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- PDB-5jno: Crystal structure of the BD1-NTPR complex from BEND3 and PICH -

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Basic information

Entry
Database: PDB / ID: 5jno
TitleCrystal structure of the BD1-NTPR complex from BEND3 and PICH
Components
  • BEN domain-containing protein 3
  • DNA excision repair protein ERCC-6-like
KeywordsCELL CYCLE / Ultra fine chromatin bridges / sister chromatids separation / anaphase
Function / homology
Function and homology information


positive regulation of ATP metabolic process / ATP-dependent chromatin remodeler activity => GO:0140658 / kinetochore => GO:0000776 / rDNA binding / DNA translocase activity / rDNA heterochromatin formation / : / negative regulation of transcription by RNA polymerase I / heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal ...positive regulation of ATP metabolic process / ATP-dependent chromatin remodeler activity => GO:0140658 / kinetochore => GO:0000776 / rDNA binding / DNA translocase activity / rDNA heterochromatin formation / : / negative regulation of transcription by RNA polymerase I / heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / DNA helicase activity / mitotic spindle organization / RHO GTPases Activate Formins / protein homooligomerization / Separation of Sister Chromatids / DNA helicase / cell division / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / membrane / cytosol
Similarity search - Function
BEN domain-containing protein 3 / BEN domain / BEN domain / BEN domain profile. / BEN / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / TPR repeat region circular profile. ...BEN domain-containing protein 3 / BEN domain / BEN domain / BEN domain profile. / BEN / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / TPR repeat region circular profile. / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA excision repair protein ERCC-6-like / BEN domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsPitchai, G. / Mesa, P. / Hickson, I.D. / Montoya, G.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation14cc0001 Denmark
CitationJournal: To Be Published
Title: Crystal structure of the BD1-NTPR complex from BEND3 and PICH
Authors: Pitchai, G. / Mesa, P. / Hickson, I.D. / Montoya, G.
History
DepositionApr 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: BEN domain-containing protein 3
B: DNA excision repair protein ERCC-6-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4743
Polymers19,3822
Non-polymers921
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-6 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.280, 47.280, 431.579
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein BEN domain-containing protein 3 / BEND3


Mass: 12866.653 Da / Num. of mol.: 1 / Fragment: UNP residues 236-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BEND3, KIAA1553 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q5T5X7
#2: Protein DNA excision repair protein ERCC-6-like / ATP-dependent helicase ERCC6-like / PLK1-interacting checkpoint helicase / Tumor antigen BJ-HCC-15


Mass: 6515.378 Da / Num. of mol.: 1 / Fragment: UNP residues 10-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC6L, PICH / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q2NKX8, DNA helicase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 mM HEPES, pH=7.0 1.56 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→71.93 Å / Num. obs: 14907 / % possible obs: 99.1 % / Redundancy: 20 % / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→71.93 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.947 / SU B: 12.399 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23748 786 5 %RANDOM
Rwork0.22151 ---
obs0.22236 14907 98.09 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 58.618 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å2-0.71 Å20 Å2
2---1.43 Å20 Å2
3---4.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→71.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 6 18 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191290
X-RAY DIFFRACTIONr_bond_other_d0.0020.021240
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.981740
X-RAY DIFFRACTIONr_angle_other_deg0.98632857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6725151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39425.07567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52815225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.303157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211441
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02294
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4113.065613
X-RAY DIFFRACTIONr_mcbond_other3.413.061612
X-RAY DIFFRACTIONr_mcangle_it5.0664.545761
X-RAY DIFFRACTIONr_mcangle_other5.0644.55762
X-RAY DIFFRACTIONr_scbond_it4.1613.555677
X-RAY DIFFRACTIONr_scbond_other4.1453.556677
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5465.085980
X-RAY DIFFRACTIONr_long_range_B_refined8.80424.41443
X-RAY DIFFRACTIONr_long_range_B_other8.80324.3831442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.197→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 41 -
Rwork0.31 810 -
obs--73.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7173-0.9686-0.91523.3325-0.73992.31690.1284-0.0094-0.051-0.1728-0.01260.10750.0791-0.0273-0.11590.2774-0.023-0.05440.17820.09010.0664-10.863-10.361-5.444
22.9820.5111-0.25717.7515-5.92066.22850.23850.55180.0969-0.1884-0.02340.26270.085-0.1307-0.21510.39460.07350.05990.34910.07480.0344-5.917-7.622-25.287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A236 - 347
2X-RAY DIFFRACTION2B10 - 66

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