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- PDB-5ean: Crystal structure of Dna2 in complex with a 5' overhang DNA -

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Basic information

Entry
Database: PDB / ID: 5ean
TitleCrystal structure of Dna2 in complex with a 5' overhang DNA
Components
  • DNA (5'-D(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)-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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA replication ATP-dependent helicase/nuclease DNA2
B: DNA (5'-D(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,6436
Polymers123,7842
Non-polymers8594
Water724
1
A: DNA replication ATP-dependent helicase/nuclease DNA2
B: DNA (5'-D(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)-3')
hetero molecules

A: DNA replication ATP-dependent helicase/nuclease DNA2
B: DNA (5'-D(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,28612
Polymers247,5684
Non-polymers1,7188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area13430 Å2
ΔGint-151 kcal/mol
Surface area90500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.153, 118.488, 149.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

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


Mass: 119180.891 Da / Num. of mol.: 1
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(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)-3')


Mass: 4603.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 80 mM MES, 20 mM CaCl2, 10 mM spermidine, 4-9 % isopropanol, 0.5 mM TCEP, pH 6.5, and 1 mM ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 63876 / % possible obs: 99 % / Redundancy: 5 % / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.063 / Rrim(I) all: 0.142 / Χ2: 1.503 / Net I/av σ(I): 16.429 / Net I/σ(I): 5.3 / Num. measured all: 316314
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.433.90.65662650.750.3660.7560.92998.6
2.43-2.534.50.58363460.8370.3010.6590.96299.6
2.53-2.655.10.49863040.880.2390.5541.01499.2
2.65-2.795.40.39163800.9260.1840.4341.0999.8
2.79-2.965.30.28663560.9570.1380.3191.18199.3
2.96-3.194.90.2163690.9580.1050.2361.43599.3
3.19-3.515.30.15963930.9740.0780.1791.71299.5
3.51-4.025.10.12264120.980.0620.1372.05999
4.02-5.0650.09864350.9860.0490.112.35698.6
5.06-504.90.0866160.9940.0390.092.06897.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EAW

5eaw


Resolution: 2.36→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 18.904 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1799 3 %RANDOM
Rwork0.2083 ---
obs0.2094 57871 92.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 176.74 Å2 / Biso mean: 66.556 Å2 / Biso min: 26.12 Å2
Baniso -1Baniso -2Baniso -3
1-5.72 Å20 Å20 Å2
2---2.1 Å20 Å2
3----3.62 Å2
Refinement stepCycle: final / Resolution: 2.36→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8302 309 37 4 8652
Biso mean--63.42 59.62 -
Num. residues----1066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198856
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.95212034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24851048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53423.619373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.871151559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2991572
X-RAY DIFFRACTIONr_chiral_restr0.1040.21363
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216439
X-RAY DIFFRACTIONr_mcbond_it1.4983.6354206
X-RAY DIFFRACTIONr_mcangle_it2.3655.6095246
X-RAY DIFFRACTIONr_scbond_it2.5824.6344650
LS refinement shellResolution: 2.355→2.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 93 -
Rwork0.329 3568 -
all-3661 -
obs--77.7 %
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)
15.33350.47820.06314.1915-0.22942.9824-0.0288-0.5441-0.66580.3739-0.0101-0.34730.78030.39940.03880.75270.1626-0.0320.59860.06840.517357.6749.37113.64
21.58660.30381.0591.6004-0.27724.49320.00370.0065-0.1960.06780.1021-0.01880.580.2166-0.10570.29850.03520.02120.2531-0.01080.232648.51720.758-13.559
31.1617-1.5145-0.89033.75472.51123.7475-0.00820.02330.1083-0.25280.1225-0.5340.12850.6114-0.11440.18360.071-0.01310.47720.03370.353955.00637.74314.606
41.5707-2.2975-1.34594.9142.7582.8326-0.08360.0629-0.1424-0.09950.01880.12640.21360.04280.06490.1287-0.0318-0.010.25490.02380.152435.4939.393-16.824
54.50670.3007-0.41132.2390.07780.6563-0.0113-0.29020.14820.0202-0.09470.99250.0837-0.71450.1060.9013-0.09260.04290.98860.05540.872825.24916.4343.813
60.9905-0.30290.23130.9669-0.41652.2307-0.0026-0.0086-0.10060.01240.03550.11570.1768-0.2235-0.03290.0196-0.00820.02320.25420.02030.150326.93151.25319.284
72.44510.38110.05442.56-0.45611.66860.0252-0.0397-0.53140.14590.05730.30080.4662-0.2964-0.08260.2489-0.11170.04170.50110.0740.386413.22227.30641.77
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 121
2X-RAY DIFFRACTION2A122 - 127
3X-RAY DIFFRACTION2A229 - 357
4X-RAY DIFFRACTION3A128 - 152
5X-RAY DIFFRACTION3A358 - 460
6X-RAY DIFFRACTION3A1101
7X-RAY DIFFRACTION4A153 - 228
8X-RAY DIFFRACTION5A461 - 567
9X-RAY DIFFRACTION6A568 - 826
10X-RAY DIFFRACTION7A827 - 1056

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