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- PDB-3q8m: Crystal Structure of Human Flap Endonuclease FEN1 (D181A) in comp... -

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Basic information

Entry
Database: PDB / ID: 3q8m
TitleCrystal Structure of Human Flap Endonuclease FEN1 (D181A) in complex with substrate 5'-flap DNA and K+
Components
  • DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
  • DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')
  • DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
  • Flap endonuclease 1
KeywordsHYDROLASE/DNA / helix-3 turn-helix / hydrophobic wedge / 3' flap binding site / hydrolase-DNA complex / DNA repair / replication / flap endonuclease / FEN / FEN1 / DNA / nuclease / 5' flap / ss-dsDNA junction / helix-2 turn-helix / H2TH / H3TH / divalent cation / metal helical gateway / cap / acid block / two metal mechanism / unpaired / 5' nuclease / human / long patch base excision repair
Function / homology
Function and homology information


positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / nucleic acid metabolic process / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / UV protection / Removal of the Flap Intermediate ...positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / nucleic acid metabolic process / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / UV protection / Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / HDR through MMEJ (alt-NHEJ) / exonuclease activity / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / double-strand break repair via homologous recombination / memory / double-strand break repair / RNA-DNA hybrid ribonuclease activity / manganese ion binding / double-stranded DNA binding / endonuclease activity / DNA replication / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / DNA repair / nucleolus / magnesium ion binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / membrane / nucleus
Similarity search - Function
Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / 5'-nuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Flap endonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsTsutakawa, S.E. / Classen, S. / Chapados, B.R. / Arvai, A. / Finger, D.L. / Guenther, G. / Tomlinson, C.G. / Thompson, P. / Sarker, A.H. / Shen, B. ...Tsutakawa, S.E. / Classen, S. / Chapados, B.R. / Arvai, A. / Finger, D.L. / Guenther, G. / Tomlinson, C.G. / Thompson, P. / Sarker, A.H. / Shen, B. / Cooper, P.K. / Grasby, J.A. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily.
Authors: Tsutakawa, S.E. / Classen, S. / Chapados, B.R. / Arvai, A.S. / Finger, L.D. / Guenther, G. / Tomlinson, C.G. / Thompson, P. / Sarker, A.H. / Shen, B. / Cooper, P.K. / Grasby, J.A. / Tainer, J.A.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_ref_seq_dif.details / _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: Flap endonuclease 1
B: Flap endonuclease 1
D: DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')
E: DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
F: DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
G: DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')
H: DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
I: DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,56710
Polymers99,4898
Non-polymers782
Water1,982110
1
A: Flap endonuclease 1
G: DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')
H: DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
I: DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7845
Polymers49,7454
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-26 kcal/mol
Surface area20540 Å2
MethodPISA
2
B: Flap endonuclease 1
D: DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')
E: DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
F: DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7845
Polymers49,7454
Non-polymers391
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-25 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.520, 94.940, 104.520
Angle α, β, γ (deg.)90.00, 105.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22G
13E
23H
14I
24F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 2:342 )A2 - 342
211chain B and (resseq 2:342 )B2 - 342
112chain D and (resseq 1:18 )D1 - 18
212chain G and (resseq 1:18 )G1 - 18
113chain E and (resseq 1:12 )E1 - 12
213chain H and (resseq 1:12 )H1 - 12
114chain I and (resseq 1:7 )I1 - 7
214chain F and (resseq 1:7 )F1 - 7

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.777042, -0.385469, -0.497613), (-0.380864, -0.917342, 0.115872), (-0.501146, 0.099485, -0.859625)-24.940201, -31.363501, -65.647102
2given(0.796222, -0.294602, -0.528432), (-0.312784, -0.948096, 0.057275), (-0.517877, 0.119682, -0.847042)-26.4821, -31.4531, -65.2715
3given(0.795372, -0.278043, -0.538586), (-0.296283, -0.953532, 0.054713), (-0.528772, 0.116057, -0.840792)-26.8449, -30.8172, -65.412804
4given(0.74235, -0.493206, -0.453503), (-0.463241, -0.86683, 0.184428), (-0.484071, 0.073171, -0.871964)-27.3578, -32.7733, -65.474998

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Flap endonuclease 1 / FEN-1 / DNase IV / Flap structure-specific endonuclease 1 / Maturation factor 1 / MF1 / hFEN-1


Mass: 38467.180 Da / Num. of mol.: 2 / Fragment: D181A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FEN1, RAD2 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3 pLysS cells
References: UniProt: P39748, Hydrolases; Acting on ester bonds

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DNA chain , 3 types, 6 molecules DGEHFI

#2: DNA chain DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')


Mass: 5476.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized
#3: DNA chain DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')


Mass: 3742.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized
#4: DNA chain DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')


Mass: 2058.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized

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Non-polymers , 2 types, 112 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 7.5
Details: 20% mPEG 2k, 20% KCl, 10 mM CaCl2, 50 mM Bis-Tris pH 7.5, 5% ethylene glycol, vapor diffusion, temperature 288K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.6→101.015 Å / Num. all: 34587 / Num. obs: 34587 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.743.40.3442.21665449610.34499
2.74-2.913.60.2043.61722647650.20499.9
2.91-3.113.60.1245.71628345060.12499.9
3.11-3.363.60.0867.11492841550.08699.9
3.36-3.683.60.06110.11383238560.06199.9
3.68-4.113.60.049121244234870.04999.8
4.11-4.753.50.04114.91091830850.04199.7
4.75-5.813.50.03915.5902426020.03999.9
5.81-8.223.30.03317.5658920160.03399.3
8.22-101.0153.60.03312415111540.033100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q8K

3q8k


Resolution: 2.6→100.93 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7354 / SU ML: 0.45 / σ(F): 1.16 / Phase error: 32.67 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 3248 4.86 %RANDOM
Rwork0.2167 ---
obs0.2195 34563 98.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.166 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso max: 248.67 Å2 / Biso mean: 86.5072 Å2 / Biso min: 19.06 Å2
Baniso -1Baniso -2Baniso -3
1-8.7985 Å20 Å2-6.6517 Å2
2--3.8173 Å20 Å2
3----12.6158 Å2
Refinement stepCycle: LAST / Resolution: 2.6→100.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5251 1496 2 110 6859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147355
X-RAY DIFFRACTIONf_angle_d1.1679759
X-RAY DIFFRACTIONf_chiral_restr0.0671080
X-RAY DIFFRACTIONf_plane_restr0.0041016
X-RAY DIFFRACTIONf_dihedral_angle_d21.3582783
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2620X-RAY DIFFRACTIONPOSITIONAL0.04
12B2620X-RAY DIFFRACTIONPOSITIONAL0.04
21D363X-RAY DIFFRACTIONPOSITIONAL0.059
22G363X-RAY DIFFRACTIONPOSITIONAL0.059
31E249X-RAY DIFFRACTIONPOSITIONAL0.032
32H249X-RAY DIFFRACTIONPOSITIONAL0.032
41I136X-RAY DIFFRACTIONPOSITIONAL0.055
42F136X-RAY DIFFRACTIONPOSITIONAL0.055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.63860.47951460.49992585273194
2.6386-2.67980.43951370.36552764290197
2.6798-2.72370.41841310.37282846297799
2.7237-2.77070.38651450.31522720286599
2.7707-2.82110.4641420.32482834297699
2.8211-2.87530.33031480.28352706285499
2.8753-2.9340.32241180.25872841295999
2.934-2.99780.35711560.24832720287699
2.9978-3.06760.38841130.26012833294699
3.0676-3.14430.34171540.25592795294999
3.1443-3.22930.32261560.26352733288999
3.2293-3.32440.28471720.2652797296999
3.3244-3.43170.3631480.28152730287899
3.4317-3.55430.29271320.24942812294499
3.5543-3.69660.32361320.24762795292799
3.6966-3.86490.30561460.22192756290298
3.8649-4.06860.33981180.19762788290699
4.0686-4.32360.22781350.17572787292298
4.3236-4.65740.21641540.16172737289198
4.6574-5.12610.19871430.16522746288998
5.1261-5.86770.24991480.20172781292998
5.8677-7.39240.23141330.19482681281496
7.3924-101.00630.17561410.15972784292599
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)
10.1531-0.12160.10430.1366-0.23390.4885-0.22430.1390.0549-0.17350.2481-0.0196-0.1919-0.2408-0.0210.4176-0.2248-0.06110.38210.13170.3145-29.926-7.4455-52.4736
20.18060.04730.00650.1089-0.0440.0853-0.08050.0712-0.1088-0.16110.05370.0206-0.08840.0140.01020.4191-0.1224-0.00730.14090.04780.2621-27.225-12.6054-53.1679
30.2222-0.01290.08060.683-0.00360.1403-0.11490.00890.19160.75080.0358-0.0024-0.2970.00720.07240.8799-0.3456-0.13110.2238-0.01550.3424-18.4675.2205-39.1748
40.145-0.1320.03840.17-0.06960.0321-0.03790.42780.0403-0.4990.0412-0.09570.20080.15370.00270.7625-0.3058-0.0920.72330.0220.2659-22.3458-13.3144-63.0278
50.5015-0.0734-0.0220.3334-0.04470.134-0.1578-0.86140.2770.70530.0497-0.2811-0.23960.1771-0.1480.44780.0836-0.06980.5185-0.2253-0.2085-19.5823-18.7197-6.0643
60.47590.09490.38750.2186-0.10070.5977-0.1277-0.20720.09690.15230.0553-0.1238-0.28340.21120.03070.3322-0.0734-0.02250.503-0.0620.3015-15.1756-15.087-7.4211
70.11070.0292-0.07420.10840.05190.1222-0.0877-0.23160.24840.17630.11240.08880.09520.03050.0660.18730.09250.00540.2554-0.03440.2387-22.1724-33.4197-21.7357
80.0553-0.03670.06820.267-0.09580.0432-0.2624-0.47770.14150.5143-0.2854-0.369-0.24990.3144-0.20430.5971-0.0875-0.25821.0355-0.32580.1966-6.1694-17.1034-1.6839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:116)A2 - 116
2X-RAY DIFFRACTION2(chain A and resid 117:175)A117 - 175
3X-RAY DIFFRACTION3(chain A and resid 176:274)A176 - 274
4X-RAY DIFFRACTION4(chain A and resid 275:342)A275 - 342
5X-RAY DIFFRACTION5(chain B and resid 2:116)B2 - 116
6X-RAY DIFFRACTION6(chain B and resid 117:175)B117 - 175
7X-RAY DIFFRACTION7(chain B and resid 176:274)B176 - 274
8X-RAY DIFFRACTION8(chain B and resid 275:342)B275 - 342

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