[English] 日本語
Yorodumi
- PDB-4ric: FAN1 Nuclease bound to 5' hydroxyl (dT-dT) single flap DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ric
TitleFAN1 Nuclease bound to 5' hydroxyl (dT-dT) single flap DNA
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
  • DNA (5'-D(*TP*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*GP*AP*GP*GP*CP*GP*TP*G)-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: 2.8 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 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Feb 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fanconi-associated nuclease 1
B: Fanconi-associated nuclease 1
X: DNA (5'-D(*TP*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')
Y: DNA (5'-D(*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
U: DNA (5'-D(*TP*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')
V: DNA (5'-D(*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
W: 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)172,78910
Polymers172,7088
Non-polymers802
Water0
1
A: Fanconi-associated nuclease 1
X: DNA (5'-D(*TP*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')
Y: DNA (5'-D(*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*CP*T)-3')
W: 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)86,3945
Polymers86,3544
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-30 kcal/mol
Surface area35770 Å2
MethodPISA
2
B: Fanconi-associated nuclease 1
U: DNA (5'-D(*TP*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')
V: DNA (5'-D(*GP*CP*TP*GP*AP*GP*GP*AP*GP*TP*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)86,3945
Polymers86,3544
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-32 kcal/mol
Surface area36780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.697, 110.989, 105.427
Angle α, β, γ (deg.)90.00, 103.75, 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
113W
213U
114X
214V
115W
215U
116X
216V

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A370 - 426
2112B370 - 426
1122A538 - 552
2122B538 - 552
1132A427 - 459
2132B427 - 459
1142A533 - 537
2142B533 - 537
1152A460 - 532
2152B460 - 532
1162A593 - 773
2162B593 - 773
1172A774 - 787
2172B774 - 787
1182A791 - 799
2182B791 - 799
1192A810 - 834
2192B810 - 834
11102A956 - 1009
21102B956 - 1009
11112A572 - 592
21112B572 - 592
11122A835 - 955
21122B835 - 955
11131W16 - 19
21131U16 - 19
11141X4 - 11
21141V4 - 11
11151W-1 - 10
21151U-1 - 10
11161X14 - 19
21161V14 - 19

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

-
Components

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


Mass: 71983.922 Da / Num. of mol.: 2 / Fragment: unp residues 370-1009
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
#2: DNA chain DNA (5'-D(*TP*TP*AP*GP*CP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*C)-3')


Mass: 6319.087 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*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
#4: 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
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, NaCl , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
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: 2.8→80 Å / Num. all: 50954 / Num. obs: 50547 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.059 / Χ2: 0.768 / Net I/σ(I): 7.7

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
DENZOdata reduction
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.727 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.546 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 2080 4.1 %RANDOM
Rwork0.2225 ---
obs0.2239 48907 94.36 %-
all-51830 --
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 184.25 Å2 / Biso mean: 90.861 Å2 / Biso min: 47.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å2-0.66 Å2
2--0.36 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9977 1592 2 0 11571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01812136
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.8216746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63251240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11223.181481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.709151832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2391591
X-RAY DIFFRACTIONr_chiral_restr0.0930.21801
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218525
X-RAY DIFFRACTIONr_mcbond_it2.1784.4194973
X-RAY DIFFRACTIONr_mcangle_it3.8099.9356200
X-RAY DIFFRACTIONr_scbond_it2.3544.627163
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A216TIGHT POSITIONAL0.040.05
1A84TIGHT POSITIONAL0.040.05
1A484TIGHT POSITIONAL0.040.05
1A77TIGHT POSITIONAL0.040.05
1A169TIGHT POSITIONAL0.040.05
1A221TIGHT POSITIONAL0.030.05
1A127TIGHT POSITIONAL0.030.05
1A251MEDIUM POSITIONAL0.050.5
1A228TIGHT THERMAL16.799
1A251MEDIUM THERMAL16.8499
2A60MEDIUM POSITIONAL0.040.5
2A60TIGHT THERMAL14.7299
2A60MEDIUM THERMAL15.4199
3A136MEDIUM POSITIONAL0.030.5
3A132TIGHT THERMAL19.7199
3A136MEDIUM THERMAL19.0799
4A21MEDIUM POSITIONAL0.040.5
4A20TIGHT THERMAL17.5299
4A21MEDIUM THERMAL15.3699
5A233MEDIUM POSITIONAL0.030.5
5A256TIGHT THERMAL15.2299
5A233MEDIUM THERMAL14.5499
6A788MEDIUM POSITIONAL0.040.5
6A724TIGHT THERMAL6.4599
6A788MEDIUM THERMAL6.8799
7A52MEDIUM POSITIONAL0.030.5
7A56TIGHT THERMAL9.0599
7A52MEDIUM THERMAL8.1699
8A24MEDIUM POSITIONAL0.020.5
8A24TIGHT THERMAL12.2799
8A24MEDIUM THERMAL14.1199
9A95MEDIUM POSITIONAL0.040.5
9A100TIGHT THERMAL9.2599
9A95MEDIUM THERMAL8.999
10A210MEDIUM POSITIONAL0.050.5
10A216TIGHT THERMAL8.899
10A210MEDIUM THERMAL8.2399
11A86MEDIUM POSITIONAL0.050.5
11A84TIGHT THERMAL10.4999
11A86MEDIUM THERMAL10.3499
12A473MEDIUM POSITIONAL0.050.5
12A484TIGHT THERMAL3.299
12A473MEDIUM THERMAL3.8899
13W77TIGHT THERMAL16.8499
14X169TIGHT THERMAL14.499
15W221TIGHT THERMAL11.499
16X127TIGHT THERMAL12.6999
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 113 -
Rwork0.396 2904 -
all-3017 -
obs--76.07 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more