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- PDB-6j2z: AtFKBP53 N-terminal Nucleoplasmin Domain -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6j2z
TitleAtFKBP53 N-terminal Nucleoplasmin Domain
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP53
KeywordsCHAPERONE / FKBP / FKBP-nucleoplasmin / histone chaperone
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nucleosome assembly / histone binding / nucleolus / nucleus
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase Fpr3/Fpr4-like / Nucleoplasmin-like domain / Nucleoplasmin-like domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP53
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSingh, A.K. / Vasudevan, D.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: AtFKBP53: a chimeric histone chaperone with functional nucleoplasmin and PPIase domains.
Authors: Singh, A.K. / Datta, A. / Jobichen, C. / Luan, S. / Vasudevan, D.
History
DepositionJan 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
F: Peptidyl-prolyl cis-trans isomerase FKBP53
G: Peptidyl-prolyl cis-trans isomerase FKBP53
H: Peptidyl-prolyl cis-trans isomerase FKBP53
I: Peptidyl-prolyl cis-trans isomerase FKBP53
J: Peptidyl-prolyl cis-trans isomerase FKBP53
A: Peptidyl-prolyl cis-trans isomerase FKBP53
B: Peptidyl-prolyl cis-trans isomerase FKBP53
C: Peptidyl-prolyl cis-trans isomerase FKBP53
D: Peptidyl-prolyl cis-trans isomerase FKBP53
E: Peptidyl-prolyl cis-trans isomerase FKBP53


Theoretical massNumber of molelcules
Total (without water)121,11610
Polymers121,11610
Non-polymers00
Water68538
1
F: Peptidyl-prolyl cis-trans isomerase FKBP53
G: Peptidyl-prolyl cis-trans isomerase FKBP53
H: Peptidyl-prolyl cis-trans isomerase FKBP53
I: Peptidyl-prolyl cis-trans isomerase FKBP53
J: Peptidyl-prolyl cis-trans isomerase FKBP53


Theoretical massNumber of molelcules
Total (without water)60,5585
Polymers60,5585
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-52 kcal/mol
Surface area19560 Å2
MethodPISA
2
A: Peptidyl-prolyl cis-trans isomerase FKBP53
B: Peptidyl-prolyl cis-trans isomerase FKBP53
C: Peptidyl-prolyl cis-trans isomerase FKBP53
D: Peptidyl-prolyl cis-trans isomerase FKBP53
E: Peptidyl-prolyl cis-trans isomerase FKBP53


Theoretical massNumber of molelcules
Total (without water)60,5585
Polymers60,5585
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-49 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.590, 97.390, 96.430
Angle α, β, γ (deg.)90.00, 94.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21H
12G
22I
13G
23J
14G
24A
15G
25B
16G
26C
17G
27D
18G
28E
19H
29I
110H
210J
111H
211A
112H
212B
113H
213C
114H
214D
115H
215E
116I
216J
117I
217A
118I
218B
119I
219C
120I
220D
121I
221E
122J
222A
123J
223B
124J
224C
125J
225D
126J
226E
127A
227B
128A
228C
129A
229D
130A
230E
131B
231C
132B
232D
133B
233E
134C
234D
135C
235E
136D
236E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEGLUGLUGB3 - 963 - 96
21PHEPHEGLUGLUHC3 - 963 - 96
12PHEPHEGLUGLUGB3 - 963 - 96
22PHEPHEGLUGLUID3 - 963 - 96
13PHEPHEGLUGLUGB3 - 963 - 96
23PHEPHEGLUGLUJE3 - 963 - 96
14PHEPHEGLUGLUGB3 - 963 - 96
24PHEPHEGLUGLUAF3 - 963 - 96
15PHEPHEGLUGLUGB3 - 963 - 96
25PHEPHEGLUGLUBG3 - 963 - 96
16PHEPHEGLUGLUGB3 - 963 - 96
26PHEPHEGLUGLUCH3 - 963 - 96
17PHEPHEGLUGLUGB3 - 963 - 96
27PHEPHEGLUGLUDI3 - 963 - 96
18PHEPHEGLUGLUGB3 - 963 - 96
28PHEPHEGLUGLUEJ3 - 963 - 96
19GLYGLYTYRTYRHC2 - 972 - 97
29GLYGLYTYRTYRID2 - 972 - 97
110PHEPHELEULEUHC3 - 953 - 95
210PHEPHELEULEUJE3 - 953 - 95
111GLYGLYTYRTYRHC2 - 972 - 97
211GLYGLYTYRTYRAF2 - 972 - 97
112GLYGLYGLUGLUHC2 - 962 - 96
212GLYGLYGLUGLUBG2 - 962 - 96
113GLYGLYTYRTYRHC2 - 972 - 97
213GLYGLYTYRTYRCH2 - 972 - 97
114GLYGLYTYRTYRHC2 - 972 - 97
214GLYGLYTYRTYRDI2 - 972 - 97
115GLYGLYTYRTYRHC2 - 972 - 97
215GLYGLYTYRTYREJ2 - 972 - 97
116PHEPHELEULEUID3 - 953 - 95
216PHEPHELEULEUJE3 - 953 - 95
117GLYGLYTYRTYRID2 - 972 - 97
217GLYGLYTYRTYRAF2 - 972 - 97
118GLYGLYGLUGLUID2 - 962 - 96
218GLYGLYGLUGLUBG2 - 962 - 96
119GLYGLYTYRTYRID2 - 972 - 97
219GLYGLYTYRTYRCH2 - 972 - 97
120GLYGLYTYRTYRID2 - 972 - 97
220GLYGLYTYRTYRDI2 - 972 - 97
121GLYGLYTYRTYRID2 - 972 - 97
221GLYGLYTYRTYREJ2 - 972 - 97
122PHEPHELEULEUJE3 - 953 - 95
222PHEPHELEULEUAF3 - 953 - 95
123PHEPHELEULEUJE3 - 953 - 95
223PHEPHELEULEUBG3 - 953 - 95
124PHEPHELEULEUJE3 - 953 - 95
224PHEPHELEULEUCH3 - 953 - 95
125PHEPHELEULEUJE3 - 953 - 95
225PHEPHELEULEUDI3 - 953 - 95
126PHEPHELEULEUJE3 - 953 - 95
226PHEPHELEULEUEJ3 - 953 - 95
127GLYGLYGLUGLUAF2 - 962 - 96
227GLYGLYGLUGLUBG2 - 962 - 96
128GLYGLYTYRTYRAF2 - 972 - 97
228GLYGLYTYRTYRCH2 - 972 - 97
129GLYGLYTYRTYRAF2 - 972 - 97
229GLYGLYTYRTYRDI2 - 972 - 97
130GLYGLYTYRTYRAF2 - 972 - 97
230GLYGLYTYRTYREJ2 - 972 - 97
131GLYGLYGLUGLUBG2 - 962 - 96
231GLYGLYGLUGLUCH2 - 962 - 96
132GLYGLYGLUGLUBG2 - 962 - 96
232GLYGLYGLUGLUDI2 - 962 - 96
133GLYGLYGLUGLUBG2 - 962 - 96
233GLYGLYGLUGLUEJ2 - 962 - 96
134GLYGLYTYRTYRCH2 - 972 - 97
234GLYGLYTYRTYRDI2 - 972 - 97
135GLYGLYTYRTYRCH2 - 972 - 97
235GLYGLYTYRTYREJ2 - 972 - 97
136GLYGLYTYRTYRDI2 - 972 - 97
236GLYGLYTYRTYREJ2 - 972 - 97

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36

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Components

#1: Protein
Peptidyl-prolyl cis-trans isomerase FKBP53 / PPIase FKBP53 / FK506-binding protein 53 / AtFKBP53 / Immunophilin FKBP53 / Rotamase


Mass: 12111.609 Da / Num. of mol.: 10 / Fragment: nucleoplasmin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FKBP53, At4g25340, T30C3_20 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93ZG9, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.38 Å3/Da / Density % sol: 43.79 % / Description: rod-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M DL-Malic acid (pH 7.0), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→68.53 Å / Num. obs: 40837 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 56.493 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Net I/σ(I): 16.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 27924 / CC1/2: 0.905 / Rpim(I) all: 0.24 / Rrim(I) all: 0.609 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
PHENIXrefinement
iMOSFLM7.1.1data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K5J
Resolution: 2.4→68.53 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 19.597 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23325 2033 5 %RANDOM
Rwork0.204 ---
obs0.20538 38867 99.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 69 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å2-2.25 Å2
2--0.47 Å20 Å2
3---1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.4→68.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7179 0 0 38 7217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137336
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176806
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.6449934
X-RAY DIFFRACTIONr_angle_other_deg1.1821.58116013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0515923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3825.968315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.903151277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.111510
X-RAY DIFFRACTIONr_chiral_restr0.1310.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021272
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_it2.722.7163734
X-RAY DIFFRACTIONr_mcbond_other2.7192.7163733
X-RAY DIFFRACTIONr_mcangle_it4.0744.0724643
X-RAY DIFFRACTIONr_mcangle_other4.0734.0724644
X-RAY DIFFRACTIONr_scbond_it3.2653.0553602
X-RAY DIFFRACTIONr_scbond_other3.2653.0563603
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8774.4585292
X-RAY DIFFRACTIONr_long_range_B_refined7.03831.7917047
X-RAY DIFFRACTIONr_long_range_B_other7.03731.7937048
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)
11G23100.13
12H23100.13
21G23290.13
22I23290.13
31G22750.14
32J22750.14
41G22820.13
42A22820.13
51G23270.12
52B23270.12
61G23290.12
62C23290.12
71G23280.11
72D23280.11
81G23360.11
82E23360.11
91H26540.09
92I26540.09
101H25070.12
102J25070.12
111H26160.1
112A26160.1
121H26320.09
122B26320.09
131H26400.1
132C26400.1
141H26030.11
142D26030.11
151H26650.09
152E26650.09
161I25110.12
162J25110.12
171I26670.09
172A26670.09
181I26130.11
182B26130.11
191I26590.1
192C26590.1
201I26310.1
202D26310.1
211I26640.08
212E26640.08
221J25260.11
222A25260.11
231J25640.12
232B25640.12
241J25410.12
242C25410.12
251J24770.13
252D24770.13
261J25230.12
262E25230.12
271A26340.09
272B26340.09
281A26680.09
282C26680.09
291A26140.1
292D26140.1
301A26370.11
302E26370.11
311B26580.09
312C26580.09
321B26220.1
322D26220.1
331B26490.1
332E26490.1
341C26470.09
342D26470.09
351C26590.1
352E26590.1
361D26470.1
362E26470.1
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 172 -
Rwork0.278 2869 -
obs--100 %
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)
14.4913-0.27790.39967.62961.54845.42170.23681.0609-0.0219-2.18540.046-0.958-0.31720.4722-0.28280.74060.08530.18320.3798-0.07310.3874-2.85-4.135127.513
24.7378-0.39780.464.31720.64084.93960.30210.2932-0.07130.05710.1856-1.83550.26171.0007-0.48770.29130.1065-0.06490.3166-0.18040.986710.709-8.852141.571
35.5796-1.1081-0.21457.14481.59295.31870.11040.57460.3803-1.1808-0.21340.954-0.5959-0.73050.1030.31870.1422-0.18250.3029-0.0590.4494-17.0065.478135.667
45.3747-1.42080.6155.33070.41875.0263-0.3009-0.9820.38991.2480.12950.6022-0.2358-0.62690.17140.49380.1227-0.00970.3931-0.18540.4263-13.3666.114154.98
54.9919-0.90350.80693.95911.76065.9065-0.1045-1.02240.32551.38410.2474-0.70080.30940.3598-0.14290.6330.0881-0.29540.3593-0.09990.53263.648-2.577158.389
64.2776-0.58860.2784.0947-0.56893.3225-0.0295-0.16170.16260.10.12330.7277-0.2076-0.328-0.09380.02420.0136-0.02390.04370.0460.3122-42.135-13.439102.871
75.00290.03750.50764.8239-0.1353.7804-0.15440.87050.1218-1.25060.20990.2315-0.1993-0.023-0.05540.389-0.0655-0.14170.17110.05090.3015-35.857-15.31184.454
84.6923-0.14711.01485.83630.54023.9527-0.0299-0.9066-0.12461.13690.0580.0143-0.0611-0.2456-0.02810.2525-0.0065-0.07750.19370.09370.2778-28.936-21.373114.712
94.28080.39670.87495.5936-0.30053.87520.0964-0.1084-0.30590.3177-0.0305-0.90710.19530.4047-0.06590.03670.0179-0.07420.05570.03960.5261-14.197-28.384103.992
103.8806-0.26681.11595.41310.63314.26280.00180.926-0.2898-1.11850.1847-1.0534-0.02850.7706-0.18650.3635-0.01760.13030.305-0.07770.5126-18.575-24.72884.987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1F2 - 96
2X-RAY DIFFRACTION2G3 - 96
3X-RAY DIFFRACTION3H2 - 97
4X-RAY DIFFRACTION4I2 - 97
5X-RAY DIFFRACTION5J3 - 96
6X-RAY DIFFRACTION6A2 - 97
7X-RAY DIFFRACTION7B2 - 98
8X-RAY DIFFRACTION8C2 - 97
9X-RAY DIFFRACTION9D2 - 97
10X-RAY DIFFRACTION10E2 - 97

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