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- EMDB-42685: Structure of Ran bound to RCC1 and the nucleosome core particle (... -

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Entry
Database: EMDB / ID: EMD-42685
TitleStructure of Ran bound to RCC1 and the nucleosome core particle (composite map)
Map dataComposite 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
  • Complex: Ran-RCC1-NCP complex
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: 153-bp Widom 601 DNA forward strand
    • DNA: 153-bp Widom 601 DNA reverse strand
    • Protein or peptide: GTP-binding nuclear protein Ran
    • Protein or peptide: Regulator of chromosome condensation
KeywordsGTPase / Guanine nucleotide exchange factor / chromatin-binding / NUCLEAR PROTEIN
Function / homology
Function and homology information


HDMs demethylate histones / PKMTs methylate histone lysines / : / 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 / positive regulation of cell cycle process ...HDMs demethylate histones / PKMTs methylate histone lysines / : / 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 / positive regulation of cell cycle process / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / polytene chromosome band / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Negative Regulation of CDH1 Gene Transcription / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RNA Polymerase I Promoter Escape / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / UCH proteinases / polytene chromosome / RNA nuclear export complex / pre-miRNA export from nucleus / sulfate binding / snRNA import into nucleus / mitotic nuclear membrane reassembly / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Rev-mediated nuclear export of HIV RNA / regulation of mitotic spindle assembly / Nuclear import of Rev protein / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / protein-containing complex localization / MicroRNA (miRNA) biogenesis / nucleosomal DNA binding / regulation of mitotic nuclear division / DNA metabolic process / nuclear chromosome / dynein intermediate chain binding / mitotic sister chromatid segregation / viral process / spermatid development / ribosomal large subunit export from nucleus / nuclear pore / sperm flagellum / ribosomal subunit export from nucleus / nucleosome binding / spindle assembly / ribosomal small subunit export from nucleus / protein export from nucleus / regulation of mitotic cell cycle / guanyl-nucleotide exchange factor activity / mitotic spindle organization / condensed nuclear chromosome / male germ cell nucleus / hippocampus development / centriole / chromosome segregation / Transcriptional regulation by small RNAs / G1/S transition of mitotic cell cycle / positive regulation of protein import into nucleus / recycling endosome / small GTPase binding / protein import into nucleus / structural constituent of chromatin / melanosome / GDP binding / nuclear envelope / nucleosome / mitotic cell cycle / heterochromatin formation / nucleosome assembly / chromosome / chromatin organization / actin cytoskeleton organization / G protein activity / midbody / histone binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 1. / : / : / RCC1-like domain / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Ran GTPase / Small GTPase Ran-type domain profile. ...Regulator of chromosome condensation (RCC1) signature 1. / : / : / RCC1-like domain / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Ran GTPase / Small GTPase Ran-type domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / : / 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 / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Rab subfamily of small GTPases / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3 / Histone H2B / Regulator of chromosome condensation / GTP-binding nuclear protein Ran / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human) / Drosophila melanogaster (fruit fly) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsHuang SK / Rubinstein JL / Kay LE
Funding support Canada, 2 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2015-04347 Canada
Canadian Institutes of Health Research (CIHR)FND-50357 Canada
CitationJournal: 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
DepositionNov 8, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42685.png

Downloads & links

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Map

FileDownload / File: emd_42685.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite 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

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.123132035 - 10.992342000000001
Average (Standard dev.)0.021685403 (±0.20942947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ran-RCC1-NCP complex

EntireName: Ran-RCC1-NCP complex
Components
  • Complex: Ran-RCC1-NCP complex
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: 153-bp Widom 601 DNA forward strand
    • DNA: 153-bp Widom 601 DNA reverse strand
    • Protein or peptide: GTP-binding nuclear protein Ran
    • Protein or peptide: Regulator of chromosome condensation

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Supramolecule #1: Ran-RCC1-NCP complex

SupramoleculeName: Ran-RCC1-NCP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 15.405036 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LSAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: 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
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 11.521611 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MITGRGKGGK GLGKGGAKRH RKVLRDNIQG ITKPAIRRLA RRGGVKRISG LIYEETRGVL KVFLENVIRD AVTYTEHAKR KTVTAMDVV YALKRQGRTL YGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.388727 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKGGKV KGKAKSRSNR AGLQFPVGRI HRLLRKGNYA ERVGAGAPVY LAAVMEYLAA EVLELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLSG VTIAQGGVLP NIQAVLLPKK TEKKA

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: 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
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.897275 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GMIPPKTSGK AAKKAGKAQK NITKTDKKKK RKRKESYAIY IYKVLKQVHP DTGISSKAMS IMNSFVNDIF ERIAAEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B

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Macromolecule #7: GTP-binding nuclear protein Ran

MacromoleculeName: GTP-binding nuclear protein Ran / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.456105 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #8: Regulator of chromosome condensation

MacromoleculeName: Regulator of chromosome condensation / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.893758 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #5: 153-bp Widom 601 DNA forward strand

MacromoleculeName: 153-bp Widom 601 DNA forward strand / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.457234 KDa
SequenceString: (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)

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Macromolecule #6: 153-bp Widom 601 DNA reverse strand

MacromoleculeName: 153-bp Widom 601 DNA reverse strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.998945 KDa
SequenceString: (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)

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: The composite map of the Ran-RCC1-NCP complex are made from stitching together two distinct portions from two separate maps. The Ran-RCC1 portion comes from a locally refined map of the Ran- ...Details: The composite map of the Ran-RCC1-NCP complex are made from stitching together two distinct portions from two separate maps. The Ran-RCC1 portion comes from a locally refined map of the Ran-RCC1 region on NCP, which used 401,603 particles and refined to 2.5 angstrom resolution. The NCP portion comes from a map of a 1-side bound Ran-RCC1-NCP complex, which used 199,434 particles and refined to 2.4 angstrom resolution.
Number images used: 401603
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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