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- PDB-5xvo: E. fae Cas1-Cas2/prespacer/target ternary complex revealing DNA s... -

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Basic information

Entry
Database: PDB / ID: 5xvo
TitleE. fae Cas1-Cas2/prespacer/target ternary complex revealing DNA sampling and half-integration states
Components
  • (CRISPR-associated ...) x 2
  • DNA (28-MER)
  • DNA (46-MER)
  • DNA (5'-D(P*CP*CP*GP*AP*G)-3')
  • DNA (69-MER)
KeywordsIMMUNE SYSTEM / CRISPR / Cas
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, NMENI subtype / CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1
Similarity search - Domain/homology
DNA / DNA (> 10) / CRISPR-associated endoribonuclease Cas2 / CRISPR-associated endonuclease Cas1
Similarity search - Component
Biological speciesEnterococcus faecalis TX0027 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsXiao, Y. / Ng, S. / Nam, K.H. / Ke, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
CitationJournal: Nature / Year: 2017
Title: How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration.
Authors: Xiao, Y. / Ng, S. / Hyun Nam, K. / Ke, A.
History
DepositionJun 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 12, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id
Revision 1.4May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2
F: CRISPR-associated endoribonuclease Cas2
G: DNA (28-MER)
H: DNA (5'-D(P*CP*CP*GP*AP*G)-3')
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endoribonuclease Cas2
N: CRISPR-associated endoribonuclease Cas2
O: DNA (28-MER)
P: DNA (28-MER)
Q: DNA (46-MER)
R: DNA (69-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,47122
Polymers382,37318
Non-polymers974
Water25214
1
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2
F: CRISPR-associated endoribonuclease Cas2
G: DNA (28-MER)
H: DNA (5'-D(P*CP*CP*GP*AP*G)-3')
Q: DNA (46-MER)
R: DNA (69-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,40012
Polymers205,35210
Non-polymers492
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33880 Å2
ΔGint-238 kcal/mol
Surface area74800 Å2
MethodPISA
2
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endoribonuclease Cas2
N: CRISPR-associated endoribonuclease Cas2
O: DNA (28-MER)
P: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,07010
Polymers177,0228
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24080 Å2
ΔGint-167 kcal/mol
Surface area63970 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60360 Å2
ΔGint-423 kcal/mol
Surface area136370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.893, 124.800, 157.905
Angle α, β, γ (deg.)90.00, 106.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24I
15A
25J
16A
26K
17A
27L
18B
28C
19B
29D
110B
210I
111B
211J
112B
212K
113B
213L
114C
214D
115C
215I
116C
216J
117C
217K
118C
218L
119D
219I
120D
220J
121D
221K
122D
222L
123E
223F
124E
224M
125E
225N
126F
226M
127F
227N
128G
228O
129G
229P
130G
230R
131I
231J
132I
232K
133I
233L
134J
234K
135J
235L
136K
236L
137M
237N
138O
238P
139O
239R
140P
240R

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
11METMETILEILEAA1 - 2881 - 288
21METMETILEILEBB1 - 2881 - 288
12METMETILEILEAA1 - 2881 - 288
22METMETILEILECC1 - 2881 - 288
13GLYGLYGLYGLYAA2 - 2872 - 287
23GLYGLYGLYGLYDD2 - 2872 - 287
14METMETILEILEAA1 - 2881 - 288
24METMETILEILEII1 - 2881 - 288
15GLYGLYGLYGLYAA2 - 2872 - 287
25GLYGLYGLYGLYJJ2 - 2872 - 287
16METMETILEILEAA1 - 2881 - 288
26METMETILEILEKK1 - 2881 - 288
17METMETILEILEAA1 - 2881 - 288
27METMETILEILELL1 - 2881 - 288
18METMETILEILEBB1 - 2881 - 288
28METMETILEILECC1 - 2881 - 288
19GLYGLYGLYGLYBB2 - 2872 - 287
29GLYGLYGLYGLYDD2 - 2872 - 287
110METMETILEILEBB1 - 2881 - 288
210METMETILEILEII1 - 2881 - 288
111GLYGLYGLYGLYBB2 - 2872 - 287
211GLYGLYGLYGLYJJ2 - 2872 - 287
112METMETILEILEBB1 - 2881 - 288
212METMETILEILEKK1 - 2881 - 288
113METMETILEILEBB1 - 2881 - 288
213METMETILEILELL1 - 2881 - 288
114GLYGLYILEILECC2 - 2882 - 288
214GLYGLYILEILEDD2 - 2882 - 288
115METMETILEILECC1 - 2881 - 288
215METMETILEILEII1 - 2881 - 288
116GLYGLYILEILECC2 - 2882 - 288
216GLYGLYILEILEJJ2 - 2882 - 288
117METMETILEILECC1 - 2881 - 288
217METMETILEILEKK1 - 2881 - 288
118METMETILEILECC1 - 2881 - 288
218METMETILEILELL1 - 2881 - 288
119GLYGLYILEILEDD2 - 2882 - 288
219GLYGLYILEILEII2 - 2882 - 288
120GLYGLYILEILEDD2 - 2882 - 288
220GLYGLYILEILEJJ2 - 2882 - 288
121GLYGLYILEILEDD2 - 2882 - 288
221GLYGLYILEILEKK2 - 2882 - 288
122GLYGLYGLYGLYDD2 - 2872 - 287
222GLYGLYGLYGLYLL2 - 2872 - 287
123ARGARGLEULEUEE4 - 1064 - 106
223ARGARGLEULEUFF4 - 1064 - 106
124TYRTYRLEULEUEE5 - 1065 - 106
224TYRTYRLEULEUMM5 - 1065 - 106
125ARGARGLEULEUEE4 - 1064 - 106
225ARGARGLEULEUNN4 - 1064 - 106
126TYRTYRLEULEUFF5 - 1065 - 106
226TYRTYRLEULEUMM5 - 1065 - 106
127ARGARGLEULEUFF4 - 1064 - 106
227ARGARGLEULEUNN4 - 1064 - 106
128DTDTDTDTGG2 - 252 - 25
228DTDTDTDTOO2 - 252 - 25
129DTDTDTDTGG2 - 252 - 25
229DTDTDTDTPP2 - 252 - 25
130DTDTDTDTGG2 - 252 - 25
230DTDTDTDTRR-21 - 22 - 25
131GLYGLYILEILEII2 - 2882 - 288
231GLYGLYILEILEJJ2 - 2882 - 288
132METMETILEILEII1 - 2881 - 288
232METMETILEILEKK1 - 2881 - 288
133METMETILEILEII1 - 2881 - 288
233METMETILEILELL1 - 2881 - 288
134GLYGLYILEILEJJ2 - 2882 - 288
234GLYGLYILEILEKK2 - 2882 - 288
135GLYGLYGLYGLYJJ2 - 2872 - 287
235GLYGLYGLYGLYLL2 - 2872 - 287
136METMETILEILEKK1 - 2881 - 288
236METMETILEILELL1 - 2881 - 288
137TYRTYRLEULEUMM5 - 1065 - 106
237TYRTYRLEULEUNN5 - 1065 - 106
138DTDTDCDCOO2 - 282 - 28
238DTDTDCDCPP2 - 282 - 28
139DTDTDCDCOO2 - 272 - 27
239DTDTDCDCRR-21 - 42 - 27
140DTDTDCDCPP2 - 272 - 27
240DTDTDCDCRR-21 - 42 - 27

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
37
38
39
40

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Components

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CRISPR-associated ... , 2 types, 12 molecules ABCDIJKLEFMN

#1: Protein
CRISPR-associated endonuclease Cas1


Mass: 33492.625 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis TX0027 (bacteria)
Gene: cas1, HMPREF9501_02814 / Production host: Escherichia coli (E. coli)
References: UniProt: E6GPD7, Hydrolases; Acting on ester bonds
#2: Protein
CRISPR-associated endoribonuclease Cas2


Mass: 12977.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis TX0027 (bacteria)
Gene: cas2, HMPREF9501_02813 / Production host: Escherichia coli (E. coli)
References: UniProt: E6GPD6, Hydrolases; Acting on ester bonds

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DNA chain , 4 types, 6 molecules GOPHQR

#3: DNA chain DNA (28-MER)


Mass: 8548.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria)
#4: DNA chain DNA (5'-D(P*CP*CP*GP*AP*G)-3')


Mass: 1505.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria)
#5: DNA chain DNA (46-MER)


Mass: 14094.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria)
#6: DNA chain DNA (69-MER)


Mass: 21279.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria)

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Non-polymers , 2 types, 18 molecules

#7: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.28 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate, 100 mM sodium citrate, pH 6.2, and 4-7% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9191 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 82547 / % possible obs: 97.3 % / Redundancy: 14.4 % / Net I/σ(I): 13.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
SHELXCDphasing
RefinementResolution: 3.1→48.95 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.899 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23334 4351 5 %RANDOM
Rwork0.1939 ---
obs0.19587 82425 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.796 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20.45 Å2
2--0.32 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 3.1→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22291 4044 4 14 26353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01827301
X-RAY DIFFRACTIONr_bond_other_d0.0080.0224577
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.81237670
X-RAY DIFFRACTIONr_angle_other_deg1.691356441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04552696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57123.8111144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.853154263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2515171
X-RAY DIFFRACTIONr_chiral_restr0.090.24008
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0227876
X-RAY DIFFRACTIONr_gen_planes_other0.0060.026575
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_it4.9238.31110829
X-RAY DIFFRACTIONr_mcbond_other4.9238.31110828
X-RAY DIFFRACTIONr_mcangle_it7.42712.46613510
X-RAY DIFFRACTIONr_mcangle_other7.42712.46613511
X-RAY DIFFRACTIONr_scbond_it5.6389.02216472
X-RAY DIFFRACTIONr_scbond_other5.6389.02216471
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.66613.39924161
X-RAY DIFFRACTIONr_long_range_B_refined11.3871.45632138
X-RAY DIFFRACTIONr_long_range_B_other11.3871.45832139
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)
11A165420.16
12B165420.16
21A160530.17
22C160530.17
31A168960.16
32D168960.16
41A162950.17
42I162950.17
51A170000.15
52J170000.15
61A164040.16
62K164040.16
71A172820.15
72L172820.15
81B173270.15
82C173270.15
91B164720.17
92D164720.17
101B169900.15
102I169900.15
111B165510.15
112J165510.15
121B171760.14
122K171760.14
131B169390.15
132L169390.15
141C163970.16
142D163970.16
151C173230.14
152I173230.14
161C164560.15
162J164560.15
171C172010.14
172K172010.14
181C164590.16
182L164590.16
191D164160.16
192I164160.16
201D173420.14
202J173420.14
211D164160.16
212K164160.16
221D171260.15
222L171260.15
231E55780.15
232F55780.15
241E55170.16
242M55170.16
251E54790.17
252N54790.17
261F53430.17
262M53430.17
271F56260.16
272N56260.16
281G19280.1
282O19280.1
291G19480.09
292P19480.09
301G19230.08
302R19230.08
311I165030.15
312J165030.15
321I174170.13
322K174170.13
331I164770.16
332L164770.16
341J165170.15
342K165170.15
351J172720.14
352L172720.14
361K165070.15
362L165070.15
371M53990.17
372N53990.17
381O21420.1
382P21420.1
391O19930.12
392R19930.12
401P20130.11
402R20130.11
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 346 -
Rwork0.304 6091 -
obs--98.29 %

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