[English] 日本語
Yorodumi
- PDB-4drx: GTP-Tubulin in complex with a DARPIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4drx
TitleGTP-Tubulin in complex with a DARPIN
Components
  • Designed ankyrin repeat protein (DARPIN) D1
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / GTPASE / MICROTUBULE / DARPin / SUBTILISIN / TUBULIN / TUBULIN DIGESTED WITH SUBTILISIN
Function / homology
Function and homology information


axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / locomotory exploration behavior / startle response / microtubule polymerization / response to tumor necrosis factor / microtubule-based process / response to mechanical stimulus / homeostasis of number of cells within a tissue / condensed chromosome / cellular response to calcium ion / adult locomotory behavior / synapse organization / intracellular protein transport / neuron migration / neuromuscular junction / visual learning / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / cerebral cortex development / memory / recycling endosome / gene expression / neuron apoptotic process / microtubule / hydrolase activity / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin ...Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha chain
Similarity search - Component
Biological speciesARTIFICIAL GENE (others)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsPecqueur, L. / Gigant, B. / Knossow, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: A designed ankyrin repeat protein selected to bind to tubulin caps the microtubule plus end.
Authors: Pecqueur, L. / Duellberg, C. / Dreier, B. / Jiang, Q. / Wang, C. / Pluckthun, A. / Surrey, T. / Gigant, B. / Knossow, M.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin alpha chain
B: Tubulin beta chain
C: Tubulin alpha chain
D: Tubulin beta chain
E: Designed ankyrin repeat protein (DARPIN) D1
F: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,40814
Polymers230,2186
Non-polymers2,1908
Water6,215345
1
A: Tubulin alpha chain
B: Tubulin beta chain
F: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2047
Polymers115,1093
Non-polymers1,0954
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-21 kcal/mol
Surface area36490 Å2
MethodPISA
2
C: Tubulin alpha chain
D: Tubulin beta chain
E: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2047
Polymers115,1093
Non-polymers1,0954
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-20 kcal/mol
Surface area36350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.884, 90.596, 117.575
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'B' and (resseq 1:42 or resseq 45: 54 or...
211chain 'D' and (resseq 1:42 or resseq 45: 54 or...
112chain 'A' and (resseq 2:37 or resseq 47: 279 or...
212chain 'C' and (resseq 2:37 or resseq 47: 279 or...
113chain 'E' and (resseq 13:167 ) and (not element H)
213chain 'F' and (resseq 13:167 ) and (not element H)

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 3 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha chain


Mass: 48665.027 Da / Num. of mol.: 2 / Fragment: UNP residues 1-437 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWZ0
#2: Protein Tubulin beta chain


Mass: 48375.348 Da / Num. of mol.: 2 / Fragment: UNP residues 1-431 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9
#3: Protein Designed ankyrin repeat protein (DARPIN) D1


Mass: 18068.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTIFICIAL GENE (others) / Plasmid: PDST067 (pQE30 derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): XLIblue

-
Non-polymers , 3 types, 353 molecules

#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsAUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN ALPHA 1B ...AUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN ALPHA 1B SEQUENCE (UNP81947) WAS USED FOR REFINEMENT BECAUSE THE SEQUENCE OF OVINE BRAIN TUBULIN IS NOT AVAILABLE. FOR BETA-TUBULIN (CHAIN B AND CHAIN D), THERE ARE THREE MAJOR ISOTYPES EXPRESSED IN THE BRAIN. THEY USED THE BETA 2B ISOTYPE SEQUENCE (NCBI NP_ 999 001003900.1)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 292 K / pH: 7
Details: PEG 6K, 0.05M KCl, 0.01 M MGCL2, 0.2M LiCl, 0.01 M HEPES pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.48
ReflectionResolution: 2.22→39.19 Å / Num. obs: 104776 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.98 % / Rmerge(I) obs: 0.015 / Net I/σ(I): 12.38
Reflection shellResolution: 2.22→2.35 Å / Mean I/σ(I) obs: 2.08 / % possible all: 95

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RYC

3ryc


Resolution: 2.22→39.19 Å / σ(F): 1.38 / Phase error: 21.33 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.194 5421 5.17 %
Rwork0.159 --
obs0.161 104776 96.1 %
all-104780 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.8 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0205 Å20 Å23.1566 Å2
2--8.373 Å2-0 Å2
3----6.3526 Å2
Refinement stepCycle: LAST / Resolution: 2.22→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15529 0 132 345 16006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116039
X-RAY DIFFRACTIONf_angle_d0.80421824
X-RAY DIFFRACTIONf_dihedral_angle_d14.5275786
X-RAY DIFFRACTIONf_chiral_restr0.0582438
X-RAY DIFFRACTIONf_plane_restr0.0042842
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3291X-RAY DIFFRACTIONPOSITIONAL0.109
12D3291X-RAY DIFFRACTIONPOSITIONAL0.109
21A3224X-RAY DIFFRACTIONPOSITIONAL0.139
22C3224X-RAY DIFFRACTIONPOSITIONAL0.139
31E1131X-RAY DIFFRACTIONPOSITIONAL0.01
32F1131X-RAY DIFFRACTIONPOSITIONAL0.01
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2196-2.25790.28332580.2364851X-RAY DIFFRACTION90
2.2579-2.29890.24842600.23494927X-RAY DIFFRACTION91
2.2989-2.34310.26122530.22714928X-RAY DIFFRACTION91
2.3431-2.39090.26722700.22175012X-RAY DIFFRACTION91
2.3909-2.44290.23862580.21124920X-RAY DIFFRACTION91
2.4429-2.49970.25772600.21754981X-RAY DIFFRACTION91
2.4997-2.56220.24112610.20984977X-RAY DIFFRACTION92
2.5622-2.63150.25252550.19934954X-RAY DIFFRACTION92
2.6315-2.70890.26912680.20114991X-RAY DIFFRACTION92
2.7089-2.79630.26972570.19725002X-RAY DIFFRACTION92
2.7963-2.89630.24762580.19084984X-RAY DIFFRACTION92
2.8963-3.01220.24452600.18015001X-RAY DIFFRACTION92
3.0122-3.14920.21192650.17145003X-RAY DIFFRACTION92
3.1492-3.31520.1992650.16344990X-RAY DIFFRACTION92
3.3152-3.52270.21092580.15564998X-RAY DIFFRACTION92
3.5227-3.79450.15522660.13465007X-RAY DIFFRACTION91
3.7945-4.1760.14262590.11984989X-RAY DIFFRACTION92
4.176-4.77940.1582550.10685058X-RAY DIFFRACTION91
4.7794-6.0180.15942580.13484922X-RAY DIFFRACTION90
6.018-39.19780.13952750.13675038X-RAY DIFFRACTION90
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)
10.8742-0.1363-0.09650.75960.41661.7158-0.0102-0.0662-0.0960.01070.0056-0.03090.12280.1458-0.00720.0948-0.006-0.04290.12550.00070.18148.824610.3846-47.882
21.54580.2410.1621.26550.0191.50060.06430.30490.1757-0.071-0.11450.1246-0.0857-0.010.05750.186-0.0255-0.0190.24690.01390.213235.652820.8709-58.4517
30.6544-0.0682-0.50410.40540.19761.8810.04040.11050.0419-0.1175-0.07560.1451-0.1578-0.1980.03910.11-0.0015-0.08110.1421-0.01240.209933.093422.4836-53.848
41.9291-1.50531.48012.7325-2.31523.9464-0.1272-0.12660.34240.0715-0.01-0.1282-0.49290.30260.15590.2511-0.0976-0.07810.1144-0.08960.27843.969731.5903-35.0257
51.10170.3153-0.04491.60360.73561.2641-0.0141-0.02-0.55840.00940.0343-0.03930.55110.2169-0.01340.40210.1631-0.03340.27060.03590.484945.6672-11.4525-13.6454
61.0837-0.05280.22771.49360.03231.18070.0312-0.1568-0.18310.098-0.0758-0.19520.23150.2980.01920.21680.0237-0.07450.32510.06730.183444.04961.2184-5.3771
71.0324-0.16330.17820.9343-0.46621.85060.02070.0473-0.3776-0.15390.12320.13920.1164-0.1522-0.08860.1797-0.0352-0.06640.2362-0.01720.267228.24836.4951-18.3007
81.2796-0.05650.02040.35840.20811.60550.1537-0.0502-0.09870.2058-0.1885-0.1092-0.36490.48820.04840.2904-0.1118-0.06950.40770.00960.251840.572717.81934.3699
90.80180.03770.0180.50140.26342.1175-0.0385-0.08490.1077-0.00330.03580.0524-0.1750.44280.01050.1203-0.0225-0.06220.2207-0.00140.1769-4.056716.388-13.1738
101.4088-0.3045-0.09341.01780.08651.15460.03650.13770.05980.0061-0.07690.11060.0516-0.00470.06740.1791-0.0113-0.04520.24970.02870.243-17.50477.0389-1.7637
110.34270.38310.00690.43780.17312.43310.0419-0.1335-0.10490.1043-0.15240.1160.1562-0.23340.09180.16060.0105-0.0430.17560.03480.1791-19.57115.1217-6.9337
122.72551.9199-2.55643.1051-2.53265.32910.1114-0.1257-0.2652-0.0846-0.1474-0.07530.36060.26840.08870.27950.0453-0.07150.2382-0.03960.242-8.8414-4.4704-25.4011
130.7519-0.3018-0.14941.45660.14421.44850.0274-0.14280.14490.1941-0.0066-0.198-0.55320.19890.01990.2827-0.1806-0.12640.13960.03520.3256-6.841338.1-42.2185
140.8298-0.1924-0.42990.64690.43211.60930.09630.070.1841-0.0482-0.0936-0.1212-0.28710.32080.00870.2365-0.0652-0.03510.14070.03070.2673-6.866427.9865-54.9299
151.0767-0.0070.03890.5258-0.59071.790.0333-0.13810.06660.0620.01920.1441-0.2032-0.2704-0.03020.19040.0144-0.02910.2149-0.01110.2279-23.718220.9357-42.0517
161.09610.0007-0.09420.66360.02112.14720.04570.1038-0.0515-0.1048-0.1381-0.0810.31410.17380.0850.30020.0591-0.04420.1478-0.00740.2059-11.71469.086-64.636
171.9249-0.0858-1.09651.92420.34024.22610.05080.25730.2033-0.6294-0.0953-0.7645-0.27390.21010.10370.4856-0.11270.05380.27930.04680.2571-6.11920.0222-96.7256
181.36290.1517-0.35970.90380.47662.2505-0.1324-0.02140.0392-0.09770.05880.0808-0.0839-0.08320.0530.27190.0692-0.04520.28040.00870.1907-21.724316.1063-86.2781
191.3844-0.2460.0462.51820.78942.0765-0.2627-0.027-0.13010.120.05110.61850.0348-0.68120.18610.315-0.02660.09310.50040.03740.3414-33.288413.1592-69.9207
202.9372-0.53070.83253.44310.67895.59420.12490.1788-0.2292-0.09810.0518-0.39330.19330.3862-0.12210.3505-0.0305-0.09820.63070.04460.363646.36297.504333.7971
211.24230.0901-0.20291.52470.41332.2978-0.13380.0037-0.03020.10360.00320.06220.0649-0.13710.09750.2922-0.0688-0.09850.31430.0420.142130.7610.746326.8295
220.6660.6780.53223.50771.15662.4068-0.1390.586-0.3497-0.21590.0681-0.0955-0.4437-0.33830.04470.3545-0.0021-0.19910.8666-0.05870.527919.448813.21228.3584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:244)
2X-RAY DIFFRACTION2(chain A and resid 245:301)
3X-RAY DIFFRACTION3(chain A and resid 302:407)
4X-RAY DIFFRACTION4(chain A and resid 408:437)
5X-RAY DIFFRACTION5(chain B and resid 1:88)
6X-RAY DIFFRACTION6(chain B and resid 89:249)
7X-RAY DIFFRACTION7(chain B and resid 250:393)
8X-RAY DIFFRACTION8(chain B and resid 394:441)
9X-RAY DIFFRACTION9(chain C and resid 2:244)
10X-RAY DIFFRACTION10(chain C and resid 245:301)
11X-RAY DIFFRACTION11(chain C and resid 302:407)
12X-RAY DIFFRACTION12(chain C and resid 408:437)
13X-RAY DIFFRACTION13(chain D and resid 1:59)
14X-RAY DIFFRACTION14(chain D and resid 60:248)
15X-RAY DIFFRACTION15(chain D and resid 249:393)
16X-RAY DIFFRACTION16(chain D and resid 394:441)
17X-RAY DIFFRACTION17(chain E and resid 13:37)
18X-RAY DIFFRACTION18(chain E and resid 38:137)
19X-RAY DIFFRACTION19(chain E and resid 138:168)
20X-RAY DIFFRACTION20(chain F and resid 13:28)
21X-RAY DIFFRACTION21(chain F and resid 29:142)
22X-RAY DIFFRACTION22(chain F and resid 143:167)

+
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