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- PDB-7nt6: CryoEM structure of the Nipah virus nucleocapsid spiral clam-shap... -

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Basic information

Entry
Database: PDB / ID: 7nt6
TitleCryoEM structure of the Nipah virus nucleocapsid spiral clam-shaped assembly
Components
  • Nucleoprotein
  • RNA (42-MER)
  • RNA (48-MER)
KeywordsVIRAL PROTEIN / Protein-RNA complex / Nucleocapsid
Function / homology
Function and homology information


negative stranded viral RNA transcription / negative stranded viral RNA replication / helical viral capsid / viral nucleocapsid / host cell cytoplasm / molecular adaptor activity / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein
Similarity search - Domain/homology
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesNipah virus
Escherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKer, D.S. / Jenkins, H.T. / Greive, S.J. / Antson, A.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: PLoS Pathog / Year: 2021
Title: CryoEM structure of the Nipah virus nucleocapsid assembly.
Authors: De-Sheng Ker / Huw T Jenkins / Sandra J Greive / Alfred A Antson /
Abstract: Nipah and its close relative Hendra are highly pathogenic zoonotic viruses, storing their ssRNA genome in a helical nucleocapsid assembly formed by the N protein, a major viral immunogen. Here, we ...Nipah and its close relative Hendra are highly pathogenic zoonotic viruses, storing their ssRNA genome in a helical nucleocapsid assembly formed by the N protein, a major viral immunogen. Here, we report the first cryoEM structure for a Henipavirus RNA-bound nucleocapsid assembly, at 3.5 Å resolution. The helical assembly is stabilised by previously undefined N- and C-terminal segments, contributing to subunit-subunit interactions. RNA is wrapped around the nucleocapsid protein assembly with a periodicity of six nucleotides per protomer, in the "3-bases-in, 3-bases-out" conformation, with protein plasticity enabling non-sequence specific interactions. The structure reveals commonalities in RNA binding pockets and in the conformation of bound RNA, not only with members of the Paramyxoviridae family, but also with the evolutionarily distant Filoviridae Ebola virus. Significant structural differences with other Paramyxoviridae members are also observed, particularly in the position and length of the exposed α-helix, residues 123-139, which may serve as a valuable epitope for surveillance and diagnostics.
History
DepositionMar 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
G: Nucleoprotein
H: Nucleoprotein
I: Nucleoprotein
J: Nucleoprotein
K: Nucleoprotein
L: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
O: Nucleoprotein
X: RNA (48-MER)
Z: RNA (42-MER)


Theoretical massNumber of molelcules
Total (without water)936,60717
Polymers936,60717
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11X
21Z
12A
22B
13A
23C
14A
24D
15A
25E
16A
26F
17A
27G
18A
28H
19A
29I
110A
210J
111A
211K
112A
212L
113A
213M
114A
214N
115A
215O
116B
216C
117B
217D
118B
218E
119B
219F
120B
220G
121B
221H
122B
222I
123B
223J
124B
224K
125B
225L
126B
226M
127B
227N
128B
228O
129C
229D
130C
230E
131C
231F
132C
232G
133C
233H
134C
234I
135C
235J
136C
236K
137C
237L
138C
238M
139C
239N
140C
240O
141D
241E
142D
242F
143D
243G
144D
244H
145D
245I
146D
246J
147D
247K
148D
248L
149D
249M
150D
250N
151D
251O
152E
252F
153E
253G
154E
254H
155E
255I
156E
256J
157E
257K
158E
258L
159E
259M
160E
260N
161E
261O
162F
262G
163F
263H
164F
264I
165F
265J
166F
266K
167F
267L
168F
268M
169F
269N
170F
270O
171G
271H
172G
272I
173G
273J
174G
274K
175G
275L
176G
276M
177G
277N
178G
278O
179H
279I
180H
280J
181H
281K
182H
282L
183H
283M
184H
284N
185H
285O
186I
286J
187I
287K
188I
288L
189I
289M
190I
290N
191I
291O
192J
292K
193J
293L
194J
294M
195J
295N
196J
296O
197K
297L
198K
298M
199K
299N
1100K
2100O
1101L
2101M
1102L
2102N
1103L
2103O
1104M
2104N
1105M
2105O
1106N
2106O

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010X7 - 47
2010Z1 - 41
1020A32 - 367
2020B32 - 367
1030A32 - 367
2030C32 - 367
1040A32 - 367
2040D32 - 367
1050A32 - 367
2050E32 - 367
1060A32 - 367
2060F32 - 367
1070A32 - 367
2070G32 - 367
1080A32 - 367
2080H32 - 367
1090A32 - 367
2090I32 - 367
10100A32 - 367
20100J32 - 367
10110A32 - 367
20110K32 - 367
10120A32 - 367
20120L32 - 367
10130A32 - 367
20130M32 - 367
10140A32 - 367
20140N32 - 367
10150A32 - 366
20150O32 - 366
10160B4 - 368
20160C4 - 368
10170B4 - 368
20170D4 - 368
10180B4 - 368
20180E4 - 368
10190B4 - 368
20190F4 - 368
10200B4 - 369
20200G4 - 369
10210B4 - 368
20210H4 - 368
10220B4 - 368
20220I4 - 368
10230B4 - 368
20230J4 - 368
10240B4 - 368
20240K4 - 368
10250B4 - 368
20250L4 - 368
10260B4 - 369
20260M4 - 369
10270B4 - 368
20270N4 - 368
10280B4 - 366
20280O4 - 366
10290C4 - 371
20290D4 - 371
10300C4 - 370
20300E4 - 370
10310C4 - 370
20310F4 - 370
10320C4 - 371
20320G4 - 371
10330C4 - 370
20330H4 - 370
10340C4 - 370
20340I4 - 370
10350C4 - 370
20350J4 - 370
10360C4 - 370
20360K4 - 370
10370C4 - 370
20370L4 - 385
10380C4 - 368
20380M4 - 368
10390C4 - 370
20390N4 - 370
10400C4 - 366
20400O4 - 366
10410D4 - 370
20410E4 - 370
10420D4 - 370
20420F4 - 370
10430D4 - 371
20430G4 - 371
10440D4 - 370
20440H4 - 370
10450D4 - 370
20450I4 - 370
10460D4 - 370
20460J4 - 370
10470D4 - 370
20470K4 - 370
10480D4 - 370
20480L4 - 385
10490D4 - 368
20490M4 - 368
10500D4 - 370
20500N4 - 370
10510D4 - 366
20510O4 - 366
10520E4 - 393
20520F4 - 393
10530E4 - 372
20530G4 - 372
10540E4 - 394
20540H4 - 394
10550E4 - 393
20550I4 - 393
10560E4 - 394
20560J4 - 394
10570E4 - 393
20570K4 - 393
10580E4 - 393
20580L4 - 393
10590E4 - 368
20590M4 - 368
10600E4 - 372
20600N4 - 372
10610E4 - 366
20610O4 - 366
10620F4 - 372
20620G4 - 372
10630F4 - 394
20630H4 - 394
10640F4 - 397
20640I4 - 397
10650F4 - 396
20650J4 - 396
10660F4 - 393
20660K4 - 393
10670F4 - 393
20670L4 - 393
10680F4 - 368
20680M4 - 368
10690F4 - 372
20690N4 - 372
10700F4 - 366
20700O4 - 366
10710G4 - 372
20710H4 - 376
10720G4 - 372
20720I4 - 372
10730G4 - 372
20730J4 - 372
10740G4 - 372
20740K4 - 372
10750G4 - 373
20750L4 - 388
10760G4 - 369
20760M4 - 369
10770G4 - 373
20770N4 - 373
10780G4 - 367
20780O4 - 367
10790H4 - 394
20790I4 - 394
10800H4 - 394
20800J4 - 394
10810H4 - 393
20810K4 - 393
10820H4 - 393
20820L4 - 393
10830H4 - 368
20830M4 - 368
10840H4 - 376
20840N4 - 372
10850H4 - 366
20850O4 - 366
10860I4 - 396
20860J4 - 396
10870I4 - 393
20870K4 - 393
10880I4 - 393
20880L4 - 393
10890I4 - 368
20890M4 - 368
10900I4 - 372
20900N4 - 372
10910I4 - 366
20910O4 - 366
10920J4 - 392
20920K4 - 392
10930J4 - 382
20930L4 - 392
10940J4 - 368
20940M4 - 368
10950J4 - 372
20950N4 - 372
10960J4 - 366
20960O4 - 366
10970K4 - 382
20970L4 - 392
10980K4 - 368
20980M4 - 368
10990K4 - 372
20990N4 - 372
101000K4 - 366
201000O4 - 366
101010L4 - 368
201010M4 - 368
101020L4 - 387
201020N4 - 372
101030L4 - 366
201030O4 - 366
101040M4 - 368
201040N4 - 368
101050M4 - 366
201050O4 - 366
101060N4 - 366
201060O4 - 366

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106

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Components

#1: Protein
Nucleoprotein / Protein N / Nucleocapsid protein


Mass: 60609.484 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9IK92
#2: RNA chain RNA (48-MER)


Mass: 14650.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: RNA chain RNA (42-MER)


Mass: 12814.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Nipah virus nucleocapsid Protein-RNA complexCOMPLEXall0RECOMBINANT
2NucleoproteinCOMPLEX#11RECOMBINANT
3RNA (48-MER)COMPLEX#21RECOMBINANT
4RNA (42-MER)COMPLEX#31RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Nipah virus121791
23Escherichia coli BL21(DE3) (bacteria)469008
34Escherichia coli BL21(DE3) (bacteria)469008
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli BL21(DE3) (bacteria)469008
23Escherichia coli BL21(DE3) (bacteria)469008
34Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2300 mMsodium chlorideNaCl1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 41 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.13model fitting
11RELION3.1betaclassification
12RELION3.1beta3D reconstruction
19REFMAC5.8.0267model refinement
20PHENIX1.17model refinement
21ERRASER2model refinement
22ISOLDE0.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 217522
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23029 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7NT5
Pdb chain-ID: H / Accession code: 7NT5 / Pdb chain residue range: 4-397 / Source name: PDB / Type: experimental model
RefinementResolution: 4.3→201.22 Å / Cor.coef. Fo:Fc: 0.983 / SU B: 81.568 / SU ML: 0.79 / ESU R: 0.757
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.27534 --
obs0.27534 155589 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 113.558 Å2
Baniso -1Baniso -2Baniso -3
1--3.36 Å22.6 Å20.4 Å2
2--5.19 Å2-7.1 Å2
3----1.82 Å2
Refinement stepCycle: 1 / Total: 24128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.01124281
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.961.53830887
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.13855557
ELECTRON MICROSCOPYr_dihedral_angle_2_deg
ELECTRON MICROSCOPYr_dihedral_angle_3_deg
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1230.2360
ELECTRON MICROSCOPYr_gen_planes_refined0.010.0223038
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it19.20621.25922303
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it28.66331.77827835
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it14.1123.1731978
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined35.2488366
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11X57200.16
12Z57200.16
21A95200.04
22B95200.04
31A95400.04
32C95400.04
41A95160.04
42D95160.04
51A94900.04
52E94900.04
61A94980.05
62F94980.05
71A94700.04
72G94700.04
81A95360.04
82H95360.04
91A95060.04
92I95060.04
101A94820.04
102J94820.04
111A95240.04
112K95240.04
121A95240.04
122L95240.04
131A95260.03
132M95260.03
141A94980.04
142N94980.04
151A94640.04
152O94640.04
161B104680.04
162C104680.04
171B104820.03
172D104820.03
181B104540.04
182E104540.04
191B104280.04
192F104280.04
201B102720.05
202G102720.05
211B104900.04
212H104900.04
221B105080.03
222I105080.03
231B104300.05
232J104300.05
241B105100.04
242K105100.04
251B104940.04
252L104940.04
261B105240.03
262M105240.03
271B104680.04
272N104680.04
281B103580.05
282O103580.05
291C105420.04
292D105420.04
301C104880.05
302E104880.05
311C104760.04
312F104760.04
321C103340.04
322G103340.04
331C105120.05
332H105120.05
341C105200.04
342I105200.04
351C104780.05
352J104780.05
361C105300.04
362K105300.04
371C104940.05
372L104940.05
381C104860.03
382M104860.03
391C105040.05
392N105040.05
401C103600.04
402O103600.04
411D105180.04
412E105180.04
421D104880.04
422F104880.04
431D103180.04
432G103180.04
441D105300.04
442H105300.04
451D105300.04
452I105300.04
461D104880.05
462J104880.05
471D105540.04
472K105540.04
481D105200.04
482L105200.04
491D105060.03
492M105060.03
501D105180.04
502N105180.04
511D103680.05
512O103680.05
521E106960.05
522F106960.05
531E103300.04
532G103300.04
541E106780.04
542H106780.04
551E107520.03
552I107520.03
561E107040.06
562J107040.06
571E107700.04
572K107700.04
581E106000.04
582L106000.04
591E104700.04
592M104700.04
601E105520.04
602N105520.04
611E103480.04
612O103480.04
621F103340.05
622G103340.05
631F106520.05
632H106520.05
641F107600.06
642I107600.06
651F107340.06
652J107340.06
661F107280.06
662K107280.06
671F105620.05
672L105620.05
681F104460.04
682M104460.04
691F105120.05
692N105120.05
701F103500.05
702O103500.05
711G103300.04
712H103300.04
721G103360.03
722I103360.03
731G102940.05
732J102940.05
741G103580.04
742K103580.04
751G103380.04
752L103380.04
761G102880.04
762M102880.04
771G103600.04
772N103600.04
781G102300.04
782O102300.04
791H107240.04
792I107240.04
801H106820.06
802J106820.06
811H107520.04
812K107520.04
821H106460.03
822L106460.03
831H104980.04
832M104980.04
841H105540.03
842N105540.03
851H103860.04
852O103860.04
861I107920.06
862J107920.06
871I108260.03
872K108260.03
881I106280.03
882L106280.03
891I105020.03
892M105020.03
901I105600.03
902N105600.03
911I103620.03
912O103620.03
921J108620.06
922K108620.06
931J105200.06
932L105200.06
941J104400.04
942M104400.04
951J104900.06
952N104900.06
961J103200.05
962O103200.05
971K106180.03
972L106180.03
981K105240.03
982M105240.03
991K105880.03
992N105880.03
1001K103820.03
1002O103820.03
1011L105220.03
1012M105220.03
1021L105500.03
1022N105500.03
1031L103880.03
1032O103880.03
1041M104920.04
1042N104920.04
1051M103740.04
1052O103740.04
1061N103980.04
1062O103980.04
LS refinement shellResolution: 4.3→4.412 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.576 11513 -
obs--100 %

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