[English] 日本語
Yorodumi
- PDB-5yis: Crystal Structure of AnkB LIR/LC3B complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yis
TitleCrystal Structure of AnkB LIR/LC3B complex
Components
  • Ankyrin-2
  • Microtubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING / Autophagy
Function / homology
Function and homology information


Receptor Mediated Mitophagy / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / TBC/RABGAPs / Macroautophagy / Pexophagy / protein localization to M-band / positive regulation of mucus secretion / PINK1-PRKN Mediated Mitophagy ...Receptor Mediated Mitophagy / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / TBC/RABGAPs / Macroautophagy / Pexophagy / protein localization to M-band / positive regulation of mucus secretion / PINK1-PRKN Mediated Mitophagy / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / paranodal junction assembly / protein localization to organelle / sarcoplasmic reticulum calcium ion transport / positive regulation of potassium ion import across plasma membrane / potassium channel activator activity / A band / regulation of atrial cardiac muscle cell action potential / mucus secretion / channel activator activity / phosphorylation-dependent protein binding / atrial cardiac muscle cell action potential / regulation of SA node cell action potential / protein localization to endoplasmic reticulum / cytoskeletal anchor activity / atrial septum development / costamere / ventricular cardiac muscle cell action potential / KEAP1-NFE2L2 pathway / regulation of ventricular cardiac muscle cell membrane repolarization / response to methylmercury / positive regulation of calcium ion transport / regulation of release of sequestered calcium ion into cytosol / M band / regulation of cardiac muscle cell contraction / protein localization to cell surface / regulation of cardiac muscle contraction by calcium ion signaling / Interaction between L1 and Ankyrins / spectrin binding / autolysosome / regulation of heart rate by cardiac conduction / regulation of calcium ion transport / autophagosome membrane / intercalated disc / axoneme / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / mitophagy / COPI-mediated anterograde transport / T-tubule / endomembrane system / regulation of heart rate / autophagosome / cellular response to starvation / protein localization to plasma membrane / establishment of localization in cell / recycling endosome / sarcolemma / mitochondrial membrane / regulation of protein stability / structural constituent of cytoskeleton / autophagy / Z disc / endocytosis / intracellular calcium ion homeostasis / intracellular protein localization / protein transport / ATPase binding / cytoplasmic vesicle / protein-macromolecule adaptor activity / basolateral plasma membrane / microtubule / transmembrane transporter binding / postsynaptic membrane / early endosome / cytoskeleton / lysosome / neuron projection / protein stabilization / apical plasma membrane / positive regulation of gene expression / protein kinase binding / enzyme binding / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ankyrin repeats (many copies) ...Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ankyrin-2 / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsLi, J. / Zhu, R. / Chen, K. / Zheng, H. / Yuan, C. / Zhang, H. / Wang, C. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Research Grants Council (RGC)AoE-M09-12 Hong Kong
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins.
Authors: Li, J. / Zhu, R. / Chen, K. / Zheng, H. / Zhao, H. / Yuan, C. / Zhang, H. / Wang, C. / Zhang, M.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
B: Microtubule-associated proteins 1A/1B light chain 3B
D: Ankyrin-2
C: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0287
Polymers35,7494
Non-polymers2793
Water64936
1
A: Microtubule-associated proteins 1A/1B light chain 3B
C: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9663
Polymers17,8742
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-10 kcal/mol
Surface area8090 Å2
MethodPISA
2
B: Microtubule-associated proteins 1A/1B light chain 3B
D: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0614
Polymers17,8742
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-16 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.802, 66.866, 74.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 13 or (resid 14...
21(chain B and (resid 5 through 23 or (resid 24...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPHEPHE(chain A and (resid 5 through 13 or (resid 14...AA5 - 135 - 13
12GLUGLUGLNGLN(chain A and (resid 5 through 13 or (resid 14...AA14 - 1514 - 15
13LYSLYSGLUGLU(chain A and (resid 5 through 13 or (resid 14...AA5 - 1175 - 117
14LYSLYSGLUGLU(chain A and (resid 5 through 13 or (resid 14...AA5 - 1175 - 117
15LYSLYSGLUGLU(chain A and (resid 5 through 13 or (resid 14...AA5 - 1175 - 117
16LYSLYSGLUGLU(chain A and (resid 5 through 13 or (resid 14...AA5 - 1175 - 117
21LYSLYSILEILE(chain B and (resid 5 through 23 or (resid 24...BB5 - 235 - 23
22ARGARGARGARG(chain B and (resid 5 through 23 or (resid 24...BB2424
23GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125
24GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125
25GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125
26GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125
27GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125
28GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125

-
Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / MAP1A/MAP1B light chain 3 B / MAP1A/MAP1B LC3 B / Microtubule-associated protein 1 light chain 3 beta


Mass: 14637.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map1lc3b, Map1alc3, Map1lc3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQV6
#2: Protein/peptide Ankyrin-2 / ANK-2 / Ankyrin-B / Brain ankyrin / Non-erythroid ankyrin


Mass: 3236.489 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1588-1614
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01484
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 2.4 M ammonium phosphate dibasic, 0.1 M Tris buffer (pH 8.5)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 16051 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.52 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.048 / Rrim(I) all: 0.122 / Χ2: 1.791 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.246.40.9547780.8090.4071.041.392100
2.24-2.286.40.8667850.7940.370.9441.433100
2.28-2.326.40.7067950.8970.3010.7691.429100
2.32-2.376.40.6977990.8840.2960.7591.486100
2.37-2.426.40.5457840.9280.2320.5941.441100
2.42-2.486.30.4977930.9360.2130.5421.444100
2.48-2.546.40.4418020.9450.1880.481.464100
2.54-2.616.40.4017870.9580.1720.4371.404100
2.61-2.696.40.3287990.9660.140.3581.495100
2.69-2.776.40.2637960.9760.1130.2871.511100
2.77-2.876.40.2297880.9820.0970.2491.559100
2.87-2.996.30.1817950.9810.0780.1981.63599.9
2.99-3.126.30.158220.9890.0650.1641.91999.9
3.12-3.296.20.1227880.990.0530.1342.21899.9
3.29-3.496.20.1028070.9930.0450.1122.5399.8
3.49-3.765.90.0797980.9970.0350.0862.77999.5
3.76-4.1460.0698270.9960.030.0762.90999.4
4.14-4.745.90.0448140.9980.0190.0482.05599.3
4.74-5.976.30.0418250.9980.0180.0451.79198.7
5.97-505.80.0428690.9980.0190.0472.06395.4

-
Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UGM

1ugm


Resolution: 2.201→28.712 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.12
RfactorNum. reflection% reflection
Rfree0.2496 763 4.76 %
Rwork0.1973 --
obs0.1997 16013 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.54 Å2 / Biso mean: 44.7684 Å2 / Biso min: 20.42 Å2
Refinement stepCycle: final / Resolution: 2.201→28.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 17 36 2214
Biso mean--72.42 38.03 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092233
X-RAY DIFFRACTIONf_angle_d1.0163027
X-RAY DIFFRACTIONf_chiral_restr0.063353
X-RAY DIFFRACTIONf_plane_restr0.006386
X-RAY DIFFRACTIONf_dihedral_angle_d7.1521599
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A964X-RAY DIFFRACTION12.45TORSIONAL
12B964X-RAY DIFFRACTION12.45TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2013-2.37120.32031530.26332955310898
2.3712-2.60970.30811700.243230083178100
2.6097-2.98690.27461470.225630333180100
2.9869-3.76190.26941300.19930913221100
3.7619-28.71460.20521630.16383163332699
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3975-0.11621.52382.2454-2.01684.45030.05090.3293-0.0742-0.1591-0.08860.1522-0.2605-0.0703-0.04450.26330.03040.01630.23230.00620.29884.148174.264312.5927
23.94841.09123.00382.94980.12544.4889-0.0507-1.33730.861.20150.40050.0303-1.5826-0.69680.12510.93250.1399-0.09870.1831-0.12120.59459.562583.998529.3438
35.0747-2.0426-0.99072.8029-0.45464.2444-0.2467-0.53590.280.36450.4409-0.2218-0.49080.1775-0.19190.3310.0590.00830.3036-0.01570.342314.656871.371127.97
42.69810.2922.56862.9592-0.21564.8276-0.3337-0.6893-0.26210.69210.2250.545-0.0934-0.85070.11380.36960.0770.10050.37070.03410.37762.766767.197128.1873
53.0121-0.77590.69773.23330.56756.0055-0.2433-0.4695-0.01790.52330.38550.18960.0567-0.1669-0.02780.31860.08170.03470.2892-0.00670.24751.863673.868623.5434
65.9745-0.03071.45117.1386-1.36618.6117-0.76320.018-0.213-0.3119-0.0278-0.6679-0.05120.86640.72310.4365-0.01760.04870.37440.00310.459431.036258.578920.5149
73.70550.84531.53994.45140.3812.7321-0.06581.4426-0.2822-1.56670.5873-0.6274-0.07830.6527-0.38440.7475-0.05150.16370.6676-0.07080.361625.197651.56299.5528
81.73390.78181.24422.74740.63454.5201-0.06620.0353-0.2185-0.10220.2503-0.38670.1190.3654-0.20950.22170.0553-0.01950.3833-0.06080.268627.534649.104927.2504
97.38470.2592-1.72683.9153-1.25844.87630.6620.8870.0246-0.2494-0.09090.27390.87190.4452-0.52110.35290.0613-0.04720.3563-0.09480.362720.947140.71920.1803
105.63942.54111.35674.64151.03753.30370.5724-0.29560.18570.4061-0.3057-0.01540.94930.2606-0.12140.39980.0449-0.07840.33370.01840.367324.312440.210930.0414
114.6938-1.83360.05074.199-0.56972.7841-0.1655-0.2985-0.30241.0678-0.116-0.33840.12470.49480.23380.4528-0.0693-0.07650.47980.0520.36223.387245.971836.0909
121.71421.0163-0.82113.3929-0.11450.9396-0.12740.02410.31480.18070.02380.278-0.0239-0.226-0.01730.23480.0072-0.00870.291-0.01930.323712.370947.415725.2685
134.1134-3.1121-2.96073.32021.81033.46740.037-0.35950.5426-1.27080.3415-0.2253-0.60210.5474-0.42150.4463-0.05610.020.39610.02880.342219.031255.154616.0384
141.3610.64261.35753.0578-0.32834.63390.0032-0.27110.08690.4180.0480.1072-0.0301-0.6735-0.0290.2620.0435-0.02470.3938-0.01760.285820.702754.025336.4359
152.8132-0.9668-0.07981.357-2.49386.15480.17710.8754-0.69360.153-0.34230.1529-0.2214-0.0017-0.20410.410.22840.11540.4878-0.16660.775329.651542.043117.9791
166.9216-0.3023.46024.28831.61976.00540.6119-0.2893-2.00420.79080.54691.44931.3140.2416-0.87390.70690.09160.13690.60240.02051.907223.810931.228123.4502
171.1409-0.78461.02871.9984-1.68464.2501-0.12330.16780.669-0.3378-0.1711-0.1797-0.02050.59980.22450.30220.009-0.04440.40440.07460.384415.665975.885112.786
185.43283.1522-0.49687.3624-4.41117.5792-0.63980.0849-0.4242-0.2865-0.1823-1.08430.35810.71010.72550.26540.02580.0240.4590.07060.443621.736864.885125.4081
194.3389-1.32391.64174.4086-3.21163.1887-1.0216-0.2057-0.20220.45140.5078-0.1952-0.6622-0.8830.52040.5430.17890.03140.7581-0.06910.414815.833259.76634.9026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 37 )A5 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 50 )A38 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 79 )A51 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 102 )A80 - 102
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 117 )A103 - 117
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 12 )B4 - 12
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 26 )B13 - 26
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 50 )B27 - 50
9X-RAY DIFFRACTION9chain 'B' and (resid 51 through 59 )B51 - 59
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 71 )B60 - 71
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 85 )B72 - 85
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 102 )B86 - 102
13X-RAY DIFFRACTION13chain 'B' and (resid 103 through 108 )B103 - 108
14X-RAY DIFFRACTION14chain 'B' and (resid 109 through 125 )B109 - 125
15X-RAY DIFFRACTION15chain 'D' and (resid 122 through 128 )D122 - 128
16X-RAY DIFFRACTION16chain 'D' and (resid 129 through 134 )D129 - 134
17X-RAY DIFFRACTION17chain 'C' and (resid 121 through 128 )C121 - 128
18X-RAY DIFFRACTION18chain 'C' and (resid 129 through 136 )C129 - 136
19X-RAY DIFFRACTION19chain 'C' and (resid 137 through 145 )C137 - 145

+
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