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- PDB-5fm7: Double-heterohexameric rings of full-length Rvb1(ADP)Rvb2(ADP) -

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Basic information

Entry
Database: PDB / ID: 5fm7
TitleDouble-heterohexameric rings of full-length Rvb1(ADP)Rvb2(ADP)
Components
  • RVB1
  • RVB2
KeywordsATP BINDING PROTEIN
Function / homology
Function and homology information


chromatin organization / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA repair / ATP hydrolysis activity / ATP binding / nucleus
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) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RuvB-like helicase / RuvB-like helicase
Similarity search - Component
Biological speciesCHAETOMIUM THERMOPHILUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 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
Revision 1.1Sep 27, 2017Group: Advisory / Data collection / Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_detector.type
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: RVB1
B: RVB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7754
Polymers103,9212
Non-polymers8542
Water00
1
A: RVB1
B: RVB2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)628,65224
Polymers623,52512
Non-polymers5,12612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z1
crystal symmetry operation4_645y+1,x-1,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area76100 Å2
ΔGint-432 kcal/mol
Surface area225600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.770, 208.770, 138.450
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: 50579.977 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: 53340.875 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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Sequence detailsN-TERMINAL GA STEMS FROM TEV CLEAVAGE SITE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.97 % / Description: NONE
Crystal growDetails: 0.1 M MES PH 6.0,1 M SUCCINATE, 1.2% MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 25695 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 118.85 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.5
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FM6

5fm6


Resolution: 2.901→48.632 Å / SU ML: 0.6 / σ(F): 1.34 / Phase error: 34.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 1283 5 %
Rwork0.2586 --
obs0.2598 25670 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.901→48.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6486 0 54 0 6540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026623
X-RAY DIFFRACTIONf_angle_d0.6148939
X-RAY DIFFRACTIONf_dihedral_angle_d12.1452557
X-RAY DIFFRACTIONf_chiral_restr0.0231048
X-RAY DIFFRACTIONf_plane_restr0.0021176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9011-3.01730.44251440.38992681X-RAY DIFFRACTION100
3.0173-3.15460.44991350.42082684X-RAY DIFFRACTION100
3.1546-3.32090.35171440.38372683X-RAY DIFFRACTION100
3.3209-3.52890.31551420.32542690X-RAY DIFFRACTION100
3.5289-3.80120.35351440.33232717X-RAY DIFFRACTION100
3.8012-4.18360.34661400.27412692X-RAY DIFFRACTION100
4.1836-4.78850.24561430.24282714X-RAY DIFFRACTION100
4.7885-6.03120.35331420.26322719X-RAY DIFFRACTION100
6.0312-48.63890.20071490.19712807X-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)
11.03871.05690.23342.8843-0.48746.2238-0.1580.0560.29-0.17240.12890.0349-0.7569-1.24890.01610.75150.2465-0.06820.8951-0.14031.1023181.203525.848239.7512
21.73660.38894.330.25360.48267.701-0.4076-0.21580.3697-0.12080.07840.276-1.5622-0.68620.26111.37240.3262-0.08191.408-0.1141.3133173.345329.3897-0.1917
32.44520.5525-0.01571.31130.16961.4802-0.3587-0.2805-0.0881-0.06130.01450.1375-0.2261-0.65190.33550.82990.1485-0.02850.9865-0.14461.1069180.995915.699945.7587
41.6506-1.4434-0.02032.0313-2.02823.50310.1181-0.04480.39860.4951-0.10860.2354-0.75450.1023-0.00791.2598-0.1699-0.10440.6715-0.05611.1443219.518139.595445.1616
52.0118-2.76390.60172.9189-0.90031.27010.19710.0930.1352-0.413-0.2649-0.0396-0.8332-0.06280.01621.6112-0.0575-0.13660.7809-0.02211.3392207.080845.52427.343
62.3502-0.20080.30871.8574-0.34421.78810.07760.06520.1219-0.3073-0.2702-0.3358-0.14750.12140.17671.0457-0.0903-0.00740.5704-0.03971.1383216.282731.201930.6828
75.17290.2876-1.35880.7955-0.08811.7640.4204-0.0520.43330.0287-0.34860.3543-1.0482-0.0597-0.06011.36480.0398-0.05120.6501-0.19391.1557201.909639.709555.7664
82.32091.5241-2.17421.0809-2.41915.6195-0.61930.3466-0.25540.6763-0.2754-0.561-0.5599-0.59870.71971.2613-0.0677-0.00991.2539-0.04791.5683191.096719.904668.6861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 132 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 133 THROUGH 247 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 248 THROUGH 450 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 8 THROUGH 108 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 109 THROUGH 206 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 207 THROUGH 339 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 340 THROUGH 434 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 435 THROUGH 455 )

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