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- PDB-3uk6: Crystal Structure of the Tip48 (Tip49b) hexamer -

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Basic information

Entry
Database: PDB / ID: 3uk6
TitleCrystal Structure of the Tip48 (Tip49b) hexamer
ComponentsRuvB-like 2
KeywordsHYDROLASE / Hexameric AAA+ ATP-ase / DNA unwinding
Function / homology
Function and homology information


promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / 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 ...promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / 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 / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / positive regulation of DNA repair / TBP-class protein binding / DNA helicase activity / telomere maintenance / cellular response to estradiol stimulus / ADP binding / euchromatin / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / beta-catenin binding / nuclear matrix / transcription corepressor activity / cellular response to UV / unfolded protein binding / nucleosome / protein folding / HATs acetylate histones / ATPase binding / regulation of apoptotic process / DNA recombination / DNA helicase / protein stabilization / regulation of cell cycle / chromatin remodeling / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / ATP hydrolysis activity / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities ...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 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RuvB-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsPetukhov, M. / Dagkessamanskaja, A. / Bommer, M. / Barrett, T. / Tsaneva, I. / Yakimov, A. / Queval, R. / Shvetsov, A. / Khodorkovskiy, M. / Kas, E. / Grigoriev, M.
CitationJournal: Structure / Year: 2012
Title: Large-Scale Conformational Flexibility Determines the Properties of AAA+ TIP49 ATPases.
Authors: Petukhov, M. / Dagkessamanskaja, A. / Bommer, M. / Barrett, T. / Tsaneva, I. / Yakimov, A. / Queval, R. / Shvetsov, A. / Khodorkovskiy, M. / Kas, E. / Grigoriev, M.
History
DepositionNov 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RuvB-like 2
B: RuvB-like 2
C: RuvB-like 2
D: RuvB-like 2
E: RuvB-like 2
F: RuvB-like 2
G: RuvB-like 2
H: RuvB-like 2
I: RuvB-like 2
J: RuvB-like 2
K: RuvB-like 2
L: RuvB-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)494,68524
Polymers489,55912
Non-polymers5,12612
Water0
1
A: RuvB-like 2
B: RuvB-like 2
C: RuvB-like 2
D: RuvB-like 2
I: RuvB-like 2
J: RuvB-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,34312
Polymers244,7796
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22560 Å2
ΔGint-226 kcal/mol
Surface area73960 Å2
MethodPISA
2
E: RuvB-like 2
F: RuvB-like 2
G: RuvB-like 2
H: RuvB-like 2
K: RuvB-like 2
L: RuvB-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,34312
Polymers244,7796
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18830 Å2
ΔGint-187 kcal/mol
Surface area74100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.070, 186.280, 129.860
Angle α, β, γ (deg.)90.00, 108.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RuvB-like 2 / 48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa ...48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa erythrocyte cytosolic protein / ECP-51 / INO80 complex subunit J / Repressing pontin 52 / Reptin 52 / TIP49b / TIP60-associated protein 54-beta / TAP54-beta


Mass: 40796.559 Da / Num. of mol.: 12 / Fragment: UNP residues 1-132, 239-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-46, INO80J, RUVBL2, TIP48, TIP49B / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold-DE3 / References: UniProt: Q9Y230, DNA helicase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris-HCL, pH 8.0, 20% PEG 3000, 5% glucose, galactose or trehalose, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2009 / Details: bent cylindrical mirror
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.95→43.19 Å / Num. all: 103557 / Num. obs: 103557 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 88.87 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.7
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.91 / Num. unique all: 7753 / % possible all: 99.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→43.19 Å / Cor.coef. Fo:Fc: 0.8933 / Cor.coef. Fo:Fc free: 0.8736 / SU R Cruickshank DPI: 0.987 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 5161 4.98 %RANDOM
Rwork0.2413 ---
all0.2425 103557 --
obs0.2425 103557 97.07 %-
Displacement parametersBiso mean: 91.97 Å2
Baniso -1Baniso -2Baniso -3
1-13.1509 Å20 Å2-2.2594 Å2
2--13.6884 Å20 Å2
3----26.8393 Å2
Refine analyzeLuzzati coordinate error obs: 0.631 Å
Refinement stepCycle: LAST / Resolution: 2.95→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22548 0 322 0 22870
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123134HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1931721HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d20.786644SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0.0071264HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0.01273912HARMONIC5
X-RAY DIFFRACTIONt_it2.2423134HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion20.74
X-RAY DIFFRACTIONt_chiral_improper_torsion20.743683SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact0.0125752SEMIHARMONIC4
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3021 424 5.48 %
Rwork0.267 7313 -
all0.2689 7737 -
obs--97.07 %
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)
11.3695-0.46620.20313.0449-0.02810.94230.2010.0025-0.4863-0.01890.079-0.33150.54430.4806-0.28-0.53450.2596-0.2159-0.3867-0.1844-0.624242.8549-30.16546.6315
22.1703-0.68290.3562.4111-0.32692.23520.1241-0.0793-0.6199-0.20290.21820.50010.6311-0.1762-0.3422-0.5761-0.0614-0.1054-0.73550.1139-0.46159.3859-25.883945.6568
32.4082-0.3364-0.24842.1423-0.49371.9440.23260.0795-0.1805-0.2008-0.05060.5077-0.0953-0.4968-0.1819-0.65730.03060.0275-0.57310.0505-0.5772-4.06193.479537.0852
42.2585-0.2627-0.85391.5960.59162.25910.64190.32140.6-0.4089-0.0394-0.0799-1.1511-0.1518-0.6025-0.03850.09920.4407-0.79160.1188-0.588216.234529.400829.6289
52.1370.5135-1.30652.7224-0.34880.90740.5349-0.88240.41080.3461-0.4166-0.3401-0.63460.7368-0.1183-0.48-0.28610.1446-0.185-0.0397-0.5788-2.014933.63676.5188
61.94030.4974-1.21491.3648-0.19941.27460.35680.02470.64260.29520.1230.5599-0.5629-0.1955-0.4798-0.47680.04290.1733-0.71780.0465-0.472-35.493929.671378.2214
71.78521.2761-1.71772.5544-1.77182.7082-0.0577-0.00940.2374-0.00790.34040.81580.389-0.5582-0.2827-0.5784-0.0750.0109-0.56370.0559-0.4962-49.05670.953188.2428
83.53481.6104-0.94653.6098-1.0542.9038-0.6717-0.6325-0.8992-0.429-0.3376-0.66891.57480.57561.00930.04670.34130.652-0.74520.3252-0.4279-29.1662-25.199395.9804
91.3056-0.1398-0.08920.27310.18920.90180.2340.10810.0319-0.1985-0.18050.2135-0.607-0.7104-0.05350.48550.6872-0.05020.00640.21280.1445-63.739226.209430.3369
100.489-0.1179-0.09650.60740.1230.93950.13650.06720.0225-0.143-0.10760.51890.079-0.6432-0.0289-0.0302-0.1131-0.33360.0398-0.08370.1328-50.2612-3.329839.5694
111.17330.3215-0.22142.67730.13990.00810.0424-0.1485-0.44490.14340.0421-0.39370.19170.0823-0.0845-0.30710.07490.0476-0.29690.0757-0.22143.7136-23.193793.2076
122.93320.0877-0.76473.1144-1.1492.5777-0.0024-0.6037-0.21050.0498-0.5377-1.10870.24461.16840.5401-0.78550.01250.07440.65830.6854-0.022917.62465.89483.2153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A24 - 1450
2X-RAY DIFFRACTION2{ B|* }B23 - 1450
3X-RAY DIFFRACTION3{ C|* }C8 - 444
4X-RAY DIFFRACTION4{ D|* }D - J23 - 1450
5X-RAY DIFFRACTION5{ E|* }E - C23 - 1450
6X-RAY DIFFRACTION6{ F|* }F - I23 - 1450
7X-RAY DIFFRACTION7{ G|* }G - D7 - 1450
8X-RAY DIFFRACTION8{ H|* }H22 - 1450
9X-RAY DIFFRACTION9{ I|* }I - F23 - 1450
10X-RAY DIFFRACTION10{ J|* }J - K8 - 1450
11X-RAY DIFFRACTION11{ K|* }K - E23 - 1450
12X-RAY DIFFRACTION12{ L|* }L34 - 1450

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