[English] 日本語
Yorodumi
- PDB-6mze: Structural Basis of Tubulin Recruitment and Assembly by Microtubu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mze
TitleStructural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with Tumor Overexpressed Gene (TOG) Domain Arrays
Components
  • Designed ankyrin repeat protein (DARPIN) D1
  • Protein Stu2p/Alp14p
  • Tubulin alpha-1A chain
  • Tubulin beta chain
KeywordsCELL CYCLE / Microtubule / Tubulin / Tubulin polymerization / Heat repeats / Microtubule polymerase / TOG arrays / and Wheel-like assembly.
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / mitotic cell cycle / microtubule / hydrolase activity / cell cycle / cell division / GTPase activity ...Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / mitotic cell cycle / microtubule / hydrolase activity / cell cycle / cell division / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin ...CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 / Armadillo-like helical / Alpha Horseshoe / Helix Hairpins / Armadillo-type fold / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Protein STU1 / Tubulin alpha-1A chain / Tubulin beta chain
Similarity search - Component
Biological speciesLachancea kluyveri NRRL Y-12651 (fungus)
Escherichia coli (E. coli)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsNithianantham, S. / Al-Bassam, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110283 United States
CitationJournal: Elife / Year: 2018
Title: Structural basis of tubulin recruitment and assembly by microtubule polymerases with Tumor Overexpressed Gene (TOG) domain arrays.
Authors: Nithianantham, S. / Cook, B.D. / Beans, M. / Guo, F. / Chang, F. / Al-Bassam, J.
History
DepositionNov 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin alpha-1A chain
B: Tubulin beta chain
C: Tubulin alpha-1A chain
D: Tubulin beta chain
E: Protein Stu2p/Alp14p
F: Designed ankyrin repeat protein (DARPIN) D1
G: Designed ankyrin repeat protein (DARPIN) D1
H: Tubulin alpha-1A chain
I: Tubulin beta chain
J: Tubulin alpha-1A chain
K: Tubulin beta chain
L: Protein Stu2p/Alp14p
M: Designed ankyrin repeat protein (DARPIN) D1
N: Designed ankyrin repeat protein (DARPIN) D1
O: Tubulin alpha-1A chain
P: Tubulin beta chain
Q: Tubulin alpha-1A chain
R: Tubulin beta chain
S: Protein Stu2p/Alp14p
T: Designed ankyrin repeat protein (DARPIN) D1
U: Designed ankyrin repeat protein (DARPIN) D1
V: Tubulin alpha-1A chain
W: Tubulin beta chain
X: Tubulin alpha-1A chain
Y: Tubulin beta chain
Z: Protein Stu2p/Alp14p
a: Designed ankyrin repeat protein (DARPIN) D1
b: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,196,45960
Polymers1,188,33928
Non-polymers8,12032
Water00
1
A: Tubulin alpha-1A chain
B: Tubulin beta chain
C: Tubulin alpha-1A chain
D: Tubulin beta chain
E: Protein Stu2p/Alp14p
F: Designed ankyrin repeat protein (DARPIN) D1
G: Designed ankyrin repeat protein (DARPIN) D1
H: Tubulin alpha-1A chain
I: Tubulin beta chain
J: Tubulin alpha-1A chain
K: Tubulin beta chain
L: Protein Stu2p/Alp14p
M: Designed ankyrin repeat protein (DARPIN) D1
N: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)598,22930
Polymers594,16914
Non-polymers4,06016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
O: Tubulin alpha-1A chain
P: Tubulin beta chain
Q: Tubulin alpha-1A chain
R: Tubulin beta chain
S: Protein Stu2p/Alp14p
T: Designed ankyrin repeat protein (DARPIN) D1
U: Designed ankyrin repeat protein (DARPIN) D1
V: Tubulin alpha-1A chain
W: Tubulin beta chain
X: Tubulin alpha-1A chain
Y: Tubulin beta chain
Z: Protein Stu2p/Alp14p
a: Designed ankyrin repeat protein (DARPIN) D1
b: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)598,22930
Polymers594,16914
Non-polymers4,06016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.480, 106.150, 282.230
Angle α, β, γ (deg.)90.000, 90.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain H
41chain J
51chain O
61chain Q
71chain V
81chain X
12(chain B and resid 1 through 600)
22(chain D and resid 1 through 600)
32(chain I and resid 1 through 600)
42chain K
52(chain P and resid 1 through 600)
62(chain R and resid 1 through 600)
72(chain W and resid 1 through 600)
82(chain Y and resid 1 through 600)
13(chain E and (resid 14 through 258 or resid 297 through 543))
23(chain L and (resid 14 through 258 or (resid 297...
33chain S
43(chain Z and (resid 14 through 258 or resid 297 through 543))
14chain F
24chain G
34chain M
44chain N
54chain T
64chain U
74chain a
84chain b

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
111ARGARGMGMGchain AAA - DA2 - 6012
211ARGARGMGMGchain CCC - HA2 - 6012
311ARGARGMGMGchain HHH - LA2 - 6012
411ARGARGMGMGchain JJJ - PA2 - 6012
511ARGARGMGMGchain OOO - TA2 - 6012
611ARGARGMGMGchain QQQ - XA2 - 6012
711ARGARGMGMGchain VVV - BB2 - 6012
811ARGARGMGMGchain XXX - FB2 - 6012
112METMETGDPGDP(chain B and resid 1 through 600)BB - EA1 - 6001
212METMETGDPGDP(chain D and resid 1 through 600)DD - IA1 - 6001
312METMETGDPGDP(chain I and resid 1 through 600)II - MA1 - 6001
412METMETMGMGchain KKK - RA1 - 6011
512METMETGDPGDP(chain P and resid 1 through 600)PP - UA1 - 6001
612METMETGDPGDP(chain R and resid 1 through 600)RR - YA1 - 6001
712METMETGDPGDP(chain W and resid 1 through 600)WW - CB1 - 6001
812METMETGDPGDP(chain Y and resid 1 through 600)YY - GB1 - 6001
113LEULEUPROPRO(chain E and (resid 14 through 258 or resid 297 through 543))EE14 - 25814 - 258
123ASNASNVALVAL(chain E and (resid 14 through 258 or resid 297 through 543))EE297 - 543279 - 525
213LEULEUPROPRO(chain L and (resid 14 through 258 or (resid 297...LL14 - 25814 - 258
223ASNASNALAALA(chain L and (resid 14 through 258 or (resid 297...LL297 - 298279 - 280
233LEULEUVALVAL(chain L and (resid 14 through 258 or (resid 297...LL14 - 54314 - 525
243LEULEUVALVAL(chain L and (resid 14 through 258 or (resid 297...LL14 - 54314 - 525
253LEULEUVALVAL(chain L and (resid 14 through 258 or (resid 297...LL14 - 54314 - 525
263LEULEUVALVAL(chain L and (resid 14 through 258 or (resid 297...LL14 - 54314 - 525
313LEULEUVALVALchain SSS14 - 54314 - 525
413LEULEUPROPRO(chain Z and (resid 14 through 258 or resid 297 through 543))ZZ14 - 25814 - 258
423ASNASNVALVAL(chain Z and (resid 14 through 258 or resid 297 through 543))ZZ297 - 543279 - 525
114ASPASPLYSLYSchain FFF13 - 16713 - 167
214ASPASPLYSLYSchain GGG13 - 16713 - 167
314ASPASPLYSLYSchain MMM13 - 16713 - 167
414ASPASPLYSLYSchain NNN13 - 16713 - 167
514ASPASPLYSLYSchain TTT13 - 16713 - 167
614ASPASPLYSLYSchain UUU13 - 16713 - 167
714ASPASPLYSLYSchain aaAA13 - 16713 - 167
814ASPASPLYSLYSchain bbBA13 - 16713 - 167

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein , 4 types, 28 molecules ACHJOQVXBDIKPRWYELSZFGMNTUab

#1: Protein
Tubulin alpha-1A chain / Alpha-tubulin 1 / Tubulin alpha-1 chain


Mass: 50121.266 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / References: UniProt: P02550
#2: Protein
Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / References: UniProt: P02554
#3: Protein
Protein Stu2p/Alp14p


Mass: 60889.758 Da / Num. of mol.: 4
Mutation: 256-297 residue linkers were replaced by the shorter linker (AVPAQSDNNSTLQTDKDGDTLMGN)
Source method: isolated from a genetically manipulated source
Details: Linker residues (256-297, QKEQEQEQEQILQTDKDGDTLMGNLLAYQDTNASAIHPATKP)were replaced by shorter linker (AVPAQSDNNSTLQTDKDGDTLMGN) Shorter linker:AVPAQSDNN - InsertionLLAYQDTNASAIHPATKP - deletion
Source: (gene. exp.) Lachancea kluyveri NRRL Y-12651 (fungus)
Gene: SKLU-Cont10078 / Plasmid: pLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A493R6X7*PLUS
#4: Protein
Designed ankyrin repeat protein (DARPIN) D1


Mass: 18068.439 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Darpin was synthesized and inserted into bacterial expression vector.
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET303 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21

-
Non-polymers , 3 types, 32 molecules

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


Mass: 523.180 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.34 % / Description: Cube-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM PIPES, 100 mM MgCl2 [pH 7.0], and 10-15% PEG-8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2014
RadiationMonochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.01
ReflectionResolution: 3.6→59.453 Å / Num. obs: 142673 / % possible obs: 95 % / Redundancy: 2.7 % / Biso Wilson estimate: 81.4 Å2 / Rpim(I) all: 0.115 / Rrim(I) all: 0.199 / Rsym value: 0.134 / Net I/av σ(I): 5.2 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3.6-3.792.70.651.2211240.5811.0070.6596.7
3.79-4.022.70.4391.7200290.3860.6710.43997.1
4.02-4.32.60.2932.6184450.2570.4440.29395
4.3-4.652.50.1784.2168010.1640.280.17892.8
4.65-5.092.80.1365.4161020.1160.2050.13696.6
5.09-5.692.70.1475.1143100.1270.220.14794.7
5.69-6.572.70.1226.1123770.1040.180.12292.6
6.57-8.052.80.0759.3107930.0610.1070.07595.4
8.05-11.382.60.03815.881060.030.0530.03892
11.38-59.4532.70.03614.445860.0280.0480.03692

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.21data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→59.453 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.94 / Details: The twin fractions were adjusted during refinement
RfactorNum. reflection% reflection
Rfree0.245 5975 4.9 %
Rwork0.2022 --
obs0.2059 121943 79.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 92.9 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 366.95 Å2 / Biso mean: 98.3165 Å2 / Biso min: 3.6 Å2
Refinement stepCycle: final / Resolution: 3.6→59.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms77382 0 496 0 77878
Biso mean--91.5 --
Num. residues----9981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.634
X-RAY DIFFRACTIONf_chiral_restr0.042
X-RAY DIFFRACTIONf_plane_restr0.006
X-RAY DIFFRACTIONf_dihedral_angle_d5.932
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10344X-RAY DIFFRACTION5.192TORSIONAL
12C10344X-RAY DIFFRACTION5.192TORSIONAL
13H10344X-RAY DIFFRACTION5.192TORSIONAL
14J10344X-RAY DIFFRACTION5.192TORSIONAL
15O10344X-RAY DIFFRACTION5.192TORSIONAL
16Q10344X-RAY DIFFRACTION5.192TORSIONAL
17V10344X-RAY DIFFRACTION5.192TORSIONAL
18X10344X-RAY DIFFRACTION5.192TORSIONAL
21B10368X-RAY DIFFRACTION5.192TORSIONAL
22D10368X-RAY DIFFRACTION5.192TORSIONAL
23I10368X-RAY DIFFRACTION5.192TORSIONAL
24K10368X-RAY DIFFRACTION5.192TORSIONAL
25P10368X-RAY DIFFRACTION5.192TORSIONAL
26R10368X-RAY DIFFRACTION5.192TORSIONAL
27W10368X-RAY DIFFRACTION5.192TORSIONAL
28Y10368X-RAY DIFFRACTION5.192TORSIONAL
31E5916X-RAY DIFFRACTION5.192TORSIONAL
32L5916X-RAY DIFFRACTION5.192TORSIONAL
33S5916X-RAY DIFFRACTION5.192TORSIONAL
34Z5916X-RAY DIFFRACTION5.192TORSIONAL
41F3704X-RAY DIFFRACTION5.192TORSIONAL
42G3704X-RAY DIFFRACTION5.192TORSIONAL
43M3704X-RAY DIFFRACTION5.192TORSIONAL
44N3704X-RAY DIFFRACTION5.192TORSIONAL
45T3704X-RAY DIFFRACTION5.192TORSIONAL
46U3704X-RAY DIFFRACTION5.192TORSIONAL
47a3704X-RAY DIFFRACTION5.192TORSIONAL
48b3704X-RAY DIFFRACTION5.192TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.64730.2195670.24261047X-RAY DIFFRACTION14
3.6473-3.71360.19951010.21172230X-RAY DIFFRACTION30
3.7136-3.7850.22351220.22991X-RAY DIFFRACTION39
3.785-3.86230.2281950.18993591X-RAY DIFFRACTION48
3.8623-3.94620.22762160.18394148X-RAY DIFFRACTION55
3.9462-4.03790.21262410.18054776X-RAY DIFFRACTION63
4.0379-4.13880.23092880.18145296X-RAY DIFFRACTION70
4.1388-4.25070.22083080.17755914X-RAY DIFFRACTION77
4.2507-4.37560.21753340.17546411X-RAY DIFFRACTION85
4.3756-4.51680.20363680.1637012X-RAY DIFFRACTION93
4.5168-4.6780.21723810.16927236X-RAY DIFFRACTION95
4.678-4.86510.23573670.17457236X-RAY DIFFRACTION95
4.8651-5.08630.23833720.187229X-RAY DIFFRACTION95
5.0863-5.3540.25423860.19667175X-RAY DIFFRACTION95
5.354-5.68890.2833550.21537206X-RAY DIFFRACTION94
5.6889-6.12710.2683330.22547180X-RAY DIFFRACTION94
6.1271-6.74190.30073730.24227276X-RAY DIFFRACTION95
6.7419-7.71330.27253630.23717268X-RAY DIFFRACTION95
7.7133-9.70220.24124020.21017236X-RAY DIFFRACTION93
9.7022-45.25870.27994030.25517436X-RAY DIFFRACTION94

+
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://pdbjlvh1.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