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- PDB-2io4: Crystal structure of PCNA12 dimer from Sulfolobus solfataricus. -

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Basic information

Entry
Database: PDB / ID: 2io4
TitleCrystal structure of PCNA12 dimer from Sulfolobus solfataricus.
Components
  • DNA polymerase sliding clamp B
  • DNA polymerase sliding clamp C
KeywordsDNA BINDING PROTEIN / PCNA12 heterodimer / protein-protein interaction / PCNA123 heterotrimer
Function / homology
Function and homology information


DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNA binding
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / Alpha Beta
Similarity search - Domain/homology
DNA polymerase sliding clamp 1 / DNA polymerase sliding clamp 2
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsHlinkova, V. / Ling, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening.
Authors: Hlinkova, V. / Xing, G. / Bauer, J. / Shin, Y.J. / Dionne, I. / Rajashankar, K.R. / Bell, S.D. / Ling, H.
History
DepositionOct 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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
Revision 1.3Feb 21, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase sliding clamp B
B: DNA polymerase sliding clamp C
C: DNA polymerase sliding clamp B
D: DNA polymerase sliding clamp C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,85910
Polymers110,2284
Non-polymers6316
Water3,081171
1
A: DNA polymerase sliding clamp B
B: DNA polymerase sliding clamp C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7458
Polymers55,1142
Non-polymers6316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-42 kcal/mol
Surface area23190 Å2
MethodPISA, PQS
2
C: DNA polymerase sliding clamp B
D: DNA polymerase sliding clamp C


Theoretical massNumber of molelcules
Total (without water)55,1142
Polymers55,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-12 kcal/mol
Surface area23220 Å2
MethodPISA, PQS
3
A: DNA polymerase sliding clamp B
B: DNA polymerase sliding clamp C
C: DNA polymerase sliding clamp B
D: DNA polymerase sliding clamp C
hetero molecules

A: DNA polymerase sliding clamp B
B: DNA polymerase sliding clamp C
C: DNA polymerase sliding clamp B
D: DNA polymerase sliding clamp C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,71820
Polymers220,4568
Non-polymers1,26212
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area15820 Å2
ΔGint-142 kcal/mol
Surface area85250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.991, 112.727, 101.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31C
41A
51C
61A
71C
81A
12C
22A
32C
42A
52C
62A
13C
23A
33C
43A
53C
63A
14B
24D
34B
44D
54B
64D
74B
84D
94B
104D
15B
25D
35B
45D
55B
65D
16B
26D
36B
46D
56B
66D
76B
86D
17B
27D
37B
47D
57B
67D
77B
87D
18B
28D
19B
29D
110B
210D
111B
211D
112C
212A
312C
412A
512C
612A
712C
812A
113C
213A
114C
214A
115C
215A
116C
216A

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSASNASN5CC3 - 83 - 8
211LYSLYSASNASN5AA3 - 83 - 8
321THRTHRTHRTHR5CC88 - 9288 - 92
421THRTHRTHRTHR5AA88 - 9288 - 92
531LYSLYSARGARG5CC99 - 10399 - 103
631LYSLYSARGARG5AA99 - 10399 - 103
741GLYGLYILEILE5CC108 - 115108 - 115
841GLYGLYILEILE5AA108 - 115108 - 115
112SERSERLEULEU5CC25 - 2825 - 28
212SERSERLEULEU5AA25 - 2825 - 28
322GLYGLYLEULEU5CC34 - 4034 - 40
422GLYGLYLEULEU5AA34 - 4034 - 40
532LEULEUPROPRO5CC46 - 5346 - 53
632LEULEUPROPRO5AA46 - 5346 - 53
113THRTHRILEILE5CC219 - 245219 - 245
213THRTHRILEILE5AA219 - 245219 - 245
323PHEPHETHRTHR5CC136 - 137136 - 137
423PHEPHETHRTHR5AA136 - 137136 - 137
533GLUGLUSERSER5CC189 - 191189 - 191
633GLUGLUSERSER5AA189 - 191189 - 191
114LYSLYSILEILE5BB3 - 73 - 7
214LYSLYSILEILE5DD3 - 73 - 7
324GLUGLUGLUGLU5BB58 - 6158 - 61
424GLUGLUGLUGLU5DD58 - 6158 - 61
534ILEILESERSER5BB90 - 9390 - 93
634ILEILESERSER5DD90 - 9390 - 93
744LEULEUTHRTHR5BB98 - 10198 - 101
844LEULEUTHRTHR5DD98 - 10198 - 101
954THRTHRPROPRO5BB107 - 113107 - 113
1054THRTHRPROPRO5DD107 - 113107 - 113
115ILEILELYSLYS5BB68 - 7268 - 72
215ILEILELYSLYS5DD68 - 7268 - 72
325ALAALAILEILE5BB26 - 4026 - 40
425ALAALAILEILE5DD26 - 4026 - 40
535LEULEUSERSER5BB48 - 5448 - 54
635LEULEUSERSER5DD48 - 5448 - 54
116GLYGLYPROPRO5BB235 - 243235 - 243
216GLYGLYPROPRO5DD235 - 243235 - 243
326LEULEULEULEU5BB225 - 231225 - 231
426LEULEULEULEU5DD225 - 231225 - 231
536SERSERPHEPHE5BB214 - 219214 - 219
636SERSERPHEPHE5DD214 - 219214 - 219
746PHEPHELEULEU5BB131 - 135131 - 135
846PHEPHELEULEU5DD131 - 135131 - 135
117VALVALGLYGLY5BB193 - 198193 - 198
217VALVALGLYGLY5DD193 - 198193 - 198
327VALVALSERSER5BB153 - 158153 - 158
427VALVALSERSER5DD153 - 158153 - 158
537LEULEUGLUGLU5BB163 - 166163 - 166
637LEULEUGLUGLU5DD163 - 166163 - 166
747THRTHRLEULEU5BB173 - 178173 - 178
847THRTHRLEULEU5DD173 - 178173 - 178
118LEULEUASPASP5BB136 - 149136 - 149
218LEULEUASPASP5DD136 - 149136 - 149
119GLUGLUARGARG5BB200 - 210200 - 210
219GLUGLUARGARG5DD200 - 210200 - 210
1110ALAALASERSER5BB9 - 249 - 24
2110ALAALASERSER5DD9 - 249 - 24
1111LEULEUARGARG5BB73 - 8273 - 82
2111LEULEUARGARG5DD73 - 8273 - 82
1112TYRTYRLEULEU5CC177 - 181177 - 181
2112TYRTYRLEULEU5AA177 - 181177 - 181
3212ILEILEILEILE5CC166 - 168166 - 168
4212ILEILEILEILE5AA166 - 168166 - 168
5312ARGARGTHRTHR5CC158 - 161158 - 161
6312ARGARGTHRTHR5AA158 - 161158 - 161
7412SERSERTYRTYR5CC195 - 200195 - 200
8412SERSERTYRTYR5AA195 - 200195 - 200
1113ASPASPGLYGLY6CC139 - 154139 - 154
2113ASPASPGLYGLY6AA139 - 154139 - 154
1114SERSERARGARG6CC201 - 213201 - 213
2114SERSERARGARG6AA201 - 213201 - 213
1115ALAALAVALVAL6CC9 - 229 - 22
2115ALAALAVALVAL6AA9 - 229 - 22
1116SERSERLYSLYS6CC73 - 8673 - 86
2116SERSERLYSLYS6AA73 - 8673 - 86

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

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Components

#1: Protein DNA polymerase sliding clamp B / Proliferating cell nuclear antigen homolog B / PCNA B


Mass: 27521.695 Da / Num. of mol.: 2 / Mutation: F2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: pcnB, pcnA-2 / Plasmid: pET33b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 (DE3) / References: UniProt: P57766
#2: Protein DNA polymerase sliding clamp C / Proliferating cell nuclear antigen homolog C / PCNA C


Mass: 27592.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: pcnC, pcnA-2 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 (DE3) / References: UniProt: Q97Z84
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% MPD, 20 mM CaCl2, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 8-BM10.979
SYNCHROTRONAPS 8-BM20.97912, 0.97928, 0.979313
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 26, 2005
ADSC QUANTUM 3152CCDOct 26, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979121
30.979281
40.9793131
ReflectionResolution: 2.6→30 Å / Num. all: 37787 / Num. obs: 37787 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 74.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 27.5
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 1.92 / Num. unique all: 2491 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.928 / SU B: 33.946 / SU ML: 0.34 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.782 / ESU R Free: 0.318
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.26036 1151 3 %RANDOM
Rwork0.23318 ---
all0.234 37787 --
obs0.234 37787 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.387 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2--1.28 Å20 Å2
3----0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.318 Å0.782 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7722 0 41 171 7934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227885
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.99110641
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2135982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7425.185324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.445151481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4971532
X-RAY DIFFRACTIONr_chiral_restr0.1750.21249
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025710
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.23402
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25305
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2334
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1740.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5131.55046
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86827995
X-RAY DIFFRACTIONr_scbond_it0.99533133
X-RAY DIFFRACTIONr_scangle_it1.7354.52646
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
1C96medium positional0.320.5
2C76medium positional0.110.5
3C128medium positional0.130.5
4B96medium positional0.220.5
5B108medium positional0.130.5
6B108medium positional0.090.5
7B88medium positional0.10.5
8B56medium positional0.110.5
9B44medium positional0.110.5
10B64medium positional0.140.5
11B40medium positional0.080.5
12C72medium positional0.160.5
1C97loose positional0.735
2C75loose positional0.465
3C122loose positional0.345
4B92loose positional0.745
5B100loose positional0.485
6B123loose positional0.45
7B85loose positional0.235
8B53loose positional0.535
9B50loose positional0.35
10B61loose positional0.235
11B44loose positional0.535
12C69loose positional0.935
13C112loose positional0.365
14C100loose positional0.55
15C113loose positional0.245
16C103loose positional0.665
1C96medium thermal1.12
2C76medium thermal0.592
3C128medium thermal2.532
4B96medium thermal0.762
5B108medium thermal1.092
6B108medium thermal3.22
7B88medium thermal3.132
8B56medium thermal22
9B44medium thermal1.932
10B64medium thermal0.572
11B40medium thermal0.452
12C72medium thermal3.192
1C97loose thermal1.4410
2C75loose thermal1.0510
3C122loose thermal2.8910
4B92loose thermal1.110
5B100loose thermal1.2210
6B123loose thermal4.1910
7B85loose thermal3.4810
8B53loose thermal2.2910
9B50loose thermal2.4310
10B61loose thermal0.6610
11B44loose thermal0.9710
12C69loose thermal4.0710
13C112loose thermal4.8310
14C100loose thermal4.6310
15C113loose thermal1.3710
16C103loose thermal2.1910
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 73 -
Rwork0.397 2657 -
obs-2491 99.8 %
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)
17.5889-1.5487-3.58551.60980.38076.20360.56450.3080.5847-0.2343-0.2249-0.2265-0.2944-0.7074-0.33960.05710.0052-0.0025-0.0733-0.0073-0.087157.8019-25.142320.8962
25.7363-0.8504-2.14751.25580.66633.18370.40690.25330.2835-0.1038-0.31320.0672-0.0581-1.008-0.0937-0.0243-0.1019-0.03850.4688-0.0944-0.166638.1132-24.349228.455
36.2617-3.5768-1.17625.8564-0.17143.53310.3751.04960.0456-0.4252-0.47330.4513-0.1025-1.77610.09830.0084-0.0341-0.05040.788-0.1429-0.108836.1775-25.510124.8107
42.82790.62010.20732.08621.65954.9366-0.18570.9920.1568-0.24420.08990.226-0.1306-0.56180.0958-0.2374-0.12-0.010.5907-0.0159-0.129322.1548-14.0263-47.8247
52.92650.71650.42013.83421.17573.0141-0.03230.57040.29530.37410.19410.46910.2076-0.431-0.1618-0.07420.07080.0540.09240.1066-0.076334.6547-2.5801-29.8079
63.45161.0121.69158.96021.95123.4682-0.2847-0.30590.59031.2280.13320.2003-0.139-0.23120.15150.320.096-0.04-0.3058-0.05840.020724.5834-4.40312.3308
72.485-0.66990.3345.89771.25932.0693-0.0363-0.1668-0.01680.81990.1865-0.36040.01840.045-0.15010.19380.0314-0.1115-0.28150.0180.064231.4229-18.3239-2.4427
82.24110.4169-1.7251.3002-0.72915.6282-0.30210.4739-1.004-0.03270.2605-0.51450.63580.31750.0416-0.0450.06970.0466-0.1374-0.35630.447847.0859-33.6309-30.3023
92.61130.01550.59052.5937-0.84474.6309-0.25561.0901-0.6214-0.25170.4867-0.36460.36030.2757-0.2311-0.2233-0.12580.10680.5232-0.4449-0.03356.2141-16.709-48.1731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1041 - 104
2X-RAY DIFFRACTION2AA105 - 186105 - 186
3X-RAY DIFFRACTION3AA187 - 249187 - 249
4X-RAY DIFFRACTION4BB1 - 1131 - 113
5X-RAY DIFFRACTION5BB114 - 246114 - 246
6X-RAY DIFFRACTION6CC1 - 831 - 83
7X-RAY DIFFRACTION7CC84 - 24984 - 249
8X-RAY DIFFRACTION8DD1 - 1211 - 121
9X-RAY DIFFRACTION9DD122 - 245122 - 245

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  • 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

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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

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