[English] 日本語
Yorodumi
- PDB-5eax: Crystal structure of Dna2 in complex with an ssDNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eax
TitleCrystal structure of Dna2 in complex with an ssDNA
Components
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA replication ATP-dependent helicase/nuclease DNA2
KeywordsHydrolase/DNA / DNA binding protein / Hydrolase-DNA complex
Function / homology
Function and homology information


Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA replication, Okazaki fragment processing / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / gamma DNA polymerase complex ...Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA replication, Okazaki fragment processing / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / gamma DNA polymerase complex / Processing of DNA double-strand break ends / site-specific endodeoxyribonuclease activity, specific for altered base / mitochondrial DNA replication / mitotic telomere maintenance via semi-conservative replication / DNA double-strand break processing / nucleic acid metabolic process / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / Regulation of TP53 Activity through Phosphorylation / nuclease activity / DNA replication checkpoint signaling / replication fork reversal / 5'-3' DNA helicase activity / single-stranded DNA helicase activity / mitochondrial DNA repair / mitochondrial nucleoid / telomere maintenance / positive regulation of DNA replication / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA helicase / DNA replication / chromosome, telomeric region / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / Dna2 Rift barrel domain / DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / PD-(D/E)XK endonuclease-like domain superfamily ...: / Dna2 Rift barrel domain / DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / PD-(D/E)XK endonuclease-like domain superfamily / DNA2/NAM7 helicase-like, C-terminal / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA replication ATP-dependent helicase/nuclease DNA2
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.05 Å
AuthorsZhou, C. / Pourmal, S. / Pavletich, N.P.
CitationJournal: Elife / Year: 2015
Title: Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.
Authors: Zhou, C. / Pourmal, S. / Pavletich, N.P.
History
DepositionOct 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA replication ATP-dependent helicase/nuclease DNA2
E: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
B: DNA replication ATP-dependent helicase/nuclease DNA2
H: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,5808
Polymers248,0224
Non-polymers1,5584
Water0
1
A: DNA replication ATP-dependent helicase/nuclease DNA2
E: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7904
Polymers124,0112
Non-polymers7792
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA replication ATP-dependent helicase/nuclease DNA2
H: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7904
Polymers124,0112
Non-polymers7792
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.234, 149.211, 172.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22A
13B
23A
14B
24A
15B
25A
16B
26A
17C
27F
18D
28G
19E
29H
110E
210H
111E
211H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B1 - 13
2111A1 - 13
1121B21 - 121
2121A21 - 121
1131B122 - 460
2131A122 - 460
1141B461 - 563
2141A461 - 563
1151B569 - 826
2151A569 - 826
1161B827 - 1056
2161A827 - 1056
1171C600
2171F600
1181D502
2181G502
1191E1 - 5
2191H1 - 5
11101E6 - 9
21101H6 - 9
11111E10 - 17
21111H10 - 17

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999883, -0.014999, 0.002877), (0.014882, -0.999197, -0.037195), (0.003433, -0.037148, 0.999304)178.852127, 3.51117, 1.26414
3given(1), (1), (1)
4given(-0.999976, 0.000952, 0.006865), (-0.000926, -0.999993, 0.003754), (0.006869, 0.003748, 0.999969)178.315536, -0.25975, -0.89068
5given(1), (1), (1)
6given(-0.999948, 0.003729, 0.009487), (-0.00372, -0.999993, 0.000902), (0.009491, 0.000867, 0.999955)178.072479, 0.16197, -1.0538
7given(1), (1), (1)
8given(-0.999988, 0.004841, -0.001175), (-0.004833, -0.999964, -0.006903), (-0.001208, -0.006897, 0.999976)178.965683, 0.80079, -0.4682
9given(1), (1), (1)
10given(-0.999686, -0.001252, 0.025031), (0.001273, -0.999999, 0.000851), (0.02503, 0.000882, 0.999686)176.82724, -0.1807, -2.15964
11given(1), (1), (1)
12given(-0.999559, -0.001663, 0.029635), (0.001835, -0.999982, 0.005778), (0.029625, 0.005829, 0.999544)176.504135, -0.55658, -2.68408
13given(1), (1), (1)
14given(-0.999519, 0.026067, 0.016796), (-0.026693, -0.998914, -0.038185), (0.015782, -0.038615, 0.999129)177.69902, 6.70938, -1.61361
15given(1), (1), (1)
16given(-0.999979, -0.005368, 0.003519), (0.005569, -0.998184, 0.059983), (0.003191, 0.060001, 0.998193)177.894028, -3.73818, 1.78466
17given(1), (1), (1)
18given(-0.999787, -0.004617, 0.020134), (0.004566, -0.999986, -0.002584), (0.020146, -0.002491, 0.999794)177.130112, -0.40463, -1.71592
19given(1), (1), (1)
20given(-0.99944, -0.006979, 0.032725), (0.006962, -0.999976, -0.000625), (0.032729, -0.000397, 0.999464)176.274612, -0.75053, -3.17819
21given(1), (1), (1)
22given(-0.999944, -0.002266, 0.010306), (0.002327, -0.99998, 0.005879), (0.010292, 0.005902, 0.99993)178.081268, -0.76323, -0.78481

-
Components

#1: Protein DNA replication ATP-dependent helicase/nuclease DNA2 / DNA replication ATP-dependent helicase-like homolog


Mass: 118884.633 Da / Num. of mol.: 2 / Mutation: D278A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dna2, Dna2l, Kiaa0083 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6ZQJ5, Hydrolases; Acting on ester bonds, DNA helicase
#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 5126.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: 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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: IPA, CaCl2, MES pH6.5 / PH range: 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 62189 / % possible obs: 99 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.066 / Rrim(I) all: 0.15 / Χ2: 1.385 / Net I/av σ(I): 13.222 / Net I/σ(I): 6.9 / Num. measured all: 379814
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3-3.11661420.7010.5711.2299.2
3.11-3.23661610.8360.3821.26799.40.8750.957
3.23-3.386.161770.9250.2391.29899.60.550.602
3.38-3.566.161980.9580.161.35699.60.3670.402
3.56-3.786.161820.980.1051.39999.50.2410.264
3.78-4.076.262420.9910.0691.39399.70.1610.176
4.07-4.486.362300.9960.0461.36699.40.1080.118
4.48-5.126.262300.9970.0361.48499.10.0840.092
5.12-6.446.162700.9960.041.61998.50.0910.1
6.44-30663570.9990.0181.43996.40.040.044

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
RefinementResolution: 3.05→29.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 21.191 / SU ML: 0.366 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1305 2.5 %RANDOM
Rwork0.2226 ---
obs0.2234 51122 87.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 178.85 Å2 / Biso mean: 75.784 Å2 / Biso min: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2---3.9 Å2-0 Å2
3---4.95 Å2
Refinement stepCycle: final / Resolution: 3.05→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16536 674 70 0 17280
Biso mean--78.1 --
Num. residues----2126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01917666
X-RAY DIFFRACTIONr_angle_refined_deg1.431.95224044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44152084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67923.595740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.587153110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.06415144
X-RAY DIFFRACTIONr_chiral_restr0.0980.22734
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112824
X-RAY DIFFRACTIONr_mcbond_it1.5663.6798360
X-RAY DIFFRACTIONr_mcangle_it2.8728.27210436
X-RAY DIFFRACTIONr_scbond_it1.5023.8879306
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B80TIGHT POSITIONAL0.020.05
1B160TIGHT POSITIONAL0.010.05
1B106TIGHT THERMAL2.0299
2B812TIGHT THERMAL5.6199
3B2686TIGHT THERMAL2.4399
4B798TIGHT THERMAL5.3399
5B2021TIGHT THERMAL2.399
6B1792TIGHT THERMAL7.9399
7A8TIGHT THERMAL1.6199
8B27TIGHT THERMAL2.699
9E97TIGHT THERMAL4.4699
10E80TIGHT THERMAL1.8499
11E160TIGHT THERMAL3.9799
LS refinement shellResolution: 3.05→3.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 76 -
Rwork0.375 2994 -
all-3070 -
obs--71.16 %

+
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