[English] 日本語
Yorodumi
- PDB-4ri8: FAN1 Nuclease bound to 5' phosphorylated p(dG)/3'(dT-dT-dT-dT) do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ri8
TitleFAN1 Nuclease bound to 5' phosphorylated p(dG)/3'(dT-dT-dT-dT) double flap DNA
Components
  • DNA (5'-D(*AP*AP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*CP*A)-3')
  • DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*TP*T)-3')
  • DNA (5'-D(P*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 / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / ubiquitin-modified protein reader activity / 5'-3' exonuclease activity / intercellular bridge / interstrand cross-link repair / nucleotide-excision repair ...flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / phosphodiesterase I activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / ubiquitin-modified protein reader activity / 5'-3' exonuclease 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 / 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 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.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_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
E: DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*TP*T)-3')
F: DNA (5'-D(P*GP*AP*GP*GP*CP*GP*TP*G)-3')
G: DNA (5'-D(*AP*AP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*CP*A)-3')
H: DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*TP*T)-3')
I: DNA (5'-D(P*GP*AP*GP*GP*CP*GP*TP*G)-3')
J: DNA (5'-D(*AP*AP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,01910
Polymers172,9388
Non-polymers802
Water00
1
A: Fanconi-associated nuclease 1
E: DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*TP*T)-3')
F: DNA (5'-D(P*GP*AP*GP*GP*CP*GP*TP*G)-3')
G: DNA (5'-D(*AP*AP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5095
Polymers86,4694
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-60 kcal/mol
Surface area33610 Å2
MethodPISA
2
B: Fanconi-associated nuclease 1
H: DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*TP*T)-3')
I: DNA (5'-D(P*GP*AP*GP*GP*CP*GP*TP*G)-3')
J: DNA (5'-D(*AP*AP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5095
Polymers86,4694
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-61 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.260, 210.880, 83.220
Angle α, β, γ (deg.)90.00, 107.61, 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
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 - 14
21131H1 - 14
11141G10 - 19
21141J10 - 19
11151F0 - 7
21151I0 - 7
11161G1 - 9
21161J1 - 9

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: 73926.023 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
#2: DNA chain DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*TP*T)-3')


Mass: 4316.811 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*GP*AP*GP*GP*CP*GP*TP*G)-3')


Mass: 2507.653 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(*AP*AP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*CP*A)-3')


Mass: 5718.727 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, NaCl, pH 7.0, hanging drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP

-
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. obs: 42278 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-37.20.833194.7
3-3.126.90.594192.2
3.12-3.277.60.332196.1
3.27-3.447.50.239196
3.44-3.657.40.188193.9
3.65-3.947.20.14192
3.94-4.337.60.098195.4
4.33-4.967.40.082192.7
4.96-6.257.60.08194.3
6.25-807.50.046190.2

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
DENZOdata reduction
SHARPphasing
RefinementResolution: 2.9→70 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 44.259 / SU ML: 0.361 / Cross valid method: THROUGHOUT / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25476 1647 4.1 %RANDOM
Rwork0.22053 ---
obs0.22193 38976 90.08 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å2-2.19 Å2
2---4.54 Å20 Å2
3---3.74 Å2
Refinement stepCycle: LAST / Resolution: 2.9→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9884 1672 2 0 11558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01811970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.82216529
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78651227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76923.151476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.793151820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9131590
X-RAY DIFFRACTIONr_chiral_restr0.0880.21778
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218418
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_it1.2881.5384916
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2523.4576132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3591.4987054
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 POSITIONAL0.060.05
1A286TIGHT POSITIONAL0.060.05
1A201TIGHT POSITIONAL0.040.05
1A171TIGHT POSITIONAL0.040.05
1A178TIGHT POSITIONAL0.050.05
1A479TIGHT THERMAL2.399
2A120TIGHT THERMAL1.5299
3A268TIGHT THERMAL2.5799
4A41TIGHT THERMAL2.5299
5A489TIGHT THERMAL3.3499
6A1512TIGHT THERMAL3.1299
7A108TIGHT THERMAL3.0599
8A48TIGHT THERMAL4.5199
9A195TIGHT THERMAL5.3699
10A426TIGHT THERMAL2.8199
11A170TIGHT THERMAL1.4799
12A957TIGHT THERMAL3.2199
13E286TIGHT THERMAL4.8399
14G201TIGHT THERMAL2.2999
15F171TIGHT THERMAL11.2799
16G178TIGHT THERMAL6.8199
LS refinement shellResolution: 2.902→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 119 -
Rwork0.361 2709 -
obs--84.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.36621.9689-4.36954.3662-4.07045.50060.1928-0.3045-0.0136-0.3761-0.6667-0.7498-0.09011.0180.47381.1105-0.0452-0.13430.7447-0.08171.179762.245-3.95191.477
27.13651.0743-1.04715.3372-2.1513.12450.3460.47890.504-0.2842-0.401-0.61330.19740.71640.0551.28150.0346-0.12950.6951-0.13230.852445.019-86.44233.65
33.4606-2.71840.273916.2168-3.38694.1681-0.05530.15580.2168-0.16020.146-0.2817-0.34620.3025-0.09081.0999-0.0468-0.14720.60560.18850.764563.964-9.54561.78
43.6008-3.47830.668514.6807-3.46013.0950.10670.2708-0.2391-0.7338-0.23490.240.21380.02820.12810.88470.2697-0.08710.58920.13050.777367.384-79.6952.403
511.33764.01030.29825.1202-0.01987.04550.0467-0.8160.61940.0491-0.56370.6616-0.3353-0.05710.5170.49240.0748-0.0120.4289-0.04220.496354.131-35.4571.745
60.9093-0.98071.05111.2374-1.37161.57030.32270.237-0.0021-0.06240.00670.3792-0.2156-0.0466-0.32941.75320.2561-0.32781.38130.21021.826141.533-8.73450.165
73.7505-1.99592.22418.32210.98657.6095-0.32890.89120.7543-1.4058-0.0850.2749-0.47330.2720.41390.9482-0.0804-0.25710.59440.03750.637854.633-28.70755.223
82.87740.82320.86726.28072.44194.9685-0.1949-0.48290.39580.4113-0.42550.693-0.3087-0.80470.62040.14980.08760.16230.6036-0.26320.765146.038-16.54896.477
96.26820.3047-0.98328.06830.26993.86410.0621-0.09870.88030.45760.0182-1.0174-0.61550.409-0.08040.2939-0.0133-0.0890.6707-0.19820.792579.601-12.01198.283
104.2123-0.77611.12383.53730.57694.1633-0.2074-0.2980.07080.64110.0731-0.26690.3690.2630.13440.29070.08440.11520.331-0.02070.292270.787-35.21595.705
1110.6946-1.283-2.75224.0522-1.23188.1163-0.2060.4772-0.1318-0.1606-0.06940.43360.4977-0.49610.27550.64810.0624-0.11510.3804-0.03790.483649.172-56.70756.871
123.26480.02851.3496.387-0.85751.1420.0116-0.5418-1.14070.82580.0321-0.09570.3950.0004-0.04371.3750.19530.03111.02570.26291.024462.684-84.15276.699
135.918-0.33842.057110.3764-2.19044.6378-0.3911-0.89010.18230.45070.1983-0.85370.3350.61030.19270.76240.1521-0.07930.6713-0.06550.404563.534-62.21965.882
144.27510.2281.10954.47221.64022.7460.1114-0.2253-0.35590.04270.03640.4580.7312-0.5731-0.14770.7878-0.20940.01530.54420.16930.465128.916-78.70144.787
157.25640.6955-2.14555.4932-1.5974.03040.06740.6014-0.8112-0.5784-0.1515-0.491.0220.52880.08411.13840.04550.04510.947-0.1080.488347.92-74.72417.348
162.3084-0.68160.29223.3196-0.85584.6526-0.08810.29510.4808-0.0331-0.0545-0.25140.23060.04680.14270.422-0.0393-0.04840.38350.10660.458240.055-54.32329.531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F0 - 7
2X-RAY DIFFRACTION1G1 - 9
3X-RAY DIFFRACTION2I0 - 7
4X-RAY DIFFRACTION2J1 - 9
5X-RAY DIFFRACTION3E1 - 14
6X-RAY DIFFRACTION3G10 - 19
7X-RAY DIFFRACTION4H1 - 14
8X-RAY DIFFRACTION4J10 - 19
9X-RAY DIFFRACTION5A370 - 410
10X-RAY DIFFRACTION5A540 - 582
11X-RAY DIFFRACTION6A457 - 532
12X-RAY DIFFRACTION7A411 - 456
13X-RAY DIFFRACTION7A533 - 539
14X-RAY DIFFRACTION8A592 - 773
15X-RAY DIFFRACTION9A774 - 835
16X-RAY DIFFRACTION9A957 - 1009
17X-RAY DIFFRACTION10A836 - 956
18X-RAY DIFFRACTION10A583 - 591
19X-RAY DIFFRACTION11B370 - 410
20X-RAY DIFFRACTION11B540 - 582
21X-RAY DIFFRACTION12B457 - 532
22X-RAY DIFFRACTION13B411 - 456
23X-RAY DIFFRACTION13B533 - 539
24X-RAY DIFFRACTION14B592 - 773
25X-RAY DIFFRACTION15B774 - 835
26X-RAY DIFFRACTION15B957 - 1009
27X-RAY DIFFRACTION16B836 - 956
28X-RAY DIFFRACTION16B583 - 591

+
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