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- PDB-5nwl: Crystal structure of a human RAD51-ATP filament. -

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Basic information

Entry
Database: PDB / ID: 5nwl
TitleCrystal structure of a human RAD51-ATP filament.
ComponentsDNA repair protein RAD51 homolog 1
KeywordsRECOMBINATION / ATPase / DNA-strand exchange / Homologous Recombination / double-strand DNA break repair
Function / homology
Function and homology information


presynaptic intermediate filament cytoskeleton / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / cellular response to camptothecin / DNA recombinase assembly / telomere maintenance via telomere lengthening / positive regulation of DNA ligation / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / mitotic recombination ...presynaptic intermediate filament cytoskeleton / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / cellular response to camptothecin / DNA recombinase assembly / telomere maintenance via telomere lengthening / positive regulation of DNA ligation / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / mitotic recombination / DNA strand invasion / cellular response to hydroxyurea / replication-born double-strand break repair via sister chromatid exchange / DNA strand exchange activity / lateral element / telomere maintenance via recombination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / single-stranded DNA helicase activity / reciprocal meiotic recombination / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / ATP-dependent DNA damage sensor activity / Impaired BRCA2 binding to RAD51 / regulation of double-strand break repair via homologous recombination / nuclear chromosome / DNA unwinding involved in DNA replication / replication fork processing / Transcriptional Regulation by E2F6 / Presynaptic phase of homologous DNA pairing and strand exchange / ATP-dependent activity, acting on DNA / interstrand cross-link repair / DNA polymerase binding / condensed chromosome / meiotic cell cycle / condensed nuclear chromosome / male germ cell nucleus / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDR through Homologous Recombination (HRR) / PML body / Meiotic recombination / single-stranded DNA binding / site of double-strand break / double-stranded DNA binding / DNA recombination / chromosome, telomeric region / mitochondrial matrix / DNA repair / centrosome / DNA damage response / chromatin binding / chromatin / nucleolus / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 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'-TRIPHOSPHATE / DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.93 Å
AuthorsPellegrini, L. / Moschetti, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust104641/Z/14/Z United Kingdom
CitationJournal: EMBO J. / Year: 2018
Title: Two distinct conformational states define the interaction of human RAD51-ATP with single-stranded DNA.
Authors: Brouwer, I. / Moschetti, T. / Candelli, A. / Garcin, E.B. / Modesti, M. / Pellegrini, L. / Wuite, G.J. / Peterman, E.J.
History
DepositionMay 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD51 homolog 1
B: DNA repair protein RAD51 homolog 1
C: DNA repair protein RAD51 homolog 1
D: DNA repair protein RAD51 homolog 1
E: DNA repair protein RAD51 homolog 1
F: DNA repair protein RAD51 homolog 1
G: DNA repair protein RAD51 homolog 1
H: DNA repair protein RAD51 homolog 1
I: DNA repair protein RAD51 homolog 1
J: DNA repair protein RAD51 homolog 1
K: DNA repair protein RAD51 homolog 1
L: DNA repair protein RAD51 homolog 1
M: DNA repair protein RAD51 homolog 1
N: DNA repair protein RAD51 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)525,56942
Polymers518,12814
Non-polymers7,44128
Water0
1
A: DNA repair protein RAD51 homolog 1
B: DNA repair protein RAD51 homolog 1
C: DNA repair protein RAD51 homolog 1
D: DNA repair protein RAD51 homolog 1
E: DNA repair protein RAD51 homolog 1
F: DNA repair protein RAD51 homolog 1
G: DNA repair protein RAD51 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,78421
Polymers259,0647
Non-polymers3,72014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26630 Å2
ΔGint-193 kcal/mol
Surface area87780 Å2
MethodPISA
2
H: DNA repair protein RAD51 homolog 1
I: DNA repair protein RAD51 homolog 1
J: DNA repair protein RAD51 homolog 1
K: DNA repair protein RAD51 homolog 1
L: DNA repair protein RAD51 homolog 1
M: DNA repair protein RAD51 homolog 1
N: DNA repair protein RAD51 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,78421
Polymers259,0647
Non-polymers3,72014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26530 Å2
ΔGint-192 kcal/mol
Surface area87960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.700, 128.000, 230.100
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA repair protein RAD51 homolog 1 / / hRAD51 / RAD51 homolog A


Mass: 37009.125 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD51, RAD51A, RECA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q06609
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: Mg
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O13P3 / Comment: ATP, 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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 MES pH 5.2 MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.93→49.14 Å / Num. obs: 61077 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 128.3 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.287 / Rpim(I) all: 0.168 / Net I/σ(I): 3.8
Reflection shellResolution: 3.93→4.02 Å / Redundancy: 3.8 % / Rmerge(I) obs: 2.888 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4149 / CC1/2: 0.263 / Rpim(I) all: 1.683 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N0W

1n0w


Resolution: 3.93→49.14 Å / SU ML: 0.76 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 35.55
RfactorNum. reflection% reflection
Rfree0.3167 5960 5.08 %
Rwork0.2684 --
obs0.2708 61077 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.93→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32767 0 0 0 32767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333271
X-RAY DIFFRACTIONf_angle_d0.42944908
X-RAY DIFFRACTIONf_dihedral_angle_d9.35820132
X-RAY DIFFRACTIONf_chiral_restr0.0385121
X-RAY DIFFRACTIONf_plane_restr0.0025774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.93-3.97470.40061780.36093475X-RAY DIFFRACTION92
3.9747-4.02140.35831940.36323565X-RAY DIFFRACTION94
4.0214-4.07040.38792400.35643615X-RAY DIFFRACTION96
4.0704-4.12190.38782250.35693634X-RAY DIFFRACTION97
4.1219-4.17610.40532060.35573670X-RAY DIFFRACTION97
4.1761-4.23330.35421940.33743653X-RAY DIFFRACTION96
4.2333-4.29380.39412270.33623617X-RAY DIFFRACTION98
4.2938-4.35780.34561910.31643841X-RAY DIFFRACTION99
4.3578-4.42590.38732040.31653692X-RAY DIFFRACTION99
4.4259-4.49840.39112310.32523676X-RAY DIFFRACTION99
4.4984-4.57590.34121940.30293815X-RAY DIFFRACTION99
4.5759-4.6590.33361790.29853683X-RAY DIFFRACTION98
4.659-4.74860.36282120.2853724X-RAY DIFFRACTION99
4.7486-4.84540.31191820.28133780X-RAY DIFFRACTION99
4.8454-4.95070.32832000.27973785X-RAY DIFFRACTION99
4.9507-5.06570.33141520.29543809X-RAY DIFFRACTION99
5.0657-5.19230.38761850.30853690X-RAY DIFFRACTION98
5.1923-5.33250.37541940.31323746X-RAY DIFFRACTION98
5.3325-5.48920.33821760.30733733X-RAY DIFFRACTION99
5.4892-5.66610.33331890.28123755X-RAY DIFFRACTION99
5.6661-5.86830.32042010.27293828X-RAY DIFFRACTION99
5.8683-6.10290.32151880.29253678X-RAY DIFFRACTION99
6.1029-6.38010.30592140.27823761X-RAY DIFFRACTION99
6.3801-6.71570.32362090.26243738X-RAY DIFFRACTION99
6.7157-7.13520.29692140.25413692X-RAY DIFFRACTION99
7.1352-7.68420.27342100.23223749X-RAY DIFFRACTION99
7.6842-8.4540.31862060.21923780X-RAY DIFFRACTION99
8.454-9.66920.23081780.18013754X-RAY DIFFRACTION99
9.6692-12.15170.21492150.16823714X-RAY DIFFRACTION99
12.1517-49.14340.25291720.22433721X-RAY DIFFRACTION98

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