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- PDB-8ux1: Cryo-EM structure of Ran bound to RCC1 and the nucleosome core pa... -

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Entry
Database: PDB / ID: 8ux1
TitleCryo-EM structure of Ran bound to RCC1 and the nucleosome core particle
Components
  • (153-bp Widom 601 DNA ...) x 2
  • GTP-binding nuclear protein Ran
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • Regulator of chromosome condensation
KeywordsNUCLEAR PROTEIN / GTPase / Guanine nucleotide exchange factor / chromatin-binding
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 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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 / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / pre-miRNA export from nucleus / RNA nuclear export complex / mitotic nuclear membrane reassembly / snRNA import into nucleus / sulfate binding / Regulation of cholesterol biosynthesis by SREBP (SREBF) / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / regulation of mitotic spindle assembly / 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 / nucleosomal DNA binding / regulation of mitotic nuclear division / DNA metabolic process / nuclear chromosome / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / viral process / nuclear pore / ribosomal subunit export from nucleus / nucleosome binding / spindle assembly / ribosomal small subunit export from nucleus / centriole / protein export from nucleus / regulation of mitotic cell cycle / guanyl-nucleotide exchange factor activity / condensed nuclear chromosome / mitotic spindle organization / chromosome segregation / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / G1/S transition of mitotic cell cycle / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / structural constituent of chromatin / positive regulation of protein binding / nucleosome / nuclear envelope / melanosome / heterochromatin formation / nucleosome assembly / mitotic cell cycle / chromatin organization / G protein activity / chromosome / midbody / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / histone binding / cadherin binding / protein heterodimerization activity / cell division / GTPase activity / chromatin binding / protein-containing complex binding / GTP binding / chromatin / nucleolus / magnesium ion binding / protein-containing complex / DNA binding / RNA binding / extracellular exosome / nucleoplasm
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 1. / : / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / small GTPase Ran family profile. / Ran GTPase / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...Regulator of chromosome condensation (RCC1) signature 1. / : / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / small GTPase Ran family profile. / Ran GTPase / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / : / Histone H2B signature. / Histone H2B / Histone H2B / Rho (Ras homology) subfamily of Ras-like small GTPases / Histone H2A conserved site / Histone H2A signature. / Ras subfamily of RAS small GTPases / Small GTPase / Histone H2A, C-terminal domain / Ras family / C-terminus of histone H2A / Histone H2A / Histone 2A / 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 / Histone-fold / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / Regulator of chromosome condensation / GTP-binding nuclear protein Ran / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsHuang, S.K. / Rubinstein, J.L. / Kay, L.E.
Funding support Canada, 2items
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, S.K. / Rubinstein, J.L. / Kay, L.E.
History
DepositionNov 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.0Nov 22, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 22, 2023Data content type: FSC / Part number: 1 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 22, 2023Data content type: FSC / Part number: 2 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 22, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 22, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
I: 153-bp Widom 601 DNA forward strand
J: 153-bp Widom 601 DNA reverse strand
K: GTP-binding nuclear protein Ran
L: Regulator of chromosome condensation


Theoretical massNumber of molelcules
Total (without water)272,23112
Polymers272,23112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 10 molecules AEBFCGDHKL

#1: Protein Histone H3


Mass: 15405.036 Da / Num. of mol.: 2 / Mutation: C110S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CALMAC_LOCUS17614 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A653DHJ5
#2: Protein Histone H4


Mass: 11521.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: An extra isoleucine was inserted at the N-terminus following the first residue methionine
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, ...Gene: His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, His4:CG33881, CG33881, His4:CG33883, CG33883, His4:CG33885, CG33885, His4:CG33887, CG33887, His4:CG33889, CG33889, His4:CG33891, CG33891, His4:CG33893, CG33893, His4:CG33895, CG33895, His4:CG33897, CG33897, His4:CG33899, CG33899, His4:CG33901, CG33901, His4:CG33903, CG33903, His4:CG33905, CG33905, His4:CG33907, CG33907, His4:CG33909, CG33909
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84040
#3: Protein Histone H2A


Mass: 13388.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A: ...Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84051
#4: Protein Histone H2B


Mass: 13897.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His2B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02283
#7: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 24456.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826
#8: Protein Regulator of chromosome condensation


Mass: 44893.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RCC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18754

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153-bp Widom 601 DNA ... , 2 types, 2 molecules IJ

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


Mass: 47457.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain 153-bp Widom 601 DNA reverse strand


Mass: 46998.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ran-RCC1-NCP complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameCategory
4cryoSPARCCTF correction
8PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 401603
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.
Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00617291
ELECTRON MICROSCOPYf_angle_d0.59124582
ELECTRON MICROSCOPYf_dihedral_angle_d28.8034383
ELECTRON MICROSCOPYf_chiral_restr0.0882765
ELECTRON MICROSCOPYf_plane_restr0.0042119

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