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- PDB-5gyk: Crystal Structure of Mdm12-deletion mutant -

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Basic information

Entry
Database: PDB / ID: 5gyk
TitleCrystal Structure of Mdm12-deletion mutant
ComponentsMitochondrial distribution and morphology protein 12
KeywordsLIPID TRANSPORT / Mdm12 / ERMES complex / SMP domain / TRANSPORT PROTEIN
Function / homology
Function and homology information


ERMES complex / outer mitochondrial membrane protein complex / mitochondrion inheritance / mitochondrial outer membrane translocase complex assembly / lipid transfer activity / aminophospholipid transport / peroxisome organization / mitochondria-associated endoplasmic reticulum membrane contact site / mitochondrial genome maintenance / phospholipid homeostasis ...ERMES complex / outer mitochondrial membrane protein complex / mitochondrion inheritance / mitochondrial outer membrane translocase complex assembly / lipid transfer activity / aminophospholipid transport / peroxisome organization / mitochondria-associated endoplasmic reticulum membrane contact site / mitochondrial genome maintenance / phospholipid homeostasis / phospholipid transport / protein insertion into mitochondrial outer membrane / mitochondrion-endoplasmic reticulum membrane tethering / mitochondrion organization / mitochondrial outer membrane / lipid binding / endoplasmic reticulum membrane / mitochondrion / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Mitochondrial distribution and morphology protein 12 / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial lipid-binding proteins (SMP) domain profile.
Similarity search - Domain/homology
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Mitochondrial distribution and morphology protein 12
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.596 Å
AuthorsJeong, H. / Park, J. / Lee, C.
CitationJournal: EMBO Rep. / Year: 2016
Title: Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex
Authors: Jeong, H. / Park, J. / Lee, C.
History
DepositionSep 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 2.0Nov 8, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial distribution and morphology protein 12
B: Mitochondrial distribution and morphology protein 12
C: Mitochondrial distribution and morphology protein 12
D: Mitochondrial distribution and morphology protein 12
E: Mitochondrial distribution and morphology protein 12
F: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,5068
Polymers159,0186
Non-polymers1,4882
Water00
1
A: Mitochondrial distribution and morphology protein 12
B: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7503
Polymers53,0062
Non-polymers7441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-32 kcal/mol
Surface area24950 Å2
MethodPISA
2
C: Mitochondrial distribution and morphology protein 12
D: Mitochondrial distribution and morphology protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7503
Polymers53,0062
Non-polymers7441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-31 kcal/mol
Surface area25330 Å2
MethodPISA
3
E: Mitochondrial distribution and morphology protein 12
F: Mitochondrial distribution and morphology protein 12


Theoretical massNumber of molelcules
Total (without water)53,0062
Polymers53,0062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-18 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.239, 148.243, 212.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Mitochondrial distribution and morphology protein 12 / Mitochondrial inheritance component MDM12


Mass: 26503.057 Da / Num. of mol.: 6 / Mutation: Deletion of UNP residues 74-114
Source method: isolated from a genetically manipulated source
Details: Mdm12 mutant residues 74-114 to linker GGSGG / Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: MDM12, YOL009C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92328
#2: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.41 Å3/Da / Density % sol: 77.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate, Tris-HCl (pH 8.5), Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 3.596→50 Å / Num. obs: 40722 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 11.1
Reflection shellResolution: 3.6→3.66 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
AutoSolphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GYD
Resolution: 3.596→41.451 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2673 1995 4.91 %
Rwork0.2197 --
obs0.222 40625 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.596→41.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10812 0 62 0 10874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711071
X-RAY DIFFRACTIONf_angle_d1.36915012
X-RAY DIFFRACTIONf_dihedral_angle_d16.744130
X-RAY DIFFRACTIONf_chiral_restr0.0481746
X-RAY DIFFRACTIONf_plane_restr0.0071911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5962-3.6860.37411390.31242682X-RAY DIFFRACTION98
3.686-3.78560.38311410.3012722X-RAY DIFFRACTION100
3.7856-3.8970.3681410.27912733X-RAY DIFFRACTION100
3.897-4.02260.32941410.26242725X-RAY DIFFRACTION100
4.0226-4.16630.30711420.24622731X-RAY DIFFRACTION100
4.1663-4.33290.29641410.21852745X-RAY DIFFRACTION100
4.3329-4.52990.28381400.1962743X-RAY DIFFRACTION100
4.5299-4.76840.21361440.17942763X-RAY DIFFRACTION100
4.7684-5.06670.21451410.17642736X-RAY DIFFRACTION100
5.0667-5.45710.23661440.21262768X-RAY DIFFRACTION100
5.4571-6.00480.29681430.23132774X-RAY DIFFRACTION100
6.0048-6.87020.27341450.23672804X-RAY DIFFRACTION100
6.8702-8.64290.27431470.21922823X-RAY DIFFRACTION100
8.6429-41.45380.18771460.18262881X-RAY DIFFRACTION97
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)
11.99030.35641.26411.74880.30822.5670.76510.6292-1.62270.2279-0.2842-1.06321.58130.39150.20540.5477-0.14320.21670.50370.26730.961713.7428-14.8957-48.4363
23.14821.09110.61080.43680.67752.2311-0.10030.5282-0.7112-0.00480.318-0.31290.83090.35210.00840.74970.02150.11440.67380.0150.651511.6291-14.0493-60.5973
32.4450.6043-1.09612.16861.07184.91420.2546-0.02810.0148-0.7351-0.3048-0.54520.2164-1.1912-0.0653-0.10160.42760.00780.28830.23820.52510.6505-1.1732-53.2117
43.99181.5296-1.22211.2499-0.74771.9472-0.54651.1493-0.0869-1.00080.45510.4383-0.1671-0.1323-0.00930.9560.0493-0.06490.74630.00040.48472.7875-11.5096-69.1366
54.0593-0.29940.55471.0469-0.83971.0101-0.1613-0.96141.72450.9920.38-0.4996-1.2308-0.5169-0.09481.04990.06180.12510.47390.1980.49412.009213.3873-42.2498
62.10950.74620.88411.4827-0.05882.1251-0.58580.07110.5645-1.01430.62450.648-0.62920.4348-0.00620.5038-0.01750.00580.53190.11120.683712.3295.5953-56.3386
72.6051-1.18261.65680.7891-1.0611.3452-0.11960.4346-0.9321-1.7270.419-0.38270.7258-0.06980.25960.7282-0.00270.37570.5254-0.02150.753113.2004-19.3666-62.2238
82.2012-1.5419-0.45891.090.29050.95820.07192.36210.4588-0.06940.0520.13790.1607-0.77450.01030.9885-0.8316-0.34141.2035-0.21260.3079-13.2889-31.7824-52.1386
91.8655-0.30330.33752.30240.99831.08970.23090.6686-0.7051-0.2777-0.3243-0.2920.1392-0.4902-0.00080.6354-0.12070.170.7911-0.05550.708-5.4421-41.0943-47.955
100.5859-1.1241-0.34942.95740.40510.2739-0.42020.1531-0.1495-0.47870.32410.31690.5875-0.64-0.00341.0816-0.3629-0.02220.89310.02210.6577-16.2286-38.2503-39.2195
112.87220.7532-0.13024.00280.46141.97530.7082-0.404-0.5982-0.8654-0.405-1.05710.06160.42090.03370.92430.15620.28090.63520.12870.60274.232-42.7759-38.9648
120.42660.24230.12080.14170.03160.5176-0.1273-0.26730.5530.44240.89381.348-1.2119-0.98110.00780.89430.19520.26761.35480.45071.5438-31.6355-35.1551-29.9761
130.886-0.76370.46970.8192-0.11640.5931-0.7016-0.269-0.2793-0.1480.48350.51290.5032-1.0757-0.02610.722-0.38690.2051.12960.01570.7535-19.0012-44.447-34.019
141.6127-0.60941.28110.2339-0.49711.0138-0.4551.1901-1.4011-0.5856-0.2922-1.2484-0.5490.8743-0.00891.39-0.37190.28180.691-0.15931.0367-2.1046-44.1541-48.4091
152.6325-1.260.21161.85041.03140.9485-0.2046-0.8-0.3430.6919-0.24370.82461.234-0.8012-0.55180.5644-0.5374-0.04280.54510.05860.5369-14.2085-70.1271-14.3969
160.60.08850.10882.2756-1.31461.56190.176-0.1754-0.28170.0510.03640.41080.1623-1.17450.18040.2927-0.0520.11711.04640.12330.5089-20.7949-59.3881-17.2367
172.5430.3428-0.39452.2917-1.1981.2497-0.1046-0.3632-0.16320.10690.1751-0.1163-0.20310.34080.02260.1683-0.106-0.03070.49730.05380.4144-8.4886-60.9753-24.821
181.838-1.50021.01152.1853-0.12954.6928-0.5971-1.03920.15340.97140.31470.2406-2.2324-0.7602-0.18340.89620.35530.24590.90910.04560.8781-19.7885-46.0547-14.213
191.8863-1.1289-1.70990.99040.98251.6102-0.0670.175-0.52940.54190.3449-0.27830.54582.29290.4587-0.21160.58780.52261.2868-0.0770.65945.7391-64.634-34.8723
201.18180.9771.20791.01550.93391.21320.5160.17971.0462-0.10610.3072-0.5424-1.8358-0.13370.01350.86850.03330.15070.69270.18530.651-7.9124-56.8112-32.2351
210.5191-0.3955-0.70840.4679-0.06874.1619-0.15391.1383-0.76260.09910.32541.61270.1613-1.9874-1.11410.01150.14950.28050.93640.22071.3982-25.8267-60.2246-15.2914
223.20840.55671.08671.2632-0.25240.742-0.08190.70270.2422-0.1162-0.13670.4284-1.6597-0.8927-0.00870.9430.1813-0.05040.63720.20860.5099-13.3555-55.455914.0397
231.49930.5924-0.75122.65170.77241.4910.22630.63360.406-0.2148-0.15380.3151-0.5255-0.87980.06560.2047-0.0589-0.1131.01310.20450.501-20.1057-65.945216.6514
242.1196-0.4146-0.35332.0731-0.68461.8506-0.06090.5359-0.1612-0.09250.5725-0.5167-0.10030.36820.09840.4234-0.2150.11980.45670.10570.3446-6.7177-64.126923.7438
251.81330.5672-0.45032.17220.73583.5088-0.35851.1243-0.1528-0.18240.0942-0.00660.9865-0.3356-0.0590.4604-0.1968-0.09490.56670.01960.5754-19.9267-79.007314.4059
260.41380.16740.37330.72820.45480.4035-0.03260.41980.6586-0.35830.07770.0731-0.94851.0439-0.1318-0.4675-1.50880.17530.68340.48211.13028.1038-61.129532.837
271.4124-0.0586-0.90542.6260.36231.30390.45910.7647-0.76820.3790.0329-0.46560.71740.7859-0.00180.720.0079-0.09690.43920.02160.534-6.0614-68.142630.6794
28-0.0144-0.105-0.11520.29580.43520.6082-0.4461.02070.4817-0.30250.08610.7633-0.2692-1.0421-0.00060.7089-0.1166-0.19430.96530.17170.898-24.9445-64.718814.1023
292.59761.06570.29291.342-0.94331.1686-0.9668-1.1564-0.55920.64191.3436-0.41510.04860.24040.09651.140.635-0.4770.24470.4789-0.0879-10.8607-90.329252.2624
302.3693-1.0683-0.79742.39210.10040.81420.1123-0.53460.63930.1526-0.1858-0.65420.07810.3625-0.01230.6028-0.063-0.18160.61090.05420.7629-2.3874-82.844246.5234
311.51310.48990.46463.426-0.33721.37740.04880.0043-0.4283-0.0530.0378-0.10240.030.0925-0.00310.5606-0.0465-0.00190.3420.09460.3428-15.0448-85.166539.1781
324.0286-0.6922-0.25952.16080.09611.61810.448-0.1957-0.06080.2204-0.4511-0.9260.32420.77960.00070.7736-0.11760.03080.75270.23730.65125.5643-83.10536.5585
331.0379-0.8829-1.67541.02511.43322.67880.43680.9608-0.5221-0.6595-1.2030.8376-0.0437-1.33850.01220.3265-0.0803-0.17960.5127-0.06270.8164-31.7881-87.108932.3064
341.21870.7632-1.11640.7477-0.30011.3659-0.22750.65150.7477-0.4248-0.21440.0430.2171-0.0802-0.0050.47410.02-0.07340.32890.07570.659-17.8161-79.610334.1952
353.3558-3.6566-1.44376.28852.21922.0928-1.57-0.29751.28081.2385-0.2290.38240.1340.545-1.79420.7567-0.2059-0.14560.72660.02160.77421.2589-82.633849.8239
361.00320.1757-0.36170.74820.30970.73120.49940.21320.7651-2.0135-0.2209-1.0924-0.14450.16220.05770.45290.23180.18910.70780.18371.20912.0898-112.250246.6875
372.2799-0.9556-0.67792.5592-1.35011.45350.0009-0.4180.33950.08830.0289-0.6471-0.6180.76910.00930.53650.1687-0.30980.9789-0.0080.694311.894-111.912559.0443
382.73790.16311.89971.4626-0.99262.2508-0.1050.4499-0.0959-0.0289-0.3162-0.14190.4693-0.0309-0.05670.6670.2198-0.08270.58230.15910.60188.3622-124.045352.5579
392.8547-2.17370.25331.7715-0.18740.4483-0.4157-0.50250.32011.91260.52670.1577-0.51180.18520.01821.25070.0827-0.18680.7136-0.05920.65633.7505-112.04669.1369
400.60240.4533-0.18420.50270.07170.34240.20031.5251-0.6080.1292-0.41980.64860.31520.4551-0.06561.73660.213-0.4030.8578-0.32170.99664.6405-140.683543.4772
413.0127-1.692-0.07911.08370.02090.6413-0.29150.2014-0.09470.6536-0.60420.80050.1694-0.1102-0.02310.78510.1203-0.12540.5785-0.01740.77958.3476-131.665256.6174
420.03460.19460.1942.3222.06741.84750.0893-0.32160.11231.78890.0129-2.05110.23721.6529-0.19670.67260.1573-1.48490.8847-0.07260.572813.5092-109.114961.9655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 171 )
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 230 )
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 255 )
7X-RAY DIFFRACTION7chain 'A' and (resid 256 through 267 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 29 )
9X-RAY DIFFRACTION9chain 'B' and (resid 30 through 118 )
10X-RAY DIFFRACTION10chain 'B' and (resid 119 through 171 )
11X-RAY DIFFRACTION11chain 'B' and (resid 172 through 217 )
12X-RAY DIFFRACTION12chain 'B' and (resid 218 through 230 )
13X-RAY DIFFRACTION13chain 'B' and (resid 231 through 255 )
14X-RAY DIFFRACTION14chain 'B' and (resid 256 through 264 )
15X-RAY DIFFRACTION15chain 'C' and (resid 0 through 29 )
16X-RAY DIFFRACTION16chain 'C' and (resid 30 through 118 )
17X-RAY DIFFRACTION17chain 'C' and (resid 119 through 171 )
18X-RAY DIFFRACTION18chain 'C' and (resid 172 through 217 )
19X-RAY DIFFRACTION19chain 'C' and (resid 218 through 230 )
20X-RAY DIFFRACTION20chain 'C' and (resid 231 through 255 )
21X-RAY DIFFRACTION21chain 'C' and (resid 256 through 267 )
22X-RAY DIFFRACTION22chain 'D' and (resid 0 through 29 )
23X-RAY DIFFRACTION23chain 'D' and (resid 30 through 118 )
24X-RAY DIFFRACTION24chain 'D' and (resid 119 through 171 )
25X-RAY DIFFRACTION25chain 'D' and (resid 172 through 217 )
26X-RAY DIFFRACTION26chain 'D' and (resid 218 through 230 )
27X-RAY DIFFRACTION27chain 'D' and (resid 231 through 255 )
28X-RAY DIFFRACTION28chain 'D' and (resid 256 through 267 )
29X-RAY DIFFRACTION29chain 'E' and (resid 0 through 29 )
30X-RAY DIFFRACTION30chain 'E' and (resid 30 through 118 )
31X-RAY DIFFRACTION31chain 'E' and (resid 119 through 171 )
32X-RAY DIFFRACTION32chain 'E' and (resid 172 through 217 )
33X-RAY DIFFRACTION33chain 'E' and (resid 218 through 230 )
34X-RAY DIFFRACTION34chain 'E' and (resid 231 through 255 )
35X-RAY DIFFRACTION35chain 'E' and (resid 256 through 266 )
36X-RAY DIFFRACTION36chain 'F' and (resid 0 through 29 )
37X-RAY DIFFRACTION37chain 'F' and (resid 30 through 118 )
38X-RAY DIFFRACTION38chain 'F' and (resid 119 through 171 )
39X-RAY DIFFRACTION39chain 'F' and (resid 172 through 217 )
40X-RAY DIFFRACTION40chain 'F' and (resid 218 through 230 )
41X-RAY DIFFRACTION41chain 'F' and (resid 231 through 255 )
42X-RAY DIFFRACTION42chain 'F' and (resid 256 through 265 )

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