[English] 日本語
Yorodumi
- PDB-6r5y: 8-bladed beta-propeller formed by two 4-bladed fragments -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r5y
Title8-bladed beta-propeller formed by two 4-bladed fragments
ComponentsWD-40 repeat protein
KeywordsUNKNOWN FUNCTION / Repeat Protein / Fragment Amplification / Protein Evolution / Protein Design
Function / homology
Function and homology information


microtubule organizing center organization / microtubule plus-end binding / retrograde axonal transport / microtubule associated complex / dynein complex binding / cytoplasmic microtubule / kinetochore / neuron projection / neuronal cell body / membrane / metal ion binding
Similarity search - Function
Borrelia P83100 / Borrelia P83/100 protein / AAA-like domain / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...Borrelia P83100 / Borrelia P83/100 protein / AAA-like domain / Quinoprotein alcohol dehydrogenase-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
WD-40 repeat protein
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMartin, J. / Lupas, A.N. / Hartmann, M.D.
Citation
Journal: Elife / Year: 2019
Title: Structural diversity of oligomeric beta-propellers with different numbers of identical blades.
Authors: Afanasieva, E. / Chaudhuri, I. / Martin, J. / Hertle, E. / Ursinus, A. / Alva, V. / Hartmann, M.D. / Lupas, A.N.
#1: Journal: Elife / Year: 2019
Title: 8-bladed beta-propeller formed by four 2-bladed fragments
Authors: Hartmann, M.D.
History
DepositionMar 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: WD-40 repeat protein
B: WD-40 repeat protein
C: WD-40 repeat protein
D: WD-40 repeat protein
E: WD-40 repeat protein
F: WD-40 repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,03312
Polymers106,6416
Non-polymers3926
Water5,945330
1
A: WD-40 repeat protein
B: WD-40 repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8096
Polymers35,5472
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: WD-40 repeat protein
D: WD-40 repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6784
Polymers35,5472
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: WD-40 repeat protein
F: WD-40 repeat protein


Theoretical massNumber of molelcules
Total (without water)35,5472
Polymers35,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.721, 127.167, 72.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLYAA5 - 1657 - 167
21SERSERGLYGLYBB5 - 1657 - 167
12SERSERGLYGLYAA5 - 1657 - 167
22SERSERGLYGLYCC5 - 1657 - 167
13SERSERLEULEUAA5 - 1637 - 165
23SERSERLEULEUDD5 - 1637 - 165
14SERSERLEULEUAA5 - 1637 - 165
24SERSERLEULEUEE5 - 1637 - 165
15ALAALAHISHISAA0 - 1662 - 168
25ALAALAHISHISFF0 - 1662 - 168
16SERSERHISHISBB5 - 1667 - 168
26SERSERHISHISCC5 - 1667 - 168
17SERSERLEULEUBB5 - 1637 - 165
27SERSERLEULEUDD5 - 1637 - 165
18SERSERLEULEUBB5 - 1637 - 165
28SERSERLEULEUEE5 - 1637 - 165
19SERSERGLYGLYBB5 - 1657 - 167
29SERSERGLYGLYFF5 - 1657 - 167
110SERSERLEULEUCC5 - 1637 - 165
210SERSERLEULEUDD5 - 1637 - 165
111SERSERLEULEUCC5 - 1637 - 165
211SERSERLEULEUEE5 - 1637 - 165
112SERSERGLYGLYCC5 - 1657 - 167
212SERSERGLYGLYFF5 - 1657 - 167
113SERSERTHRTHRDD5 - 1647 - 166
213SERSERTHRTHREE5 - 1647 - 166
114SERSERLEULEUDD5 - 1637 - 165
214SERSERLEULEUFF5 - 1637 - 165
115SERSERLEULEUEE5 - 1637 - 165
215SERSERLEULEUFF5 - 1637 - 165

NCS ensembles :
ID
6
1
2
3
4
5
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
WD-40 repeat protein / 8-bladed beta-propeller formed by two 4-bladed fragments


Mass: 17773.471 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Gene: Npun_R6612 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J0I0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.01M Zinc chloride 0.1M Hepes pH 7 20% w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→38.7 Å / Num. obs: 49886 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 3.51 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 7918 / CC1/2: 0.726 / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YMU
Resolution: 2.15→38.7 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 15.751 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.224 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25368 2485 5 %RANDOM
Rwork0.2229 ---
obs0.22445 47400 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å20 Å2
2---0.37 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.15→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7350 0 6 330 7686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197510
X-RAY DIFFRACTIONr_bond_other_d0.0090.026894
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.90810246
X-RAY DIFFRACTIONr_angle_other_deg1.467315835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10125.419310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.636151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5661524
X-RAY DIFFRACTIONr_chiral_restr0.0790.21170
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028752
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021780
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6741.4333906
X-RAY DIFFRACTIONr_mcbond_other0.6741.4333905
X-RAY DIFFRACTIONr_mcangle_it1.1322.1484872
X-RAY DIFFRACTIONr_mcangle_other1.1322.1484873
X-RAY DIFFRACTIONr_scbond_it0.7351.5253603
X-RAY DIFFRACTIONr_scbond_other0.7351.5253603
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1872.2535373
X-RAY DIFFRACTIONr_long_range_B_refined4.58212.2238442
X-RAY DIFFRACTIONr_long_range_B_other4.54512.058373
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A86220.13
12B86220.13
21A86350.13
22C86350.13
31A85760.14
32D85760.14
41A85950.14
42E85950.14
51A89740.14
52F89740.14
61B89810.11
62C89810.11
71B89320.11
72D89320.11
81B89510.1
82E89510.1
91B86670.12
92F86670.12
101C90810.1
102D90810.1
111C89660.09
112E89660.09
121C87180.12
122F87180.12
131D90110.1
132E90110.1
141D86390.13
142F86390.13
151E86740.12
152F86740.12
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 184 -
Rwork0.333 3410 -
obs--98.28 %
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)
10.48071.954-1.31488.0904-5.38633.8448-0.0495-0.00480.0492-0.20670.09030.3450.3099-0.1123-0.04080.1722-0.01310.04440.2091-0.01160.271128.812675.465126.8014
26.723-0.37850.04521.32381.70644.21230.1204-0.66570.01590.25570.02710.16140.203-0.2994-0.14750.12510.03360.00610.12140.00690.247633.737184.837339.0566
36.81551.5017-0.97653.50120.65655.90290.0059-0.4472-0.07590.2456-0.05280.13660.12610.01470.04690.01950.00240.01260.0336-0.01680.208942.634279.551532.4654
44.25480.7774-0.87594.6844-0.60383.2598-0.12940.1155-0.17360.01930.189-0.29080.16310.1944-0.05960.01160.00910.00720.0275-0.0220.161143.087373.400322.224
52.23631.55350.46133.59352.29875.6511-0.1150.2948-0.1031-0.3304-0.05920.05220.17110.17960.17420.0710.04340.02320.093-0.0160.27134.616571.8313.4104
64.0032-0.78650.82162.0845-0.24722.96050.12490.3055-0.1661-0.3132-0.12740.10650.1227-0.06410.00250.08120.0117-0.0250.0329-0.00430.202322.409169.617612.2826
73.9963-0.97011.17054.1035-1.69634.84720.02370.1324-0.3664-0.39880.09950.31010.277-0.241-0.12310.0445-0.0198-0.02680.0224-0.00970.220312.699375.176216.0234
84.34610.22150.36193.0491-0.21134.4341-0.06610.0092-0.1481-0.01750.02120.33030.1255-0.43330.0450.0069-0.0130.0170.0433-0.01080.200512.248782.73225.4302
91.54010.64531.96893.57032.86473.7783-0.0132-0.03070.03570.27370.0208-0.08410.1584-0.017-0.00760.04920.01810.01420.00970.00790.264921.53486.978132.81
106.9381-0.1188-0.26895.864-3.68994.9437-0.00730.07970.1535-0.0631-0.04130.0829-0.2413-0.21030.04860.21080.0035-0.02540.1552-0.00890.249526.447351.0774-0.0522
116.6176-1.0037-1.5024.6984-0.90524.5440.1398-0.09560.3034-0.08860.0429-0.122-0.4091-0.0226-0.18270.0699-0.03610.00190.0595-0.00540.213737.540247.70832.3629
124.5754-0.5294-0.70127.322.72944.5327-0.0722-0.12170.06180.09690.1203-0.22540.03240.1884-0.04810.0073-0.01130.00080.05-0.00250.178741.03336.88576.0524
133.24560.5083-2.25418.3120.54061.6942-0.2498-0.0251-0.31280.51590.0916-0.16070.3004-0.01270.15820.2044-0.0412-0.08170.12590.00060.283234.021926.80598.2573
145.54650.96290.7318.00580.61862.79570.1492-0.3169-0.22650.7488-0.1547-0.42020.08710.18380.00560.18530.0105-0.00940.12720.01560.312122.666921.736912.7711
156.34740.58173.33624.4290.16026.116-0.0374-0.39-0.33330.3241-0.05170.16280.0118-0.21660.08910.0481-0.00020.00360.0825-0.00420.276111.444925.075210.8837
165.1498-0.21810.99514.28630.6738.3691-0.0795-0.1389-0.10650.0607-0.14480.3556-0.0493-0.47580.22440.13060.0022-0.03450.0832-0.00930.26518.043835.07715.1659
171.50830.03641.3486.9714-1.0011.928-0.21020.18950.2234-0.21410.070.0942-0.531-0.08050.14010.32570.0646-0.040.22310.05520.28414.919143.64290.0533
183.2553-1.61940.10639.8153-1.88322.52640.0212-0.2322-0.1997-0.13820.2351.0753-0.0916-0.5759-0.25620.08060.0052-0.00490.16920.07290.291716.159346.870129.0157
194.1994-0.5670.52387.5681-1.32232.16520.04010.2882-0.057-0.2737-0.02670.0511-0.0409-0.2162-0.01340.01770.01390.0210.0529-0.00710.159727.332843.424128.1782
204.25990.7645-0.313.90840.79491.68230.0660.14420.00090.0976-0.0432-0.2575-0.04160.1016-0.02280.0093-0.0065-0.03730.01840.02390.232936.272546.217835.6933
210.9002-0.79360.12737.37990.080.05560.1093-0.25970.00620.6628-0.0968-0.255-0.00940.0152-0.01250.3461-0.1135-0.07420.22510.02220.243236.255852.847345.7966
220.08520.9068-0.554210.6052-6.45283.92760.010.028-0.02590.4192-0.3281-0.5407-0.26090.17660.31810.4544-0.0417-0.04460.53420.0510.469122.716457.637141.2419
233.83013.42860.33236.5994.20084.7152-0.4980.2699-0.6239-0.37750.6839-0.9687-0.36060.7391-0.18590.7185-0.0545-0.11610.41290.10780.657529.996962.804354.1833
249.14464.48552.27348.40721.93033.8712-0.32860.50230.48050.31960.32160.2227-0.12870.19570.0070.31840.06090.09290.15520.03930.284217.819964.347154.3076
256.18784.5341-0.11687.56350.72954.9244-0.27750.13860.75980.25360.00261.0905-0.3244-0.05690.2750.1642-0.01810.05870.15860.04350.46888.9960.504447.2766
263.60820.9801-0.88193.66262.50079.5214-0.19480.3434-0.1309-0.195-0.21440.69930.1217-0.21240.40920.2031-0.0160.07190.3363-0.00960.40239.378651.836638.2329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9
2X-RAY DIFFRACTION2A10 - 42
3X-RAY DIFFRACTION3A43 - 83
4X-RAY DIFFRACTION4A84 - 124
5X-RAY DIFFRACTION5A125 - 9999
6X-RAY DIFFRACTION6B-10 - 42
7X-RAY DIFFRACTION7B43 - 83
8X-RAY DIFFRACTION8B84 - 124
9X-RAY DIFFRACTION9B125 - 9999
10X-RAY DIFFRACTION10C-10 - 42
11X-RAY DIFFRACTION11C43 - 83
12X-RAY DIFFRACTION12C84 - 124
13X-RAY DIFFRACTION13C125 - 9999
14X-RAY DIFFRACTION14D-10 - 42
15X-RAY DIFFRACTION15D43 - 83
16X-RAY DIFFRACTION16D84 - 124
17X-RAY DIFFRACTION17D125 - 9999
18X-RAY DIFFRACTION18E-10 - 42
19X-RAY DIFFRACTION19E43 - 83
20X-RAY DIFFRACTION20E84 - 124
21X-RAY DIFFRACTION21E125 - 9999
22X-RAY DIFFRACTION22F-10 - 9
23X-RAY DIFFRACTION23F10 - 42
24X-RAY DIFFRACTION24F43 - 83
25X-RAY DIFFRACTION25F84 - 124
26X-RAY DIFFRACTION26F125 - 9999

+
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