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- PDB-3q8k: Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex... -

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Basic information

Entry
Database: PDB / ID: 3q8k
TitleCrystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with product 5'-flap DNA, SM3+, 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(P*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
  • Flap endonuclease 1Flap structure-specific 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 / 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 / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand / exonuclease activity / Early Phase of HIV Life Cycle / PCNA-Dependent Long Patch Base Excision Repair / POLB-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 / damaged DNA binding / chromosome, telomeric region / 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
: / HYDROXIDE ION / SAMARIUM (III) ION / DNA / DNA (> 10) / Flap endonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2001 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_alt_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_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_alt_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.pdbx_ptnr1_label_alt_id / _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
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(P*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)50,14210
Polymers49,4844
Non-polymers6586
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-71 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.438, 105.438, 105.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-396-

HOH

21A-571-

HOH

31A-637-

HOH

41A-651-

HOH

51A-713-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 38511.188 Da / Num. of mol.: 1
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, 3 molecules DEF

#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.: 1 / Source method: obtained synthetically / Details: synthesized
#3: DNA chain DNA (5'-D(P*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')


Mass: 3438.259 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Details: synthesized

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Non-polymers , 4 types, 574 molecules

#5: Chemical
ChemComp-SM / SAMARIUM (III) ION / Samarium


Mass: 150.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sm
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 7
Details: 16% mPEG 2k, 20% saturated KCl, 0.5 mM Sm2(SO4)3, 10 mM Mg(NO3)2, 100 mM Hepes pH 7.0, 5% ethylene glycol, VAPOR DIFFUSION, temperature 288K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.9796
SYNCHROTRONALS 12.3.121.116
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDApr 1, 2010
ADSC QUANTUM 315r2CCDMar 1, 2010
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHx-ray1
2Si(111)SINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
21.1161
ReflectionResolution: 2.2→34.462 Å / Num. all: 34291 / Num. obs: 34291 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym value% possible all
2.2-2.323.60.5570.60.557100
2.32-2.463.60.3392.10.339100
2.46-2.633.60.2412.70.241100
2.63-2.843.60.1783.40.178100
2.84-3.113.60.1244.70.12499.9
3.11-3.483.60.0866.20.08699.8
3.48-4.023.60.0735.30.07399.6
4.02-4.923.60.05411.40.05499
4.92-6.963.60.05510.30.05597.9
6.96-34.5033.40.049130.04979.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASERphasing
PHENIX1.7_629refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RXW

1rxw


Resolution: 2.2001→34.46 Å / Occupancy max: 1 / Occupancy min: 0.03 / SU ML: 0.37 / σ(F): 0.99 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 3236 5.1 %
Rwork0.1679 --
obs0.1702 34291 95.55 %
all-63390 -
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.56 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0229 Å20 Å2-0 Å2
2--4.0229 Å20 Å2
3----8.0458 Å2
Refinement stepCycle: LAST / Resolution: 2.2001→34.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 732 6 568 3997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123793
X-RAY DIFFRACTIONf_angle_d0.8645222
X-RAY DIFFRACTIONf_dihedral_angle_d19.2821507
X-RAY DIFFRACTIONf_chiral_restr0.053571
X-RAY DIFFRACTIONf_plane_restr0.004566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.23290.32881660.30092642X-RAY DIFFRACTION98
2.2329-2.26780.3481350.32462668X-RAY DIFFRACTION96
2.2678-2.3050.37731240.30012649X-RAY DIFFRACTION97
2.305-2.34470.27821820.27152655X-RAY DIFFRACTION97
2.3447-2.38730.29741340.24942629X-RAY DIFFRACTION97
2.3873-2.43320.31581430.24442667X-RAY DIFFRACTION97
2.4332-2.48290.30451660.24532637X-RAY DIFFRACTION97
2.4829-2.53690.28571250.24142647X-RAY DIFFRACTION97
2.5369-2.59590.23931140.2212666X-RAY DIFFRACTION97
2.5959-2.66070.30281480.21012662X-RAY DIFFRACTION96
2.6607-2.73270.26691210.19972668X-RAY DIFFRACTION96
2.7327-2.8130.28371470.20452623X-RAY DIFFRACTION96
2.813-2.90380.24211270.20012629X-RAY DIFFRACTION96
2.9038-3.00750.26351180.18752679X-RAY DIFFRACTION96
3.0075-3.12790.26151690.17272555X-RAY DIFFRACTION96
3.1279-3.27010.2061210.15222661X-RAY DIFFRACTION96
3.2701-3.44240.20241430.15512616X-RAY DIFFRACTION96
3.4424-3.65780.21361650.1582612X-RAY DIFFRACTION96
3.6578-3.93990.18721430.13992583X-RAY DIFFRACTION96
3.9399-4.33570.14891390.12142630X-RAY DIFFRACTION95
4.3357-4.96150.1251540.11022587X-RAY DIFFRACTION95
4.9615-6.24480.21481420.12732573X-RAY DIFFRACTION94
6.2448-34.46430.16871100.16892215X-RAY DIFFRACTION81
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)
10.15680.05720.09280.22080.25070.29380.0408-0.0997-0.02040.14780.0817-0.1030.15650.0846-0.06020.31480.0352-0.03690.2607-0.02490.278424.0506-6.24165.4535
20.13740.07430.07420.19620.15750.3805-0.0346-0.0523-0.06120.01660.0465-0.10090.1565-0.0330.00060.31050.02310.01350.2571-0.0050.34518.7747-4.41026.4634
30.5290.0293-0.11430.0718-0.17440.4418-0.0867-0.1718-0.18480.05430.1106-0.15160.29410.0292-0.00010.38080.0595-0.05310.19390.00520.350522.7842-23.3633-7.4051
40.0267-0.024-0.03020.0784-0.050.1498-0.0244-0.00510.0445-0.03840.04040.1074-0.0182-0.0633-0.00860.3157-0.01440.01450.3078-0.01710.364516.54816.1971-0.5776
50.3387-0.0176-0.0520.494-0.56130.65220.0357-0.0763-0.01550.0609-0.0048-0.4815-0.05140.021-0.0380.8740.1838-0.08340.3913-0.18130.742734.5115-32.32144.5985
60.8062-0.3077-0.3220.11770.12320.1284-0.0992-0.0475-0.14560.0786-0.00620.0860.0918-0.01370.05940.42670.23060.08760.2695-0.08810.559335.1173-9.591410.2881
70.4628-0.13350.56970.22260.18441.36030.229-0.249-0.03360.0411-0.1398-0.5256-0.12010.3736-0.08170.2809-0.1140.03380.63220.05690.740739.778310.18088.0426
80.7503-0.5372-0.19181.08770.50910.31190.07860.00940.14040.0286-0.0241-0.18750.15190.0208-0.04250.73310.3519-0.12570.4083-0.19250.705134.4099-29.37915.1172
91.6439-0.2929-0.86230.18720.19070.4617-0.1669-0.36960.07940.00780.1937-0.15040.04970.42-0.0630.27020.00820.06650.7415-0.02910.497840.86295.863512.73
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:116)
2X-RAY DIFFRACTION2(chain A and resid 117:175)
3X-RAY DIFFRACTION3(chain A and resid 176:274)
4X-RAY DIFFRACTION4(chain A and resid 275:342)
5X-RAY DIFFRACTION5(chain D and resid 1:9)
6X-RAY DIFFRACTION6(chain D and resid 10:13)
7X-RAY DIFFRACTION7(chain D and resid 14:18)
8X-RAY DIFFRACTION8(chain E)
9X-RAY DIFFRACTION9(chain F)

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