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- PDB-3mvd: Crystal structure of the chromatin factor RCC1 in complex with th... -

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Basic information

Entry
Database: PDB / ID: 3mvd
TitleCrystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle
Components
  • (DNA (146-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Regulator of chromosome condensation
KeywordsSIGNALING PROTEIN/STRUCTURAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / NUCLEOSOME CORE PARTICLE (NCP) / NCP-chromatin factor complex / 7-bladed beta-propeller / SIGNALING PROTEIN-STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


Postmitotic nuclear pore complex (NPC) reformation / guanyl-nucleotide exchange factor activity => GO:0005085 / Ran protein signal transduction / ventral cord development / regulation of nucleocytoplasmic transport / chromatin => GO:0000785 / regulation of mitotic spindle assembly / NLS-bearing protein import into nucleus / regulation of mitotic cell cycle / regulation of neurogenesis ...Postmitotic nuclear pore complex (NPC) reformation / guanyl-nucleotide exchange factor activity => GO:0005085 / Ran protein signal transduction / ventral cord development / regulation of nucleocytoplasmic transport / chromatin => GO:0000785 / regulation of mitotic spindle assembly / NLS-bearing protein import into nucleus / regulation of mitotic cell cycle / regulation of neurogenesis / condensed chromosome / central nervous system development / structural constituent of chromatin / nucleosome / cell cycle / protein heterodimerization activity / cell division / chromatin binding / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 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 / Histone, subunit A / Histone, subunit A / 7 Propeller ...Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 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 / Histone, subunit A / Histone, subunit A / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Regulator of chromosome condensation / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMakde, R.D. / England, J.R. / Yennawar, H.P. / Tan, S.
CitationJournal: Nature / Year: 2010
Title: Structure of RCC1 chromatin factor bound to the nucleosome core particle.
Authors: Makde, R.D. / England, J.R. / Yennawar, H.P. / Tan, S.
History
DepositionMay 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (146-MER)
J: DNA (146-MER)
K: Regulator of chromosome condensation
L: Regulator of chromosome condensation


Theoretical massNumber of molelcules
Total (without water)289,62212
Polymers289,62212
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.681, 183.036, 107.030
Angle α, β, γ (deg.)90.00, 101.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 5 types, 10 molecules AEBFCGDHKL

#1: Protein Histone H3.2


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: HISTONE H3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLYSS / References: UniProt: P84233
#2: Protein Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: HISTONE H4 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLYSS / References: UniProt: P62799
#3: Protein Histone H2A /


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLYSS / References: UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: HISTONE H2B / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLYSS / References: UniProt: P02281
#7: Protein Regulator of chromosome condensation / Chromatin-binding protein Bj1


Mass: 45366.457 Da / Num. of mol.: 2 / Fragment: N-terminal region (residues 2-422)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Bj1, CG10480, RCC1 (Bj1) / Plasmid: pST50Tr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLYSS / References: UniProt: P25171

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (146-MER)


Mass: 45138.770 Da / Num. of mol.: 1 / Fragment: 147 BP Widom 601 DNA FRAGMENT (+ strand) / Source method: obtained synthetically
#6: DNA chain DNA (146-MER)


Mass: 45610.043 Da / Num. of mol.: 1 / Fragment: 147 BP Widom 601 DNA FRAGMENT (- strand) / Source method: obtained synthetically

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Details

Sequence detailsAUTHORS STATE THAT THE DNA CODING SEQUENCES OF ALL THE PROTEINS PRESENT IN THIS STRUCTURE WERE ...AUTHORS STATE THAT THE DNA CODING SEQUENCES OF ALL THE PROTEINS PRESENT IN THIS STRUCTURE WERE VERIFIED BY DNA SEQUENCING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25 mM sodium acetate buffer, 25 mM sodium citrate, 1 mM DTT, 6 % PEG2000-MME, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium acetate11
2sodium citrate11
3DTT11
4PEG2000-MME11
5sodium acetate12
6sodium citrate12
7DTT12
8PEG2000-MME12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2009 / Details: MIRRORS
RadiationMonochromator: Si(111), side bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 86335 / Num. obs: 85040 / % possible obs: 98.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 75.8 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.25
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.67 / Num. unique all: 4232

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASER(CCP4-6.1.1)phasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KX5, and Drosophila RCC1(not yet deposited in PDB)

1kx5


Resolution: 2.9→34.701 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 1988 2.47 %RANDOM
Rwork0.1749 ---
obs0.1759 80508 94.08 %-
all-85574 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.174 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso mean: 87.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.4139 Å2-0 Å20.8833 Å2
2---6.053 Å2-0 Å2
3---12.4669 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11757 5986 0 0 17743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218640
X-RAY DIFFRACTIONf_angle_d0.62626466
X-RAY DIFFRACTIONf_dihedral_angle_d23.0287299
X-RAY DIFFRACTIONf_chiral_restr0.0313043
X-RAY DIFFRACTIONf_plane_restr0.0022374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.00360.31671710.27836740X-RAY DIFFRACTION81
3.0036-3.12380.31871860.26747226X-RAY DIFFRACTION87
3.1238-3.26580.29511860.25017613X-RAY DIFFRACTION92
3.2658-3.43790.30022040.22797940X-RAY DIFFRACTION95
3.4379-3.65310.23942080.18898029X-RAY DIFFRACTION96
3.6531-3.93480.19232180.17228086X-RAY DIFFRACTION97
3.9348-4.33010.20552010.14588141X-RAY DIFFRACTION98
4.3301-4.95510.17472090.13478232X-RAY DIFFRACTION99
4.9551-6.2370.18581950.15048291X-RAY DIFFRACTION99
6.237-34.70350.17522100.15038222X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 31.1295 Å / Origin y: 16.9013 Å / Origin z: 31.8271 Å
111213212223313233
T0.2777 Å20.0731 Å20.0077 Å2-0.3052 Å20.001 Å2--0.2897 Å2
L1.2164 °20.5635 °2-0.0873 °2-0.9826 °2-0.1908 °2--0.2429 °2
S0.0308 Å °0.1199 Å °-0.0057 Å °0.018 Å °0.0196 Å °0.0891 Å °-0.0238 Å °-0.0486 Å °-0.0506 Å °
Refinement TLS groupSelection details: all

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