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- PDB-6o5m: Tubulin-RB3_SLD-TTL in complex with compound 10bb -

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Basic information

Entry
Database: PDB / ID: 6o5m
TitleTubulin-RB3_SLD-TTL in complex with compound 10bb
Components
  • Stathmin-4
  • Tubulin Tyrosine Ligase
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / Microtubule Inhibitor / Colchicine / Cancer
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Recruitment of NuMA to mitotic centrosomes / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / COPI-mediated anterograde transport / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / growth cone / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 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 / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-G8K / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin tyrosine ligase / Tubulin beta chain / Tubulin alpha-1B chain / Stathmin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKumar, G. / Wang, Y. / Li, W. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA148706 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Guided Design, Synthesis, and Biological Evaluation of (2-(1H-Indol-3-yl)-1H-imidazol-4-yl)(3,4,5-trimethoxyphenyl) Methanone (ABI-231) Analogues Targeting the Colchicine Binding Site in Tubulin.
Authors: Wang, Q. / Arnst, K.E. / Wang, Y. / Kumar, G. / Ma, D. / White, S.W. / Miller, D.D. / Li, W. / Li, W.
History
DepositionMar 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_label_seq_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.ptnr1_label_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,33023
Polymers261,3056
Non-polymers4,02517
Water13,836768
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.966, 157.721, 181.615
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 1 through 283 or (resid 284...
21(chain C and (resid 1 through 89 or (resid 90...
12(chain B and (resid 2 through 14 or (resid 15...
22(chain D and (resid 2 through 319 or (resid 320...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETHISHIS(chain A and (resid 1 through 283 or (resid 284...AA1 - 2831 - 283
121GLUGLUGLNGLN(chain A and (resid 1 through 283 or (resid 284...AA284 - 285284 - 285
131METMETGTPGTP(chain A and (resid 1 through 283 or (resid 284...AA - G1 - 5011
141METMETGTPGTP(chain A and (resid 1 through 283 or (resid 284...AA - G1 - 5011
151METMETGTPGTP(chain A and (resid 1 through 283 or (resid 284...AA - G1 - 5011
161METMETGTPGTP(chain A and (resid 1 through 283 or (resid 284...AA - G1 - 5011
211METMETPROPRO(chain C and (resid 1 through 89 or (resid 90...CC1 - 891 - 89
221GLUGLUGLUGLU(chain C and (resid 1 through 89 or (resid 90...CC9090
231METMETGTPGTP(chain C and (resid 1 through 89 or (resid 90...CC - Q1 - 5011
112ARGARGASNASN(chain B and (resid 2 through 14 or (resid 15...BB2 - 142 - 14
122GLNGLNGLNGLN(chain B and (resid 2 through 14 or (resid 15...BB1515
132ARGARGGDPGDP(chain B and (resid 2 through 14 or (resid 15...BB - K2 - 5012
142ARGARGGDPGDP(chain B and (resid 2 through 14 or (resid 15...BB - K2 - 5012
152ARGARGGDPGDP(chain B and (resid 2 through 14 or (resid 15...BB - K2 - 5012
212ARGARGGLYGLY(chain D and (resid 2 through 319 or (resid 320...DD2 - 3192 - 319
222ARGARGARGARG(chain D and (resid 2 through 319 or (resid 320...DD320320
232METMETGTPGTP(chain D and (resid 2 through 319 or (resid 320...DD - T1 - 5011

NCS ensembles :
ID
1
2

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7, UniProt: P02554*PLUS
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STMN4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H169
#4: Protein Tubulin Tyrosine Ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

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Non-polymers , 9 types, 785 molecules

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


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-G8K / [2-(1H-indol-4-yl)-1H-imidazol-4-yl](3,4,5-trimethoxyphenyl)methanone


Mass: 377.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19N3O4 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG 4000, 5% Glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 135595 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 29.88 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.032 / Rrim(I) all: 0.113 / Χ2: 0.999 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.3-2.341367250.7980.2890.98299.8
2.34-2.381366570.8360.2530.97599.90.8890.925
2.38-2.4312.966960.8630.2210.98799.90.7730.804
2.43-2.4812.867330.9040.1870.99599.90.6520.679
2.48-2.5312.567250.9210.165199.90.5660.59
2.53-2.5911.866810.9250.1471.02899.80.4920.514
2.59-2.6613.467630.9570.1171.0351000.4190.436
2.66-2.7313.567120.9650.1071.0531000.3840.399
2.73-2.8113.567510.9780.0850.9971000.3050.317
2.81-2.913.467410.9850.070.9931000.250.26
2.9-313.267490.9890.060.9961000.210.219
3-3.1212.667490.9910.0480.9891000.1640.171
3.12-3.2613.167470.9940.0391.021000.1360.141
3.26-3.4413.967970.9960.0311.0121000.1120.116
3.44-3.6513.868000.9970.0261.0151000.0920.096
3.65-3.9313.568120.9970.0221.0031000.0780.081
3.93-4.3312.868290.9970.020.96399.80.0680.071
4.33-4.951468540.9980.0170.9691000.0630.066
4.95-6.2412.968900.9970.0180.91699.50.0650.067
6.24-5013.171840.9980.0181.05799.60.0610.064

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.763 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.29
RfactorNum. reflection% reflection
Rfree0.2233 7667 5.67 %
Rwork0.1899 --
obs0.1918 135167 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.05 Å2 / Biso mean: 43.5603 Å2 / Biso min: 14.01 Å2
Refinement stepCycle: final / Resolution: 2.3→49.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16842 0 253 768 17863
Biso mean--42.19 41.74 -
Num. residues----2172
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2620X-RAY DIFFRACTION6.519TORSIONAL
12C2620X-RAY DIFFRACTION6.519TORSIONAL
21B2478X-RAY DIFFRACTION6.519TORSIONAL
22D2478X-RAY DIFFRACTION6.519TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2876-2.31360.26472040.24373570377484
2.3136-2.34080.28232380.23774189442798
2.3408-2.36930.26072380.23714203444199
2.3693-2.39930.28632720.24074210448299
2.3993-2.43090.25822420.230342334475100
2.4309-2.46420.26582650.226842034468100
2.4642-2.49940.26922490.222742814530100
2.4994-2.53670.25932450.221641784423100
2.5367-2.57630.24582490.219442674516100
2.5763-2.61860.26292730.207542344507100
2.6186-2.66370.26132470.206442294476100
2.6637-2.71210.23992370.216542934530100
2.7121-2.76430.27082700.212542654535100
2.7643-2.82070.25412660.217542284494100
2.8207-2.88210.25972670.208342264493100
2.8821-2.94910.24532790.21642464525100
2.9491-3.02280.27492490.212742704519100
3.0228-3.10450.25282560.209842934549100
3.1045-3.19590.22012260.19942954521100
3.1959-3.2990.24012580.196242734531100
3.299-3.41690.21962500.191242814531100
3.4169-3.55370.2072500.181642814531100
3.5537-3.71540.2212810.176142764557100
3.7154-3.91120.17952440.163743304574100
3.9112-4.15610.18592690.157842784547100
4.1561-4.47680.18082690.14943064575100
4.4768-4.9270.17512680.145843404608100
4.927-5.63910.21792630.172943534616100
5.6391-7.10130.22712640.19734376464099
7.1013-49.77470.19322790.17914493477298
Refinement TLS params.Method: refined / Origin x: 17.2025 Å / Origin y: -44.2781 Å / Origin z: -25.8948 Å
111213212223313233
T0.0934 Å2-0.0071 Å2-0.0109 Å2-0.1951 Å2-0.0195 Å2--0.2391 Å2
L0.1328 °20.0194 °20.0867 °2-0.6557 °20.6274 °2--1.083 °2
S-0.0332 Å °-0.0138 Å °-0.0118 Å °-0.009 Å °0.0918 Å °-0.0205 Å °0.0002 Å °0.0687 Å °-0.0432 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 501
2X-RAY DIFFRACTION1allB2 - 501
3X-RAY DIFFRACTION1allC1 - 501
4X-RAY DIFFRACTION1allD1 - 501
5X-RAY DIFFRACTION1allE6 - 140
6X-RAY DIFFRACTION1allF1 - 380
7X-RAY DIFFRACTION1allM1 - 2
8X-RAY DIFFRACTION1allN1 - 2
9X-RAY DIFFRACTION1allH1 - 4
10X-RAY DIFFRACTION1allP1
11X-RAY DIFFRACTION1allG2 - 3
12X-RAY DIFFRACTION1allI1 - 2
13X-RAY DIFFRACTION1allS1 - 768

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