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- PDB-4ria: FAN1 Nuclease bound to 5' phosphorylated nicked DNA -

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Basic information

Entry
Database: PDB / ID: 4ria
TitleFAN1 Nuclease bound to 5' phosphorylated nicked DNA
Components
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*G*AP*GP*GP*CP*GP*TP*G)-3')
  • DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')
  • DNA (5'-D(P*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')
  • DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*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: 3 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.ptnr2_auth_asym_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_label_asym_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
F: DNA (5'-D(P*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')
K: DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')
G: DNA (5'-D(*TP*TP*TP*TP*TP*TP*G*AP*GP*GP*CP*GP*TP*G)-3')
L: DNA (5'-D(P*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')
I: DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')
J: DNA (5'-D(*TP*TP*TP*TP*TP*TP*G*AP*GP*GP*CP*GP*TP*G)-3')
E: DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
H: DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,56112
Polymers175,28610
Non-polymers2752
Water0
1
A: Fanconi-associated nuclease 1
F: DNA (5'-D(P*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')
K: DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')
G: DNA (5'-D(*TP*TP*TP*TP*TP*TP*G*AP*GP*GP*CP*GP*TP*G)-3')
E: DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7806
Polymers87,6435
Non-polymers1371
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-49 kcal/mol
Surface area33700 Å2
MethodPISA
2
B: Fanconi-associated nuclease 1
L: DNA (5'-D(P*AP*GP*CP*CP*AP*CP*GP*CP*CP*T)-3')
I: DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')
J: DNA (5'-D(*TP*TP*TP*TP*TP*TP*G*AP*GP*GP*CP*GP*TP*G)-3')
H: DNA (5'-D(P*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7806
Polymers87,6435
Non-polymers1371
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-47 kcal/mol
Surface area33990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.813, 100.317, 212.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
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
113E
213H
114G
214J
115F
215I
116G
216J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A370 - 426
2111B370 - 426
1121A538 - 552
2121B538 - 552
1131A427 - 459
2131B427 - 459
1141A533 - 537
2141B533 - 537
1151A460 - 532
2151B460 - 532
1161A593 - 773
2161B593 - 773
1171A774 - 787
2171B774 - 787
1181A791 - 799
2181B791 - 799
1191A810 - 834
2191B810 - 834
11101A956 - 1009
21101B956 - 1009
11111A572 - 592
21111B572 - 592
11121A835 - 955
21121B835 - 955
11131E1 - 9
21131H1 - 9
11141G11 - 19
21141J11 - 19
11151F1 - 10
21151I1 - 10
11161G1 - 10
21161J1 - 10

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16

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Components

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DNA chain , 4 types, 8 molecules FLKIGJEH

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


Mass: 2989.970 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')


Mass: 2675.775 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*G*AP*GP*GP*CP*GP*TP*G)-3')


Mass: 4332.810 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: 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

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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: 73926.023 Da / Num. of mol.: 2 / Fragment: unp residues 370-1017
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: 2.86 Å3/Da / Density % sol: 57.02 %
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: 3→50 Å / Num. all: 38468 / Num. obs: 37660 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3-3.1130.709190.6
3.11-3.233.90.568194.3
3.23-3.384.50.446197.3
3.38-3.564.70.341198.6
3.56-3.784.70.272199
3.78-4.075.30.205199.6
4.07-4.486.10.1691100
4.48-5.135.60.138199.7
5.13-6.466.20.15199.9
6.46-505.50.064199.5

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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: 3→40 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.882 / SU B: 19.828 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26733 1460 4.1 %RANDOM
Rwork0.22431 ---
obs0.22605 34554 93.63 %-
all-36916 --
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.505 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0 Å2
2--3.73 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9854 1554 2 0 11410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01811806
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.8316285
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5451223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57723.151476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.89151810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4431590
X-RAY DIFFRACTIONr_chiral_restr0.0860.21756
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218338
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_it2.0563.3064898
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6567.4276112
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1223.3146907
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 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A426TIGHT POSITIONAL0.040.05
1A170TIGHT POSITIONAL0.050.05
1A957TIGHT POSITIONAL0.050.05
1A180TIGHT POSITIONAL0.030.05
1A189TIGHT POSITIONAL0.030.05
1A202TIGHT POSITIONAL0.030.05
1A206TIGHT POSITIONAL0.040.05
1A479TIGHT THERMAL4.0599
2A120TIGHT THERMAL2.299
3A268TIGHT THERMAL2.8399
4A41TIGHT THERMAL2.1199
5A489TIGHT THERMAL5.1299
6A1512TIGHT THERMAL5.8699
7A108TIGHT THERMAL5.5199
8A33TIGHT THERMAL4.7699
9A195TIGHT THERMAL3.2999
10A426TIGHT THERMAL4.9299
11A170TIGHT THERMAL4.6499
12A957TIGHT THERMAL3.499
13G180TIGHT THERMAL2.2999
14I189TIGHT THERMAL1.8999
15F202TIGHT THERMAL3.6599
16I206TIGHT THERMAL3.499
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 85 -
Rwork0.322 2064 -
obs--77.58 %

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