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- PDB-5fm6: Double-heterohexameric rings of full-length Rvb1(ADP)Rvb2(apo) -

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Basic information

Entry
Database: PDB / ID: 5fm6
TitleDouble-heterohexameric rings of full-length Rvb1(ADP)Rvb2(apo)
Components
  • RVB1
  • RVB2
KeywordsATP BINDING PROTEIN / UNKNOWN FUNCTION / RVB1 / RVB2 / ADP
Function / homology
Function and homology information


ATP-dependent activity, acting on DNA / helicase activity / chromatin organization / DNA helicase / DNA repair / ATP hydrolysis activity / ATP binding / nucleus
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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / RuvB-like helicase / RuvB-like helicase
Similarity search - Component
Biological speciesCHAETOMIUM THERMOPHILUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.997 Å
AuthorsSilva-Martin, N. / Dauden, M.I. / Glatt, S. / Hoffmann, N.A. / Mueller, C.W.
CitationJournal: PLoS One / Year: 2016
Title: The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex.
Authors: Noella Silva-Martin / María I Daudén / Sebastian Glatt / Niklas A Hoffmann / Panagiotis Kastritis / Peer Bork / Martin Beck / Christoph W Müller /
Abstract: The Rvb1/Rvb2 complex is an essential component of many cellular pathways. The Rvb1/Rvb2 complex forms a dodecameric assembly where six copies of each subunit form two heterohexameric rings. However, ...The Rvb1/Rvb2 complex is an essential component of many cellular pathways. The Rvb1/Rvb2 complex forms a dodecameric assembly where six copies of each subunit form two heterohexameric rings. However, due to conformational variability, the way the two rings pack together is still not fully understood. Here, we present the crystal structure and two cryo-electron microscopy reconstructions of the dodecameric, full-length Rvb1/Rvb2 complex, all showing that the interaction between the two heterohexameric rings is mediated through the Rvb1/Rvb2-specific domain II. Two conformations of the Rvb1/Rvb2 dodecamer are present in solution: a stretched conformation also present in the crystal, and a compact conformation. Novel asymmetric features observed in the reconstruction of the compact conformation provide additional insight into the plasticity of the Rvb1/Rvb2 complex.
History
DepositionNov 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RVB1
B: RVB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7575
Polymers105,1402
Non-polymers6173
Water0
1
A: RVB1
B: RVB2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)634,54430
Polymers630,84112
Non-polymers3,70318
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
Buried area71410 Å2
ΔGint-518.4 kcal/mol
Surface area231510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.610, 209.610, 137.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein RVB1


Mass: 51048.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: G0RYI5
#2: Protein RVB2


Mass: 54091.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: G0RYC2
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
Sequence detailsN-TERMINAL GA FROM TEV CLEAVAGE SITE, CHAIN A N-TERMINAL GA FROM TEV CLEAVAGE SITE, CHAIN B

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.64 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS PH 5.7; 1.8 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97923
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 45338 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 105.27 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.4
Reflection shellResolution: 3→3.09 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.997→48.635 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 30.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 2262 5 %
Rwork0.2299 --
obs0.2312 45327 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.997→48.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 0 37 0 6558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036637
X-RAY DIFFRACTIONf_angle_d0.5828953
X-RAY DIFFRACTIONf_dihedral_angle_d14.1832553
X-RAY DIFFRACTIONf_chiral_restr0.0221049
X-RAY DIFFRACTIONf_plane_restr0.0021168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9973-3.06250.45141380.40042637X-RAY DIFFRACTION98
3.0625-3.13370.36931390.35742707X-RAY DIFFRACTION100
3.1337-3.21210.35851450.34642684X-RAY DIFFRACTION100
3.2121-3.29890.32511430.32092712X-RAY DIFFRACTION100
3.2989-3.39590.35261400.3042687X-RAY DIFFRACTION100
3.3959-3.50550.31831400.27052694X-RAY DIFFRACTION100
3.5055-3.63080.31381400.27172686X-RAY DIFFRACTION100
3.6308-3.77610.28961430.25272677X-RAY DIFFRACTION100
3.7761-3.94790.28951430.24912707X-RAY DIFFRACTION100
3.9479-4.15590.24331360.22792691X-RAY DIFFRACTION100
4.1559-4.41610.23511450.20842689X-RAY DIFFRACTION100
4.4161-4.75680.22891390.20382725X-RAY DIFFRACTION100
4.7568-5.2350.2361410.21272690X-RAY DIFFRACTION100
5.235-5.99140.33821390.23542676X-RAY DIFFRACTION100
5.9914-7.54390.22681430.22512705X-RAY DIFFRACTION100
7.5439-48.64110.18651480.17862698X-RAY DIFFRACTION100
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)
14.4207-1.4352-1.5743.51540.06094.23670.06230.43220.3744-0.144-0.0226-0.4377-0.71480.6911-0.05040.7833-0.1506-0.12250.80110.09820.79235.9643132.065763.4873
20.42610.21990.40812.2329-3.69297.49420.25580.3989-0.2786-0.279-0.548-0.38330.07941.56080.66051.1889-0.0855-0.10261.66020.03371.047342.5747137.422123.7978
32.2997-0.19130.02613.68730.7932.0711-0.1228-0.03170.28780.293-0.1711-0.1538-0.430.26960.27050.804-0.116-0.18280.82260.11540.779827.5924137.297469.5473
44.342-0.90020.09913.4910.8844.7305-0.16220.0981-0.06570.13630.046-0.56680.29590.74330.0180.88220.20790.01770.83670.09540.896327.546392.702467.0517
57.3178-0.5951-0.37212.0523-0.69282.0071-0.11560.41030.2068-0.1635-0.0794-0.61060.28470.95630.23190.84180.16090.05221.01550.11620.901539.65698.513648.3119
65.93761.88382.60363.9425-3.25177.0762-0.2448-0.16840.40041.18850.0303-0.4775-0.2767-0.13440.20511.13220.44260.08011.38030.02481.136949.044695.768751.3515
73.1839-0.0304-0.70312.8753-0.70476.8301-0.04820.0914-0.03530.18550.05860.3845-0.2441-0.3455-0.01520.51690.0885-0.02880.60670.02870.847118.2633100.120756.0042
81.40291.97170.52825.58781.09521.481-0.0594-0.1547-0.03190.82980.0468-0.6189-0.0110.52250.02170.93580.1726-0.22141.09420.10880.767938.6119111.846381.5256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 130 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 131 THROUGH 257 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 258 THROUGH 450 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 7 THROUGH 114 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 115 THROUGH 168 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 169 THROUGH 232 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 233 THROUGH 350 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 351 THROUGH 455 )

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