emd-42685-v30.xml emd-42685.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42685_fsc.xml emd_42685_fsc_2.xml | 8.4 KB 8.4 KB | Display Display | FSC data file |
Images | emd_42685.png | 64.8 KB | ||
Filedesc metadata | emd-42685.cif.gz | 7.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42685 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42685 | HTTPS FTP |
-Validation report
Summary document | emd_42685_validation.pdf.gz | 469.4 KB | Display | EMDB validaton report |
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Full document | emd_42685_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | emd_42685_validation.xml.gz | 11 KB | Display | |
Data in CIF | emd_42685_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42685 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42685 | HTTPS FTP |
-Related structure data
Related structure data | 8ux1MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_42685.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of the Ran-RCC1-NCP complex. The Ran-RCC1 portion was taken from a focus-refined Ran-RCC1 map. The NCP portion was taken from a 1-side bound Ran-RCC1-NCP map. Both local-sharpened. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Ran-RCC1-NCP complex
Entire | Name: Ran-RCC1-NCP complex |
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Components |
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-Supramolecule #1: Ran-RCC1-NCP complex
Supramolecule | Name: Ran-RCC1-NCP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Histone H3
Macromolecule | Name: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 15.405036 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LSAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3 |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 Details: An extra isoleucine was inserted at the N-terminus following the first residue methionine Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 11.521611 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MITGRGKGGK GLGKGGAKRH RKVLRDNIQG ITKPAIRRLA RRGGVKRISG LIYEETRGVL KVFLENVIRD AVTYTEHAKR KTVTAMDVV YALKRQGRTL YGFGG UniProtKB: Histone H4 |
-Macromolecule #3: Histone H2A
Macromolecule | Name: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 13.388727 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSGRGKGGKV KGKAKSRSNR AGLQFPVGRI HRLLRKGNYA ERVGAGAPVY LAAVMEYLAA EVLELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLSG VTIAQGGVLP NIQAVLLPKK TEKKA UniProtKB: Histone H2A |
-Macromolecule #4: Histone H2B
Macromolecule | Name: Histone H2B / type: protein_or_peptide / ID: 4 Details: An extra glycine was left at the N-terminus as a result of TEV cleavage. An extra isoleucine (residue 3) was inserted after the initiation methionine. Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 13.897275 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GMIPPKTSGK AAKKAGKAQK NITKTDKKKK RKRKESYAIY IYKVLKQVHP DTGISSKAMS IMNSFVNDIF ERIAAEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK UniProtKB: Histone H2B |
-Macromolecule #7: GTP-binding nuclear protein Ran
Macromolecule | Name: GTP-binding nuclear protein Ran / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.456105 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAAQGEPQVQ FKLVLVGDGG TGKTTFVKRH LTGEFEKKYV ATLGVEVHPL VFHTNRGPIK FNVWDTAGQE KFGGLRDGYY IQAQCAIIM FDVTSRVTYK NVPNWHRDLV RVCENIPIVL CGNKVDIKDR KVKAKSIVFH RKKNLQYYDI SAKSNYNFEK P FLWLARKL ...String: MAAQGEPQVQ FKLVLVGDGG TGKTTFVKRH LTGEFEKKYV ATLGVEVHPL VFHTNRGPIK FNVWDTAGQE KFGGLRDGYY IQAQCAIIM FDVTSRVTYK NVPNWHRDLV RVCENIPIVL CGNKVDIKDR KVKAKSIVFH RKKNLQYYDI SAKSNYNFEK P FLWLARKL IGDPNLEFVA MPALAPPEVV MDPALAAQYE HDLEVAQTTA LPDEDDDL UniProtKB: GTP-binding nuclear protein Ran |
-Macromolecule #8: Regulator of chromosome condensation
Macromolecule | Name: Regulator of chromosome condensation / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.893758 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: SPKRIAKRRS PPADAIPKSK KVKVSHRSHS TEPGLVLTLG QGDVGQLGLG ENVMERKKPA LVSIPEDVVQ AEAGGMHTVC LSKSGQVYS FGCNDEGALG RDTSVEGSEM VPGKVELQEK VVQVSAGDSH TAALTDDGRV FLWGSFRDNN GVIGLLEPMK K SMVPVQVQ ...String: SPKRIAKRRS PPADAIPKSK KVKVSHRSHS TEPGLVLTLG QGDVGQLGLG ENVMERKKPA LVSIPEDVVQ AEAGGMHTVC LSKSGQVYS FGCNDEGALG RDTSVEGSEM VPGKVELQEK VVQVSAGDSH TAALTDDGRV FLWGSFRDNN GVIGLLEPMK K SMVPVQVQ LDVPVVKVAS GNDHLVMLTA DGDLYTLGCG EQGQLGRVPE LFANRGGRQG LERLLVPKCV MLKSRGSRGH VR FQDAFCG AYFTFAISHE GHVYGFGLSN YHQLGTPGTE SCFIPQNLTS FKNSTKSWVG FSGGQHHTVC MDSEGKAYSL GRA EYGRLG LGEGAEEKSI PTLISRLPAV SSVACGASVG YAVTKDGRVF AWGMGTNYQL GTGQDEDAWS PVEMMGKQLE NRVV LSVSS GGQHTVLLVK DKEQS UniProtKB: Regulator of chromosome condensation |
-Macromolecule #5: 153-bp Widom 601 DNA forward strand
Macromolecule | Name: 153-bp Widom 601 DNA forward strand / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 47.457234 KDa |
Sequence | String: (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(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) ...String: (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(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)(DC)(DC)(DG)(DG) (DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DA)(DT) |
-Macromolecule #6: 153-bp Widom 601 DNA reverse strand
Macromolecule | Name: 153-bp Widom 601 DNA reverse strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 46.998945 KDa |
Sequence | String: (DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG)(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) ...String: (DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG)(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)(DT)(DA)(DT)(DA) (DT)(DA)(DC) (DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG)(DA)(DT) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |