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- PDB-4ri9: FAN1 Nuclease bound to 5' phosphorylated p(dT)/3'(dT-dT-dT-dT-dT-... -

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Basic information

Entry
Database: PDB / ID: 4ri9
TitleFAN1 Nuclease bound to 5' phosphorylated p(dT)/3'(dT-dT-dT-dT-dT-dT-dT-dT) double flap DNA
Components
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*GP*AP*GP*GP*CP*GP*TP*G)-3')
  • DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*CP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
  • DNA (5'-D(P*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')
  • Fanconi-associated nuclease 1
Keywordshydrolase/dna / nuclease / hydrolase-dna complex
Function / homology
Function and homology information


flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / phosphodiesterase I activity / 5'-3' exonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / ubiquitin-modified protein reader activity / intercellular bridge / interstrand cross-link repair / nucleotide-excision repair ...flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / phosphodiesterase I activity / 5'-3' exonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / ubiquitin-modified protein reader activity / intercellular bridge / interstrand cross-link repair / nucleotide-excision repair / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / DNA repair / magnesium ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Fanconi-associated nuclease 1, SAP subdomain / Fanconi-associated nuclease 1, TPR domain / Fanconi-associated nuclease 1-like / : / FAN1, HTH domain / VRR-NUC domain / VRR-NUC domain ...: / : / : / Fanconi-associated nuclease 1, SAP subdomain / Fanconi-associated nuclease 1, TPR domain / Fanconi-associated nuclease 1-like / : / FAN1, HTH domain / VRR-NUC domain / VRR-NUC domain / VRR_NUC / Rad18-like CCHC zinc finger / tRNA endonuclease-like domain superfamily / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile.
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Fanconi-associated nuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPavletich, N.P. / Wang, R.
CitationJournal: Science / Year: 2014
Title: DNA repair. Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1.
Authors: Wang, R. / Persky, N.S. / Yoo, B. / Ouerfelli, O. / Smogorzewska, A. / Elledge, S.J. / Pavletich, N.P.
History
DepositionOct 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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: Fanconi-associated nuclease 1
B: Fanconi-associated nuclease 1
S: DNA (5'-D(P*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')
U: DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*CP*TP*TP*TP*TP*TP*TP*TP*T)-3')
V: DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
W: DNA (5'-D(P*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')
X: DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
Z: DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*CP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Y: DNA (5'-D(*TP*TP*TP*TP*TP*TP*GP*AP*GP*GP*CP*GP*TP*G)-3')
T: DNA (5'-D(*TP*TP*TP*TP*TP*TP*GP*AP*GP*GP*CP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,21012
Polymers180,93610
Non-polymers2752
Water0
1
A: Fanconi-associated nuclease 1
S: DNA (5'-D(P*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')
X: DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
Z: DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*CP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Y: DNA (5'-D(*TP*TP*TP*TP*TP*TP*GP*AP*GP*GP*CP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6056
Polymers90,4685
Non-polymers1371
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-53 kcal/mol
Surface area33650 Å2
MethodPISA
2
B: Fanconi-associated nuclease 1
U: DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*CP*TP*TP*TP*TP*TP*TP*TP*T)-3')
V: DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
W: DNA (5'-D(P*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')
T: DNA (5'-D(*TP*TP*TP*TP*TP*TP*GP*AP*GP*GP*CP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6056
Polymers90,4685
Non-polymers1371
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-61 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.865, 211.574, 69.273
Angle α, β, γ (deg.)90.00, 99.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110A
210B
111A
211B
112A
212B
113A
213B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A370 - 426
2112B370 - 426
1122A538 - 554
2122B538 - 554
1132A555 - 571
2132B555 - 571
1142A427 - 459
2142B427 - 459
1152A533 - 537
2152B533 - 537
1162A460 - 532
2162B460 - 532
1172A593 - 773
2172B593 - 773
1182A774 - 787
2182B774 - 787
1192A791 - 799
2192B791 - 799
11102A810 - 834
21102B810 - 834
11112A956 - 1009
21112B956 - 1009
11122A572 - 592
21122B572 - 592
11132A835 - 955
21132B835 - 955

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
DetailsThe biological unit is a monomer.

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Components

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DNA chain , 4 types, 8 molecules SWUZVXYT

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


Mass: 3294.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 3
#3: DNA chain DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*CP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 5109.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 2
#4: DNA chain DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')


Mass: 3718.427 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*GP*AP*GP*GP*CP*GP*TP*G)-3')


Mass: 4332.810 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein / Non-polymers , 2 types, 4 molecules AB

#1: Protein Fanconi-associated nuclease 1 / FANCD2/FANCI-associated nuclease 1 / Myotubularin-related protein 15


Mass: 74013.102 Da / Num. of mol.: 2 / Fragment: unp residues 370-1017 / Mutation: V487A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAN1, KIAA1018, MTMR15 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y2M0, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters, phosphodiesterase I
#6: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba

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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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2013
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.9→80 Å / Num. all: 41488 / Num. obs: 38210 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-33.60.642188.5
3-3.123.60.459189
3.12-3.2740.306194.1
3.27-3.443.90.23193.4
3.44-3.653.80.17193.1
3.65-3.943.70.123191.9
3.94-4.333.90.094195
4.33-4.963.80.075192.2
4.96-6.2540.071193.3
6.25-803.80.041190.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
DENZOdata reduction
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 19.229 / SU ML: 0.355 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26606 1566 4.1 %RANDOM
Rwork0.22666 ---
obs0.22827 36918 91.6 %-
all-40303 --
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.321 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.14 Å2
2---3.3 Å2-0 Å2
3---2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9884 1720 2 0 11606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01812011
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.82116587
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30851227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55823.151476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.356151820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2721590
X-RAY DIFFRACTIONr_chiral_restr0.0920.21784
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218434
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0513.8324914
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6278.6156132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3374.0567097
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1100TIGHT POSITIONAL0.030.05
1216TIGHT POSITIONAL0.030.05
184TIGHT POSITIONAL0.040.05
1484TIGHT POSITIONAL0.050.05
1251MEDIUM POSITIONAL0.040.5
1228TIGHT THERMAL2.9799
1251MEDIUM THERMAL3.3999
266MEDIUM POSITIONAL0.050.5
268TIGHT THERMAL3.3699
266MEDIUM THERMAL3.4999
349MEDIUM POSITIONAL0.030.5
368TIGHT THERMAL8.699
349MEDIUM THERMAL9.0499
4136MEDIUM POSITIONAL0.040.5
4132TIGHT THERMAL5.8899
4136MEDIUM THERMAL6.3399
521MEDIUM POSITIONAL0.050.5
520TIGHT THERMAL2.6199
521MEDIUM THERMAL3.299
6233MEDIUM POSITIONAL0.020.5
6256TIGHT THERMAL5.3499
6233MEDIUM THERMAL6.2999
7788MEDIUM POSITIONAL0.040.5
7724TIGHT THERMAL6.9799
7788MEDIUM THERMAL7.4799
852MEDIUM POSITIONAL0.040.5
856TIGHT THERMAL4.4899
852MEDIUM THERMAL5.8499
924MEDIUM POSITIONAL0.030.5
924TIGHT THERMAL11.1699
924MEDIUM THERMAL10.5799
1095MEDIUM POSITIONAL0.030.5
10100TIGHT THERMAL3.0899
1095MEDIUM THERMAL3.6999
11210MEDIUM POSITIONAL0.050.5
11216TIGHT THERMAL2.9199
11210MEDIUM THERMAL3.6599
1286MEDIUM POSITIONAL0.050.5
1284TIGHT THERMAL4.999
1286MEDIUM THERMAL5.1599
13473MEDIUM POSITIONAL0.060.5
13484TIGHT THERMAL2.7899
13473MEDIUM THERMAL3.699
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 84 -
Rwork0.356 1956 -
obs--66.64 %

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