[English] 日本語
Yorodumi
- PDB-11fh: RNA Vault cap (MVP/PARP4/TEP1 sample) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 11fh
TitleRNA Vault cap (MVP/PARP4/TEP1 sample)
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / RNA Vault / BAD / benzamide adenine dinucleotide / Major Vault Protein
Function / homology
Function and homology information


protein activation cascade / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / nuclear pore / mRNA transport / protein transport / secretory granule lumen / protein phosphatase binding / ficolin-1-rich granule lumen / cytoskeleton ...protein activation cascade / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / nuclear pore / mRNA transport / protein transport / secretory granule lumen / protein phosphatase binding / ficolin-1-rich granule lumen / cytoskeleton / cell population proliferation / intracellular signal transduction / ribonucleoprotein complex / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain ...Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain / Shoulder domain / Major Vault Protein repeat domain / Major Vault Protein Repeat domain / Major Vault Protein repeat domain / MVP (vault) repeat profile. / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.92 Å
AuthorsOsinski, A. / Tagliabracci, V.S.
Funding support United States, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Welch FoundationI-1911 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137419 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM158265 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150033 United States
CitationJournal: Biorxiv / Year: 2026
Title: TIR-like NADases act in bacterial immunity and the RNA vault
Authors: Osinski, A. / Mayro, B. / Lopez, V.A. / Schrad, J. / Choi, H. / Tomchick, D.R. / Pawlowski, K. / Forsberg, K. / Shahmoradian, S.H. / Tagliabracci, V.S.
History
DepositionFeb 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major vault protein
B: Major vault protein
C: Major vault protein
D: Major vault protein
E: Major vault protein
F: Major vault protein
G: Major vault protein
H: Major vault protein
I: Major vault protein
J: Major vault protein
K: Major vault protein
L: Major vault protein
M: Major vault protein
N: Major vault protein
O: Major vault protein
P: Major vault protein
Q: Major vault protein
R: Major vault protein
S: Major vault protein
T: Major vault protein
U: Major vault protein
V: Major vault protein
W: Major vault protein
X: Major vault protein
Y: Major vault protein
Z: Major vault protein
a: Major vault protein
b: Major vault protein
c: Major vault protein
d: Major vault protein
e: Major vault protein
f: Major vault protein
g: Major vault protein
h: Major vault protein
i: Major vault protein
j: Major vault protein
k: Major vault protein
l: Major vault protein
m: Major vault protein


Theoretical massNumber of molelcules
Total (without water)3,878,65839
Polymers3,878,65839
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "P"
d_3ens_1chain "G"
d_4ens_1chain "J"
d_5ens_1chain "M"
d_6ens_1chain "D"
d_7ens_1chain "S"
d_8ens_1chain "V"
d_9ens_1chain "Y"
d_10ens_1chain "b"
d_11ens_1chain "e"
d_12ens_1chain "h"
d_13ens_1chain "k"
d_1ens_2chain "T"
d_2ens_2chain "E"
d_3ens_2chain "H"
d_4ens_2chain "K"
d_5ens_2chain "N"
d_6ens_2chain "Q"
d_7ens_2chain "Z"
d_8ens_2chain "W"
d_9ens_2chain "B"
d_10ens_2chain "c"
d_11ens_2chain "f"
d_12ens_2chain "i"
d_13ens_2chain "l"
d_1ens_3chain "O"
d_2ens_3chain "F"
d_3ens_3chain "I"
d_4ens_3chain "C"
d_5ens_3chain "X"
d_6ens_3chain "R"
d_7ens_3chain "U"
d_8ens_3chain "d"
d_9ens_3chain "a"
d_10ens_3chain "L"
d_11ens_3chain "g"
d_12ens_3chain "j"
d_13ens_3chain "m"

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1METMETAA766 - 851766 - 851
d_2ens_1METMETPP766 - 851766 - 851
d_3ens_1METMETGG766 - 851766 - 851
d_4ens_1METMETJJ766 - 851766 - 851
d_5ens_1METMETMM766 - 851766 - 851
d_6ens_1METMETDD766 - 851766 - 851
d_7ens_1METMETSS766 - 851766 - 851
d_8ens_1METMETVV766 - 851766 - 851
d_9ens_1METMETYY766 - 851766 - 851
d_10ens_1METMETbBA766 - 851766 - 851
d_11ens_1METMETeEA766 - 851766 - 851
d_12ens_1METMEThHA766 - 851766 - 851
d_13ens_1METMETkKA766 - 851766 - 851
d_1ens_2ASNASNTT766 - 843766 - 843
d_2ens_2ASNASNEE766 - 843766 - 843
d_3ens_2ASNASNHH766 - 843766 - 843
d_4ens_2ASNASNKK766 - 843766 - 843
d_5ens_2ASNASNNN766 - 843766 - 843
d_6ens_2ASNASNQQ766 - 843766 - 843
d_7ens_2ASNASNZZ766 - 843766 - 843
d_8ens_2ASNASNWW766 - 843766 - 843
d_9ens_2ASNASNBB766 - 843766 - 843
d_10ens_2ASNASNcCA766 - 843766 - 843
d_11ens_2ASNASNfFA766 - 843766 - 843
d_12ens_2ASNASNiIA766 - 843766 - 843
d_13ens_2ASNASNlLA766 - 843766 - 843
d_1ens_3LEULEUOO766 - 858766 - 858
d_2ens_3LEULEUFF766 - 858766 - 858
d_3ens_3LEULEUII766 - 858766 - 858
d_4ens_3LEULEUCC766 - 858766 - 858
d_5ens_3LEULEUXX766 - 858766 - 858
d_6ens_3LEULEURR766 - 858766 - 858
d_7ens_3LEULEUUU766 - 858766 - 858
d_8ens_3LEULEUdDA766 - 858766 - 858
d_9ens_3LEULEUaAA766 - 858766 - 858
d_10ens_3LEULEULL766 - 858766 - 858
d_11ens_3LEULEUgGA766 - 858766 - 858
d_12ens_3LEULEUjJA766 - 858766 - 858
d_13ens_3LEULEUmMA766 - 858766 - 858

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.748504468162, -0.66312974682, 4.90773773958E-6), (0.663129746814, -0.748504468177, -3.12770761703E-6), (5.74753958693E-6, 9.13363758228E-7, 0.999999999983)515.846707095, 232.162882166, -0.00226447895821
2given(0.568073487981, -0.822977832173, -2.11741381487E-6), (0.822977832129, 0.568073487974, -9.21252058564E-6), (8.78454687172E-6, 3.4908040711E-6, 0.999999999955)268.424880052, -83.6429912012, -0.00365447583187
3given(0.120545561495, -0.992707795679, 1.09690593927E-6), (0.992707795658, 0.120545561485, -6.72180770359E-6), (6.54056376606E-6, 1.89919116091E-6, 0.999999999977)400.455314932, -24.2225217504, -0.0026901782291
4given(-0.354595212868, -0.935019911538, 6.19537476658E-6), (0.935019911512, -0.354595212909, -7.6581927078E-6), (9.35741290259E-6, 3.07724029262E-6, 0.999999999951)489.746862175, 89.7496292787, -0.0037284630844
5given(0.885460552752, -0.464714546241, -5.5888160704E-6), (0.464714546218, 0.885460552768, -4.96400090277E-6), (7.25551959409E-6, 1.79822285918E-6, 0.999999999972)123.904442863, -74.9008264173, -0.00287115610968
6given(-0.970939583964, -0.239324725474, 8.24502766926E-6), (0.239324725486, -0.970939583996, 4.67193586108E-7), (7.89361275849E-6, 2.4268557297E-6, 0.999999999966)472.772818785, 370.392428967, -0.00318289678592
7given(-0.970944902421, 0.239303147496, 7.78966717114E-6), (-0.239303147451, -0.970944902443, 6.25445512924E-6), (9.06004842984E-6, 4.2086394535E-6, 0.99999999995)370.39561899, 472.770153409, -0.00388188088192
8given(-0.748511416222, 0.663121904166, 6.7827788685E-7), (-0.663121904167, -0.748511416222, -2.17926709723E-7), (3.63186766958E-7, -6.1290155401E-7, 1)232.164712932, 515.848361098, 2.5995486709E-5
9given(-0.354605226463, 0.93501611396, 1.12621532695E-6), (-0.93501611396, -0.354605226462, -6.44611852046E-7), (-2.03360627856E-7, -1.28161221026E-6, 0.999999999999)89.7498781902, 489.750138987, 0.000322116002195
10given(0.120537345317, 0.992708793345, 3.8397630583E-7), (-0.992708793344, 0.120537345317, 1.19070271715E-6), (1.13573757301E-6, -5.2470079982E-7, 0.999999999999)-24.2234533816, 400.457215747, -0.000208907924474
11given(0.568066019732, 0.822982987203, 1.04755166723E-6), (-0.822982987203, 0.568066019732, -5.73773884106E-7), (-1.06728465119E-6, -5.36175753774E-7, 0.999999999999)-83.6456960631, 268.426784244, 0.000409523754513
12given(0.885455942242, 0.46472333097, 2.66588406799E-7), (-0.46472333097, 0.885455942242, -1.48194605622E-8), (-2.42939238009E-7, -1.1076787299E-7, 1)-74.9033920786, 123.905313513, 8.97331358942E-5
13given(-0.748526550262, 0.663104820918, 5.24579685461E-6), (-0.663104820729, -0.748526550201, 1.92550249702E-5), (1.66947181073E-5, 1.09343842333E-5, 0.999999999801)232.170425998, 515.845998332, -0.00517937324639
14given(-0.354659346881, 0.934995586951, 7.21724922589E-6), (-0.934995586524, -0.354659346939, 2.84433076183E-5), (2.91540319986E-5, 3.33958873E-6, 0.999999999569)89.7618302575, 489.755201823, -0.00532786672082
15given(0.120535443645, 0.992709024248, 1.24110738393E-6), (-0.992709024249, 0.120535443645, 1.28702643225E-7), (-2.18331537589E-8, -1.24757173029E-6, 0.999999999999)-24.2233162931, 400.457897137, 0.000287175288747
16given(0.568063917025, 0.822984438598, 2.0381024098E-7), (-0.822984438598, 0.568063917025, 3.98581790302E-7), (2.12249367106E-7, -3.94152589808E-7, 1)-83.6453490345, 268.42736524, 5.27112163979E-5
17given(0.88544008003, 0.464753552558, -7.81709538136E-6), (-0.464753552437, 0.885440080026, 1.34222904801E-5), (1.31596267441E-5, -8.2516111087E-6, 0.999999999879)-74.9071908158, 123.910987831, -0.000108207787065
18given(0.568092381473, -0.822964790193, -1.46531489561E-5), (0.822964790224, 0.568092381591, -5.40248403173E-6), (1.2770396426E-5, -8.98991563735E-6, 0.999999999878)268.421294036, -83.6485031847, 0.000119811089462
19given(0.885455789321, -0.464723622337, -4.80016423536E-7), (0.464723622337, 0.885455789321, 1.68748363741E-7), (3.46611970328E-7, -3.7249418674E-7, 1)123.905490181, -74.9034095586, 3.03659713552E-5
20given(-0.970941862925, 0.239315479692, 1.82636365825E-7), (-0.239315479692, -0.970941862924, -7.95193619533E-7), (-1.29728492344E-8, -8.15794483832E-7, 1)370.394830017, 472.774222786, 0.00018754807121
21given(0.120536961057, -0.992708840002, -1.21334110595E-6), (0.992708840002, 0.120536961057, -2.02550245029E-7), (3.47325868422E-7, -1.18007965082E-6, 0.999999999999)400.45780998, -24.223252817, 0.000209821187269
22given(-0.354582358188, -0.935024786303, 1.6114574566E-5), (0.935024786298, -0.354582358384, -1.14455651789E-5), (1.64158309895E-5, 1.10091311479E-5, 0.999999999805)489.745592685, 89.7451712345, -0.00515244334264
23given(-0.748511232115, -0.663122111981, -3.31947822367E-7), (0.663122111981, -0.748511232115, -5.09681048413E-7), (8.95140997423E-8, -6.01623930568E-7, 1)515.848417155, 232.164787507, 0.000123477952513
24given(-0.970936273644, -0.23933815444, 1.87345476403E-5), (0.239338154606, -0.970936273758, 7.13375238477E-6), (1.64826727464E-5, 1.14103110172E-5, 0.999999999799)472.77538907, 370.388606181, -0.00525136611014
25given(0.120514331885, 0.992711587173, -2.24061835473E-5), (-0.992711587035, 0.120514332441, 2.53602161642E-5), (2.78756466922E-5, 1.91866085211E-5, 0.999999999427)-24.2159952482, 400.458386588, -0.0111378682497
26given(0.56802759355, 0.823009509643, 1.93256903928E-6), (-0.823009509087, 0.568027593249, -3.5497491267E-5), (-3.03125254214E-5, 1.85730318451E-5, 0.999999999368)-83.6463343693, 268.448618543, 0.000663329459655
27given(-0.354606099583, 0.935015782829, 2.11918976952E-7), (-0.935015782827, -0.354606099582, -1.86186203436E-6), (-1.66572262574E-6, -8.58375222097E-7, 0.999999999998)89.7502923537, 489.750553077, 0.000531356919907
28given(0.120515304159, -0.992711469365, -7.36397803263E-6), (0.992711467836, 0.120515304382, -5.50983171039E-5), (5.55842033858E-5, -6.70114997481E-7, 0.999999998455)400.463818408, -24.206385387, -0.0109908474501
29given(0.885446047506, -0.46474218076, -4.87699290899E-5), (0.464742180141, 0.885446048848, -2.40223352304E-5), (5.43473334772E-5, -1.39496138899E-6, 0.999999998522)123.922465337, -74.8991124948, -0.010573693771
30given(0.568065094039, -0.822983626164, -3.70595635717E-7), (0.822983626164, 0.568065094037, 1.63776004819E-6), (-1.13732725859E-6, -1.23534845591E-6, 0.999999999999)268.427162682, -83.6456860288, 0.000533182966052
31given(-0.748525108891, -0.663106446725, 4.08833419922E-5), (0.663106445657, -0.748525110006, -3.76663552249E-5), (5.55790110364E-5, -1.0842050512E-6, 0.999999998455)515.838077583, 232.17929981, -0.010882643718
32given(-0.354603243387, -0.935016866038, -1.70539985802E-6), (0.935016866038, -0.35460324339, 1.38659529744E-6), (-1.9012303104E-6, -1.10288644085E-6, 0.999999999998)489.750169242, 89.7491803574, 0.000636898046452
33given(0.885466104201, 0.464703965953, -4.83635666523E-5), (-0.464703965205, 0.885466105521, 2.63871816176E-5), (5.50865269607E-5, -8.90213713018E-7, 0.999999998482)-74.8898709171, 123.893437256, -0.0108407351599
34given(-0.970930835051, -0.239360215776, -2.55037569682E-5), (0.239360215151, -0.970930835211, 2.53018868114E-5), (-3.08186491408E-5, 1.84617973351E-5, 0.999999999355)472.789317328, 370.379314909, 0.000789443675387
35given(-0.970936990228, 0.239335241922, 5.46030760666E-5), (-0.239335241562, -0.970936991763, 1.31363094585E-5), (5.61601282193E-5, -3.13911632034E-7, 0.999999998423)370.377177726, 472.773591714, -0.0111907766364
36given(-0.748525891451, 0.663105564582, 6.83546554463E-6), (-0.663105564116, -0.748525891246, 3.11862481874E-5), (2.57962976504E-5, 1.88110789895E-5, 0.99999999949)232.169645039, 515.84324658, -0.010659915631

-
Components

#1: Protein ...
Major vault protein / MVP / Lung resistance-related protein


Mass: 99452.766 Da / Num. of mol.: 39
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MVP, LRP / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q14764
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: RNA Vault cap (MVP/PARP4/TEP1 sample) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: 293F
Buffer solutionpH: 8
Details: 50 mM Tris 150 mM NaCl 1 mM DTT 1 mM NADP 0.025% DDM
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris1
2150 mMsodium chlorideNaCl1
31 mMDithiothreitolDTT1
41 mMNicotinamide adenine dinucleotide phosphateNADP1
50.025 %n-dodecyl-Beta-D-maltosideDDM1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C13 (13 fold cyclic)
3D reconstructionResolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115486
Details: Vault particles were symmetry-expanded in D1 symmetry, centered around the cap region and re-extracted.
Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002624648
ELECTRON MICROSCOPYf_angle_d0.428133176
ELECTRON MICROSCOPYf_chiral_restr0.03194030
ELECTRON MICROSCOPYf_plane_restr0.00384238
ELECTRON MICROSCOPYf_dihedral_angle_d3.49923289
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints4.00697820633E-12
ens_1d_3AAELECTRON MICROSCOPYNCS constraints4.49596578611E-13
ens_1d_4AAELECTRON MICROSCOPYNCS constraints3.77076674187E-13
ens_1d_5AAELECTRON MICROSCOPYNCS constraints1.87864139189E-13
ens_1d_6AAELECTRON MICROSCOPYNCS constraints5.0622259773E-13
ens_1d_7AAELECTRON MICROSCOPYNCS constraints5.3500628539E-10
ens_1d_8AAELECTRON MICROSCOPYNCS constraints6.49351519297E-13
ens_1d_9AAELECTRON MICROSCOPYNCS constraints6.20981031233E-13
ens_1d_10AAELECTRON MICROSCOPYNCS constraints1.33919075363E-12
ens_1d_11AAELECTRON MICROSCOPYNCS constraints2.07972579402E-13
ens_1d_12AAELECTRON MICROSCOPYNCS constraints2.78808870648E-10
ens_1d_13AAELECTRON MICROSCOPYNCS constraints1.04656848328E-10
ens_2d_2TTELECTRON MICROSCOPYNCS constraints1.79202390065E-10
ens_2d_3TTELECTRON MICROSCOPYNCS constraints8.48349730282E-10
ens_2d_4TTELECTRON MICROSCOPYNCS constraints1.73452110683E-12
ens_2d_5TTELECTRON MICROSCOPYNCS constraints3.3506460004E-13
ens_2d_6TTELECTRON MICROSCOPYNCS constraints8.80090577487E-12
ens_2d_7TTELECTRON MICROSCOPYNCS constraints2.24181933691E-11
ens_2d_8TTELECTRON MICROSCOPYNCS constraints5.3831940269E-13
ens_2d_9TTELECTRON MICROSCOPYNCS constraints2.95883955329E-12
ens_2d_10TTELECTRON MICROSCOPYNCS constraints4.55902597658E-13
ens_2d_11TTELECTRON MICROSCOPYNCS constraints4.10609928531E-12
ens_2d_12TTELECTRON MICROSCOPYNCS constraints1.03782405466E-12
ens_2d_13TTELECTRON MICROSCOPYNCS constraints5.2236094315E-10
ens_3d_2OOELECTRON MICROSCOPYNCS constraints2.23303913648E-11
ens_3d_3OOELECTRON MICROSCOPYNCS constraints4.60231695436E-10
ens_3d_4OOELECTRON MICROSCOPYNCS constraints6.23381653445E-13
ens_3d_5OOELECTRON MICROSCOPYNCS constraints9.87335985992E-11
ens_3d_6OOELECTRON MICROSCOPYNCS constraints9.91642780575E-11
ens_3d_7OOELECTRON MICROSCOPYNCS constraints4.42760771301E-12
ens_3d_8OOELECTRON MICROSCOPYNCS constraints8.64428412131E-13
ens_3d_9OOELECTRON MICROSCOPYNCS constraints1.95401258227E-11
ens_3d_10OOELECTRON MICROSCOPYNCS constraints6.03323636726E-11
ens_3d_11OOELECTRON MICROSCOPYNCS constraints6.13030776909E-12
ens_3d_12OOELECTRON MICROSCOPYNCS constraints1.47351274971E-10
ens_3d_13OOELECTRON MICROSCOPYNCS constraints2.67212508683E-12

+
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