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- PDB-2c9o: 3D Structure of the human RuvB-like helicase RuvBL1 -

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Basic information

Entry
Database: PDB / ID: 2c9o
Title3D Structure of the human RuvB-like helicase RuvBL1
ComponentsRUVB-LIKE 1
KeywordsHYDROLASE / HEXAMERIC HELICASE / AAA+-ATPASE / ATP-BINDING / CHROMATIN REGULATOR / GROWTH REGULATION / NUCLEAR PROTEIN / DNA RECOMBINATION / TRANSCRIPTION / TRANSCRIPTION REGULATION / ACTIVATOR / HELICASE / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / R2TP complex / Swr1 complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / box C/D snoRNP assembly ...regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / R2TP complex / Swr1 complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / box C/D snoRNP assembly / protein folding chaperone complex / NuA4 histone acetyltransferase complex / regulation of chromosome organization / positive regulation of double-strand break repair via homologous recombination / regulation of DNA replication / MLL1 complex / TFIID-class transcription factor complex binding / regulation of embryonic development / Telomere Extension By Telomerase / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of DNA repair / DNA helicase activity / TBP-class protein binding / telomere maintenance / ADP binding / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / nuclear matrix / positive regulation of canonical Wnt signaling pathway / UCH proteinases / nucleosome / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA helicase / DNA recombination / transcription coactivator activity / protein stabilization / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / cadherin binding / cell cycle / ribonucleoprotein complex / cell division / DNA repair / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
RuvBL1 DNA/RNA binding domain / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...RuvBL1 DNA/RNA binding domain / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RuvB-like 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMatias, P.M. / Gorynia, S. / Donner, P. / Carrondo, M.A.
Citation
Journal: J. Biol. Chem. / Year: 2006
Title: Crystal structure of the human AAA+ protein RuvBL1.
Authors: Matias, P.M. / Gorynia, S. / Donner, P. / Carrondo, M.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, Purification, Crystallization and Preliminary X-Ray Analysis of the Human Ruvb-Like Protein Ruvbl1.
Authors: Gorynia, S. / Matias, P.M. / Goncalves, S. / Coelho, R. / Lopes, G. / Thomaz, M. / Huber, M. / Haendler, B. / Donner, P. / Carrondo, M.A.
History
DepositionDec 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUVB-LIKE 1
B: RUVB-LIKE 1
C: RUVB-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,1726
Polymers150,8913
Non-polymers1,2823
Water2,846158
1
A: RUVB-LIKE 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)304,34512
Polymers301,7816
Non-polymers2,5636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation4_555-x,-y,z1
MethodPQS
2
B: RUVB-LIKE 1
C: RUVB-LIKE 1
hetero molecules

B: RUVB-LIKE 1
C: RUVB-LIKE 1
hetero molecules

B: RUVB-LIKE 1
C: RUVB-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,34512
Polymers301,7816
Non-polymers2,5636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)207.080, 207.080, 60.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein RUVB-LIKE 1 / / RUVBL1 / 49-KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN / 49 KDA TBP-INTERACTING PROTEIN / ...RUVBL1 / 49-KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN / 49 KDA TBP-INTERACTING PROTEIN / TIP49A / PONTIN 52 / NUCLEAR MATRIX PROTEIN 238 / NMP 238 / 54 KDA ERYTHROCYTE CYTOSOLIC PROTEIN / ECP-54 / TIP60-ASSOCIATED PROTEIN 54-ALPHA / TAP54-ALPHA


Mass: 50296.914 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-15B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y265, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHAS SINGLE-STRANDED DNA-STIMULATED ATPASE AND ATP-DEPENDENT DNA HELICASE (3' TO 5') ACTIVITY.

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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: 3.09 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PROTEIN WAS CRYSTALLISED USING THE VAPOR DIFFUSION METHOD (SITTING DROP). THE WELLS CONTAINED 500 MICROLITERS OF PRECIPITANT SOLUTION AND THE DROPS WERE COMPOSED OF 1.5 MICROLITERS OF ...Details: PROTEIN WAS CRYSTALLISED USING THE VAPOR DIFFUSION METHOD (SITTING DROP). THE WELLS CONTAINED 500 MICROLITERS OF PRECIPITANT SOLUTION AND THE DROPS WERE COMPOSED OF 1.5 MICROLITERS OF PROTEIN SOLUTION (15 MG/ML) AND 1.5 MICROLITERS OF RESERVOIR SOLUTION. THE BEST CRYSTALS WERE OBTAINED FROM A SOLUTION CONTAINING 1.6 M SODIUM MALONATE PH 6 AT 293 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→45.4 Å / Num. obs: 73593 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.2 / % possible all: 80

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Processing

Software
NameVersionClassification
SHARPmodel building
SCALAdata scaling
SHELXCDphasing
SHELXDphasing
SHELXEphasing
SHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→179.61 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.316 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BECAUSE THEIR ELECTRON DENSITY COULD NOT BE SEEN, THE FOLLOWING RESIDUES ARE MISSING FROM THE FINAL MODEL 1-8, 142-155, 248-276 AND 450-456 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BECAUSE THEIR ELECTRON DENSITY COULD NOT BE SEEN, THE FOLLOWING RESIDUES ARE MISSING FROM THE FINAL MODEL 1-8, 142-155, 248-276 AND 450-456 IN CHAIN A, 1-10, 142-154, 245-278 AND 449-456 IN CHAIN B, AND 1-7, 129-230, 247-276 AND 450-456 IN CHAIN C. ALSO, ZERO (0.01) OCCUPANCY WAS GIVEN TO 26 ATOMS IN CHAIN A, 48 IN CHAIN B AND 84 IN CHAIN C.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3705 5 %RANDOM
Rwork0.206 ---
obs0.209 70028 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.28 Å20 Å2
2--0.55 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→179.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8467 0 81 158 8706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228659
X-RAY DIFFRACTIONr_bond_other_d0.0010.028193
X-RAY DIFFRACTIONr_angle_refined_deg1.51.99911694
X-RAY DIFFRACTIONr_angle_other_deg0.804319142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95851093
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70925.146342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.104151645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8721545
X-RAY DIFFRACTIONr_chiral_restr0.0810.21395
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021523
X-RAY DIFFRACTIONr_nbd_refined0.1970.21738
X-RAY DIFFRACTIONr_nbd_other0.1790.28161
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24216
X-RAY DIFFRACTIONr_nbtor_other0.0870.25123
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.2141
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9721.57049
X-RAY DIFFRACTIONr_mcbond_other0.1641.52254
X-RAY DIFFRACTIONr_mcangle_it1.16528821
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.99533583
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0114.52873
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 206 -
Rwork0.244 3977 -
obs--75.22 %

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