[English] 日本語
Yorodumi
- PDB-4ww4: Double-heterohexameric rings of full-length Rvb1(ADP)/Rvb2(ADP) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ww4
TitleDouble-heterohexameric rings of full-length Rvb1(ADP)/Rvb2(ADP)
Components
  • RuvB-like 1
  • RuvB-like 2
KeywordsHYDROLASE / AAA+ ATPases / hexameric ring / dodecameric assemblies / full-length proteins / ADP-bound states
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 / RuvB-like helicase / RuvB-like helicase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsLakomek, K. / Hopfner, K.-P.
CitationJournal: Structure / Year: 2015
Title: Structural Basis for Dodecameric Assembly States and Conformational Plasticity of the Full-Length AAA+ ATPases Rvb1Rvb2.
Authors: Lakomek, K. / Stoehr, G. / Tosi, A. / Schmailzl, M. / Hopfner, K.P.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RuvB-like 1
B: RuvB-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2464
Polymers106,3922
Non-polymers8542
Water25214
1
A: RuvB-like 1
B: RuvB-like 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)643,47624
Polymers638,34912
Non-polymers5,12612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area78150 Å2
ΔGint-498 kcal/mol
Surface area222370 Å2
MethodPISA
2
A: RuvB-like 1
B: RuvB-like 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)643,47624
Polymers638,34912
Non-polymers5,12612
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area81260 Å2
ΔGint-501 kcal/mol
Surface area219260 Å2
MethodPISA
3
A: RuvB-like 1
B: RuvB-like 2
hetero molecules

A: RuvB-like 1
B: RuvB-like 2
hetero molecules

A: RuvB-like 1
B: RuvB-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,73812
Polymers319,1756
Non-polymers2,5636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area34610 Å2
ΔGint-228 kcal/mol
Surface area115650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.848, 206.848, 137.441
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Detailsbiological unit form 1 is a hetero-hexameric ring, generated from the hetero-dimer in the asymmetric unit by the following two operations: \cf0\f1\fs22\lang1031 -Y,X-Y,Z and -X+Y,-X,Z\cf1\f0\fs18\lang1033 / biological unit form 2a is a dodecameric head-to-head assembly, generated from the hetero-dimer in the asymmetric unit by the following five operations: \cf0\f1\fs22\lang1031 -Y,X-Y,Z and -X+Y,-X,Z and Y,X,-Z and \par -X,-X+Y,-Z and X-Y,-Y,-Z\cf1\f0\fs18\lang1033 / biological unit form 2b is a dodecameric tail-to-tail assembly, generated from the hetero-dimer in the asymmetric unit by the following five operations: \cf0\f1\fs22\lang1031 -Y,X-Y,Z and -X+Y,-X,Z and Y,X,-Z+1 and \par -X,-X+Y,-Z+1 and X-Y,-Y,-Z+1\cf1\f0\fs18\lang1033

-
Components

#1: Protein RuvB-like 1 /


Mass: 50451.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0006820 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: G0RYI5, DNA helicase
#2: Protein RuvB-like 2


Mass: 55939.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0006170 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: G0RYC2, DNA helicase
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1 M sodium malonate, ADP-BeF3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionRedundancy: 4.4 % / Number: 103751 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / D res high: 2.94 Å / D res low: 75.04 Å / Num. obs: 23417 / % possible obs: 97.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
2.943.110.690.0383.2
9.375.0410.0380.0465.1
ReflectionResolution: 2.94→64.161 Å / Num. all: 23417 / Num. obs: 23417 / % possible obs: 97.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 79.28 Å2 / Rpim(I) all: 0.052 / Rrim(I) all: 0.116 / Rsym value: 0.103 / Net I/av σ(I): 5.438 / Net I/σ(I): 8.3 / Num. measured all: 103751
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.94-3.13.20.691.11088333740.4320.691.796.9
3.1-3.293.30.4991.51035431840.3090.4992.396.4
3.29-3.513.20.3241.8928529280.20.3243.594.7
3.51-3.850.2662.11426028580.130.2665.899.3
3.8-4.165.50.164.31449026470.0730.169.399.1
4.16-4.655.20.1046.51233623820.0490.10412.498.8
4.65-5.375.40.09571131721140.0440.09514.698.3
5.37-6.575.50.0897.6967217720.040.08915.297.9
6.57-9.35.20.04613.1717713820.0210.04618.997.3
9.3-64.1615.10.03813.539777760.0190.03821.995.5

-
Processing

Software
NameVersionClassification
BUSTER-TNTrefinement
MOSFLMdata reduction
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WVY

4wvy


Resolution: 2.94→64.16 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.339
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 1193 5.1 %RANDOM
Rwork0.1975 ---
obs0.1989 23414 97.2 %-
Displacement parametersBiso max: 205.26 Å2 / Biso mean: 99.77 Å2 / Biso min: 35.37 Å2
Baniso -1Baniso -2Baniso -3
1-5.1559 Å20 Å20 Å2
2--5.1559 Å20 Å2
3----10.3119 Å2
Refine analyzeLuzzati coordinate error obs: 0.554 Å
Refinement stepCycle: final / Resolution: 2.94→64.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6535 0 54 14 6603
Biso mean--80.06 56.45 -
Num. residues----851
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2436SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes170HARMONIC2
X-RAY DIFFRACTIONt_gen_planes982HARMONIC5
X-RAY DIFFRACTIONt_it6668HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion918SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7570SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6668HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg8994HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion23.11
LS refinement shellResolution: 2.94→3.07 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2698 136 4.82 %
Rwork0.2352 2686 -
all0.2369 2822 -
obs--97.2 %
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)
10.7122-0.20820.12241.28391.0421.8426-0.0515-0.06630.0982-0.2034-0.2450.1497-1.0305-0.25240.29650.2280.0748-0.147-0.33240.07940.0146-4.128735.770933.9151
21.6140.07530.6521.23750.64662.2382-0.1462-0.08130.2891-0.16590.08550.0089-0.50760.86890.0607-0.1212-0.3966-0.02180.13530.1522-0.001931.141920.312828.5593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 458
2X-RAY DIFFRACTION2{ B|* }B7 - 456

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more