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- PDB-5gwn: Crystal structure of human RCC2 -

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Basic information

Entry
Database: PDB / ID: 5gwn
TitleCrystal structure of human RCC2
ComponentsProtein RCC2
KeywordsPROTEIN BINDING / seven-bladed propeller
Function / homology
Function and homology information


chromosome passenger complex localization to kinetochore / chromosome, centromeric core domain / regulation of fibroblast migration / regulation of ruffle assembly / negative regulation of substrate adhesion-dependent cell spreading / positive regulation of attachment of spindle microtubules to kinetochore / mitotic spindle midzone / negative regulation of focal adhesion assembly / focal adhesion assembly / activation of GTPase activity ...chromosome passenger complex localization to kinetochore / chromosome, centromeric core domain / regulation of fibroblast migration / regulation of ruffle assembly / negative regulation of substrate adhesion-dependent cell spreading / positive regulation of attachment of spindle microtubules to kinetochore / mitotic spindle midzone / negative regulation of focal adhesion assembly / focal adhesion assembly / activation of GTPase activity / negative regulation of GTPase activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / regulation of cell migration / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / positive regulation of G2/M transition of mitotic cell cycle / guanyl-nucleotide exchange factor activity / mitotic spindle organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / establishment of protein localization / small GTPase binding / Separation of Sister Chromatids / midbody / microtubule binding / early endosome membrane / microtubule / cell division / protein domain specific binding / nucleolus / protein kinase binding / RNA binding / plasma membrane / cytosol
Similarity search - Function
Protein RCC2 / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.309 Å
AuthorsLiang, L. / Yun, C.H. / Yin, Y.X.
CitationJournal: Oncogene / Year: 2018
Title: RCC2 is a novel p53 target in suppressing metastasis.
Authors: Song, C. / Liang, L. / Jin, Y. / Li, Y. / Liu, Y. / Guo, L. / Wu, C. / Yun, C.H. / Yin, Y.
History
DepositionSep 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein RCC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4376
Polymers47,9561
Non-polymers4805
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.447, 84.056, 60.671
Angle α, β, γ (deg.)90.00, 101.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-967-

HOH

21A-1124-

HOH

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Components

#1: Protein Protein RCC2 / Regulator of chromosome condensation 2 / RCC1-like protein TD-60 / Telophase disk protein of 60 kDa


Mass: 47956.461 Da / Num. of mol.: 1 / Fragment: UNP residues 89-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RCC2, KIAA1470, TD60 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9P258
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M BIS-TRIS 5.5, 0.2M (NH4)2SO4, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.309→40.676 Å / Num. obs: 109282 / % possible obs: 98.1 % / Redundancy: 12.8 % / Net I/σ(I): 9.3
Reflection shellResolution: 1.309→1.36 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A12

1a12


Resolution: 1.309→40.676 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.18
RfactorNum. reflection% reflection
Rfree0.1889 5474 5.01 %
Rwork0.1712 --
obs0.1721 109281 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.309→40.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 25 555 3847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073401
X-RAY DIFFRACTIONf_angle_d1.0844609
X-RAY DIFFRACTIONf_dihedral_angle_d15.0831250
X-RAY DIFFRACTIONf_chiral_restr0.25493
X-RAY DIFFRACTIONf_plane_restr0.005595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3092-1.32410.30231810.26283150X-RAY DIFFRACTION89
1.3241-1.33970.2911820.25423381X-RAY DIFFRACTION96
1.3397-1.3560.27321570.23993409X-RAY DIFFRACTION97
1.356-1.37320.24891730.22923438X-RAY DIFFRACTION97
1.3732-1.39130.2411530.22243419X-RAY DIFFRACTION97
1.3913-1.41030.24241900.21013432X-RAY DIFFRACTION97
1.4103-1.43050.22631650.20683393X-RAY DIFFRACTION97
1.4305-1.45180.22471770.19563447X-RAY DIFFRACTION97
1.4518-1.47450.2061930.20133426X-RAY DIFFRACTION97
1.4745-1.49870.21561950.18783437X-RAY DIFFRACTION98
1.4987-1.52450.18741810.19163428X-RAY DIFFRACTION98
1.5245-1.55230.22351960.17593409X-RAY DIFFRACTION98
1.5523-1.58210.1921930.17663457X-RAY DIFFRACTION98
1.5821-1.61440.19711720.17173456X-RAY DIFFRACTION98
1.6144-1.64950.20282050.17493454X-RAY DIFFRACTION98
1.6495-1.68790.17331530.17233496X-RAY DIFFRACTION99
1.6879-1.73010.19831690.17183459X-RAY DIFFRACTION99
1.7301-1.77690.19761780.17593479X-RAY DIFFRACTION99
1.7769-1.82920.18141950.17393486X-RAY DIFFRACTION99
1.8292-1.88820.19151470.17163526X-RAY DIFFRACTION99
1.8882-1.95570.18221930.16713498X-RAY DIFFRACTION99
1.9557-2.0340.17322020.16933485X-RAY DIFFRACTION99
2.034-2.12650.17011600.15983508X-RAY DIFFRACTION99
2.1265-2.23870.17011930.1643532X-RAY DIFFRACTION99
2.2387-2.37890.18571710.17063511X-RAY DIFFRACTION100
2.3789-2.56260.19681950.17743506X-RAY DIFFRACTION100
2.5626-2.82040.21391890.17743542X-RAY DIFFRACTION100
2.8204-3.22830.18942060.16973547X-RAY DIFFRACTION100
3.2283-4.06680.15381950.14613543X-RAY DIFFRACTION100
4.0668-40.69610.18742150.15983553X-RAY DIFFRACTION99

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