[English] 日本語
Yorodumi
- PDB-3wvl: Crystal structure of the football-shaped GroEL-GroES complex (Gro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wvl
TitleCrystal structure of the football-shaped GroEL-GroES complex (GroEL: GroES2:ATP14) from Escherichia coli
Components
  • 10 kDa chaperonin
  • 60 kDa chaperonin
KeywordsHYDROLASE / Protein folding / ATP Hydrolysis / Denaturing proteins
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / protein folding chaperone / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / protein folding chaperone / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / membrane / cytosol
Similarity search - Function
10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GroEL / GroEL / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. ...10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GroEL / GroEL / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / GroES-like superfamily / 3-Layer(bba) Sandwich / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Chaperonin GroEL / Co-chaperonin GroES
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.788 Å
AuthorsKoike-Takeshita, A. / Arakawa, T. / Taguchi, H. / Shimamura, T.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Crystal structure of a symmetric football-shaped GroEL:GroES2-ATP14 complex determined at 3.8 angstrom reveals rearrangement between two GroEL rings.
Authors: Koike-Takeshita, A. / Arakawa, T. / Taguchi, H. / Shimamura, T.
History
DepositionMay 23, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 60 kDa chaperonin
B: 60 kDa chaperonin
C: 60 kDa chaperonin
D: 60 kDa chaperonin
E: 60 kDa chaperonin
F: 60 kDa chaperonin
G: 60 kDa chaperonin
H: 60 kDa chaperonin
I: 60 kDa chaperonin
J: 60 kDa chaperonin
K: 60 kDa chaperonin
L: 60 kDa chaperonin
M: 60 kDa chaperonin
N: 60 kDa chaperonin
O: 10 kDa chaperonin
P: 10 kDa chaperonin
Q: 10 kDa chaperonin
R: 10 kDa chaperonin
S: 10 kDa chaperonin
T: 10 kDa chaperonin
U: 10 kDa chaperonin
V: 10 kDa chaperonin
W: 10 kDa chaperonin
X: 10 kDa chaperonin
Y: 10 kDa chaperonin
Z: 10 kDa chaperonin
a: 10 kDa chaperonin
b: 10 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)955,85370
Polymers947,86528
Non-polymers7,98842
Water00
1
A: 60 kDa chaperonin
B: 60 kDa chaperonin
C: 60 kDa chaperonin
D: 60 kDa chaperonin
E: 60 kDa chaperonin
F: 60 kDa chaperonin
G: 60 kDa chaperonin
O: 10 kDa chaperonin
P: 10 kDa chaperonin
Q: 10 kDa chaperonin
R: 10 kDa chaperonin
S: 10 kDa chaperonin
T: 10 kDa chaperonin
U: 10 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)477,92635
Polymers473,93214
Non-polymers3,99421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43320 Å2
ΔGint-208 kcal/mol
Surface area183090 Å2
MethodPISA
2
H: 60 kDa chaperonin
I: 60 kDa chaperonin
J: 60 kDa chaperonin
K: 60 kDa chaperonin
L: 60 kDa chaperonin
M: 60 kDa chaperonin
N: 60 kDa chaperonin
V: 10 kDa chaperonin
W: 10 kDa chaperonin
X: 10 kDa chaperonin
Y: 10 kDa chaperonin
Z: 10 kDa chaperonin
a: 10 kDa chaperonin
b: 10 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)477,92635
Polymers473,93214
Non-polymers3,99421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43580 Å2
ΔGint-208 kcal/mol
Surface area183380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.280, 217.117, 198.481
Angle α, β, γ (deg.)90.00, 98.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESID 2:136 OR RESID 411:602)
21CHAIN B AND (RESID 2:136 OR RESID 411:602)
31CHAIN C AND (RESID 2:136 OR RESID 411:602)
41CHAIN D AND (RESID 2:136 OR RESID 411:602)
51CHAIN E AND (RESID 2:136 OR RESID 411:602)
61CHAIN F AND (RESID 2:136 OR RESID 411:602)
71CHAIN G AND (RESID 2:136 OR RESID 411:602)
81CHAIN H AND (RESID 2:136 OR RESID 411:602)
91CHAIN I AND (RESID 2:136 OR RESID 411:602)
101CHAIN J AND (RESID 2:136 OR RESID 411:602)
111CHAIN K AND (RESID 2:136 OR RESID 411:602)
121CHAIN L AND (RESID 2:136 OR RESID 411:602)
131CHAIN M AND (RESID 2:136 OR RESID 411:602)
141CHAIN N AND (RESID 2:136 OR RESID 411:602)
12CHAIN A AND (RESID 137:192 OR RESID 375:410)
22CHAIN B AND (RESID 137:192 OR RESID 375:410)
32CHAIN C AND (RESID 137:192 OR RESID 375:410)
42CHAIN D AND (RESID 137:192 OR RESID 375:410)
52CHAIN E AND (RESID 137:192 OR RESID 375:410)
62CHAIN F AND (RESID 137:192 OR RESID 375:410)
72CHAIN G AND (RESID 137:192 OR RESID 375:410)
82CHAIN H AND (RESID 137:192 OR RESID 375:410)
92CHAIN I AND (RESID 137:192 OR RESID 375:410)
102CHAIN J AND (RESID 137:192 OR RESID 375:410)
112CHAIN K AND (RESID 137:192 OR RESID 375:410)
122CHAIN L AND (RESID 137:192 OR RESID 375:410)
132CHAIN M AND (RESID 137:192 OR RESID 375:410)
142CHAIN N AND (RESID 137:192 OR RESID 375:410)
13CHAIN A RESID 193:374
23CHAIN B RESID 193:374
33CHAIN C RESID 193:374
43CHAIN D RESID 193:374
53CHAIN E RESID 193:374
63CHAIN F RESID 193:374
73CHAIN G RESID 193:374
83CHAIN H RESID 193:374
93CHAIN I RESID 193:374
103CHAIN J RESID 193:374
113CHAIN K RESID 193:374
123CHAIN L RESID 193:374
133CHAIN M RESID 193:374
143CHAIN N RESID 193:374
14CHAIN O RESID 1:97
24CHAIN P RESID 1:97
34CHAIN Q RESID 1:97
44CHAIN R RESID 1:97
54CHAIN S RESID 1:97
64CHAIN T RESID 1:97
74CHAIN U RESID 1:97
84CHAIN V RESID 1:97
94CHAIN W RESID 1:97
104CHAIN X RESID 1:97
114CHAIN Y RESID 1:97
124CHAIN Z RESID 1:97
134CHAIN a RESID 1:97
144CHAIN b RESID 1:97

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESID 2:136 OR RESID 411:602)A2 - 136
121CHAIN A AND (RESID 2:136 OR RESID 411:602)A411 - 602
211CHAIN B AND (RESID 2:136 OR RESID 411:602)B2 - 136
221CHAIN B AND (RESID 2:136 OR RESID 411:602)B411 - 602
311CHAIN C AND (RESID 2:136 OR RESID 411:602)C2 - 136
321CHAIN C AND (RESID 2:136 OR RESID 411:602)C411 - 602
411CHAIN D AND (RESID 2:136 OR RESID 411:602)D2 - 136
421CHAIN D AND (RESID 2:136 OR RESID 411:602)D411 - 602
511CHAIN E AND (RESID 2:136 OR RESID 411:602)E2 - 136
521CHAIN E AND (RESID 2:136 OR RESID 411:602)E411 - 602
611CHAIN F AND (RESID 2:136 OR RESID 411:602)F2 - 136
621CHAIN F AND (RESID 2:136 OR RESID 411:602)F411 - 602
711CHAIN G AND (RESID 2:136 OR RESID 411:602)G2 - 136
721CHAIN G AND (RESID 2:136 OR RESID 411:602)G411 - 602
811CHAIN H AND (RESID 2:136 OR RESID 411:602)H2 - 136
821CHAIN H AND (RESID 2:136 OR RESID 411:602)H411 - 602
911CHAIN I AND (RESID 2:136 OR RESID 411:602)I2 - 136
921CHAIN I AND (RESID 2:136 OR RESID 411:602)I411 - 602
1011CHAIN J AND (RESID 2:136 OR RESID 411:602)J2 - 136
1021CHAIN J AND (RESID 2:136 OR RESID 411:602)J411 - 602
1111CHAIN K AND (RESID 2:136 OR RESID 411:602)K2 - 136
1121CHAIN K AND (RESID 2:136 OR RESID 411:602)K411 - 602
1211CHAIN L AND (RESID 2:136 OR RESID 411:602)L2 - 136
1221CHAIN L AND (RESID 2:136 OR RESID 411:602)L411 - 602
1311CHAIN M AND (RESID 2:136 OR RESID 411:602)M2 - 136
1321CHAIN M AND (RESID 2:136 OR RESID 411:602)M411 - 602
1411CHAIN N AND (RESID 2:136 OR RESID 411:602)N2 - 136
1421CHAIN N AND (RESID 2:136 OR RESID 411:602)N411 - 602
112CHAIN A AND (RESID 137:192 OR RESID 375:410)A137 - 192
122CHAIN A AND (RESID 137:192 OR RESID 375:410)A375 - 410
212CHAIN B AND (RESID 137:192 OR RESID 375:410)B137 - 192
222CHAIN B AND (RESID 137:192 OR RESID 375:410)B375 - 410
312CHAIN C AND (RESID 137:192 OR RESID 375:410)C137 - 192
322CHAIN C AND (RESID 137:192 OR RESID 375:410)C375 - 410
412CHAIN D AND (RESID 137:192 OR RESID 375:410)D137 - 192
422CHAIN D AND (RESID 137:192 OR RESID 375:410)D375 - 410
512CHAIN E AND (RESID 137:192 OR RESID 375:410)E137 - 192
522CHAIN E AND (RESID 137:192 OR RESID 375:410)E375 - 410
612CHAIN F AND (RESID 137:192 OR RESID 375:410)F137 - 192
622CHAIN F AND (RESID 137:192 OR RESID 375:410)F375 - 410
712CHAIN G AND (RESID 137:192 OR RESID 375:410)G137 - 192
722CHAIN G AND (RESID 137:192 OR RESID 375:410)G375 - 410
812CHAIN H AND (RESID 137:192 OR RESID 375:410)H137 - 192
822CHAIN H AND (RESID 137:192 OR RESID 375:410)H375 - 410
912CHAIN I AND (RESID 137:192 OR RESID 375:410)I137 - 192
922CHAIN I AND (RESID 137:192 OR RESID 375:410)I375 - 410
1012CHAIN J AND (RESID 137:192 OR RESID 375:410)J137 - 192
1022CHAIN J AND (RESID 137:192 OR RESID 375:410)J375 - 410
1112CHAIN K AND (RESID 137:192 OR RESID 375:410)K137 - 192
1122CHAIN K AND (RESID 137:192 OR RESID 375:410)K375 - 410
1212CHAIN L AND (RESID 137:192 OR RESID 375:410)L137 - 192
1222CHAIN L AND (RESID 137:192 OR RESID 375:410)L375 - 410
1312CHAIN M AND (RESID 137:192 OR RESID 375:410)M137 - 192
1322CHAIN M AND (RESID 137:192 OR RESID 375:410)M375 - 410
1412CHAIN N AND (RESID 137:192 OR RESID 375:410)N137 - 192
1422CHAIN N AND (RESID 137:192 OR RESID 375:410)N375 - 410
113CHAIN A AND RESID 193:374A0
213CHAIN B AND RESID 193:374B0
313CHAIN C AND RESID 193:374C0
413CHAIN D AND RESID 193:374D0
513CHAIN E AND RESID 193:374E0
613CHAIN F AND RESID 193:374F0
713CHAIN G AND RESID 193:374G0
813CHAIN H AND RESID 193:374H0
913CHAIN I AND RESID 193:374I0
1013CHAIN J AND RESID 193:374J0
1113CHAIN K AND RESID 193:374K0
1213CHAIN L AND RESID 193:374L0
1313CHAIN M AND RESID 193:374M0
1413CHAIN N AND RESID 193:374N0
114CHAIN O AND RESID 1:97O0
214CHAIN P AND RESID 1:97P0
314CHAIN Q AND RESID 1:97Q0
414CHAIN R AND RESID 1:97R0
514CHAIN S AND RESID 1:97S0
614CHAIN T AND RESID 1:97T0
714CHAIN U AND RESID 1:97U0
814CHAIN V AND RESID 1:97V0
914CHAIN W AND RESID 1:97W0
1014CHAIN X AND RESID 1:97X0
1114CHAIN Y AND RESID 1:97Y0
1214CHAIN Z AND RESID 1:97Z0
1314CHAIN a AND RESID 1:97a0
1414CHAIN b AND RESID 1:97b0

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein
60 kDa chaperonin / GroEL protein / Protein Cpn60


Mass: 57303.688 Da / Num. of mol.: 14 / Mutation: D52A, D398A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: groL, groEL, mopA, b4143, JW4103 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5, EC: 3.6.4.9
#2: Protein
10 kDa chaperonin / GroES protein / Protein Cpn10


Mass: 10400.938 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: groS, groES, mopB, b4142, JW4102 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F9, EC: 3.6.4.9
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% PEG 550 MME, 0.1M HEPES, 1mM ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 28, 2012
RadiationMonochromator: liquid-nitrogen-cooled double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. all: 134954 / Num. obs: 129961 / % possible obs: 96.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 4.6
Reflection shellResolution: 3.77→3.91 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 1.4 / % possible all: 82.6

-
Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1589)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PCQ

1pcq


Resolution: 3.788→49.557 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 29.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 6081 5.01 %
Rwork0.2114 --
obs0.2134 121466 91.03 %
all-134900 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.788→49.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms64078 0 462 0 64540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00464988
X-RAY DIFFRACTIONf_angle_d0.73387808
X-RAY DIFFRACTIONf_dihedral_angle_d13.92924556
X-RAY DIFFRACTIONf_chiral_restr0.03310668
X-RAY DIFFRACTIONf_plane_restr0.00311396
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A16005X-RAY DIFFRACTION15.559TORSIONAL
12B16005X-RAY DIFFRACTION15.559TORSIONAL
13C16005X-RAY DIFFRACTION15.559TORSIONAL
14D16005X-RAY DIFFRACTION15.559TORSIONAL
15E16005X-RAY DIFFRACTION15.559TORSIONAL
16F16005X-RAY DIFFRACTION15.559TORSIONAL
17G16005X-RAY DIFFRACTION15.559TORSIONAL
18H16005X-RAY DIFFRACTION15.559TORSIONAL
19I16005X-RAY DIFFRACTION15.559TORSIONAL
110J16005X-RAY DIFFRACTION15.559TORSIONAL
111K16005X-RAY DIFFRACTION15.559TORSIONAL
112L16005X-RAY DIFFRACTION15.559TORSIONAL
113M16005X-RAY DIFFRACTION15.559TORSIONAL
114N16005X-RAY DIFFRACTION15.559TORSIONAL
21A5748X-RAY DIFFRACTION15.559TORSIONAL
22B5748X-RAY DIFFRACTION15.559TORSIONAL
23C5748X-RAY DIFFRACTION15.559TORSIONAL
24D5748X-RAY DIFFRACTION15.559TORSIONAL
25E5748X-RAY DIFFRACTION15.559TORSIONAL
26F5748X-RAY DIFFRACTION15.559TORSIONAL
27G5748X-RAY DIFFRACTION15.559TORSIONAL
28H5748X-RAY DIFFRACTION15.559TORSIONAL
29I5748X-RAY DIFFRACTION15.559TORSIONAL
210J5748X-RAY DIFFRACTION15.559TORSIONAL
211K5748X-RAY DIFFRACTION15.559TORSIONAL
212L5748X-RAY DIFFRACTION15.559TORSIONAL
213M5748X-RAY DIFFRACTION15.559TORSIONAL
214N5748X-RAY DIFFRACTION15.559TORSIONAL
31A11946X-RAY DIFFRACTION15.559TORSIONAL
32B11946X-RAY DIFFRACTION15.559TORSIONAL
33C11946X-RAY DIFFRACTION15.559TORSIONAL
34D11946X-RAY DIFFRACTION15.559TORSIONAL
35E11946X-RAY DIFFRACTION15.559TORSIONAL
36F11946X-RAY DIFFRACTION15.559TORSIONAL
37G11946X-RAY DIFFRACTION15.559TORSIONAL
38H11946X-RAY DIFFRACTION15.559TORSIONAL
39I11946X-RAY DIFFRACTION15.559TORSIONAL
310J11946X-RAY DIFFRACTION15.559TORSIONAL
311K11946X-RAY DIFFRACTION15.559TORSIONAL
312L11946X-RAY DIFFRACTION15.559TORSIONAL
313M11946X-RAY DIFFRACTION15.559TORSIONAL
314N11946X-RAY DIFFRACTION15.559TORSIONAL
41O6247X-RAY DIFFRACTION15.559TORSIONAL
42P6247X-RAY DIFFRACTION15.559TORSIONAL
43Q6247X-RAY DIFFRACTION15.559TORSIONAL
44R6247X-RAY DIFFRACTION15.559TORSIONAL
45S6247X-RAY DIFFRACTION15.559TORSIONAL
46T6247X-RAY DIFFRACTION15.559TORSIONAL
47U6247X-RAY DIFFRACTION15.559TORSIONAL
48V6247X-RAY DIFFRACTION15.559TORSIONAL
49W6247X-RAY DIFFRACTION15.559TORSIONAL
410X6247X-RAY DIFFRACTION15.559TORSIONAL
411Y6247X-RAY DIFFRACTION15.559TORSIONAL
412Z6247X-RAY DIFFRACTION15.559TORSIONAL
413a6247X-RAY DIFFRACTION15.559TORSIONAL
414b6247X-RAY DIFFRACTION15.559TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7881-3.83110.2987360.2492703X-RAY DIFFRACTION17
3.8311-3.87620.30991310.27922459X-RAY DIFFRACTION59
3.8762-3.92340.32541950.28153613X-RAY DIFFRACTION87
3.9234-3.97310.32112100.26863997X-RAY DIFFRACTION95
3.9731-4.02530.28942070.27244079X-RAY DIFFRACTION96
4.0253-4.08050.32092030.26183995X-RAY DIFFRACTION96
4.0805-4.13870.30362240.24693995X-RAY DIFFRACTION95
4.1387-4.20050.25612340.24594016X-RAY DIFFRACTION96
4.2005-4.26610.30412210.24434034X-RAY DIFFRACTION96
4.2661-4.3360.30382210.24914032X-RAY DIFFRACTION96
4.336-4.41070.28282140.25384009X-RAY DIFFRACTION95
4.4107-4.49080.28412080.23364020X-RAY DIFFRACTION96
4.4908-4.57720.29962000.22864115X-RAY DIFFRACTION96
4.5772-4.67050.26492200.22733977X-RAY DIFFRACTION96
4.6705-4.7720.25342330.21454042X-RAY DIFFRACTION96
4.772-4.88290.26211790.21474087X-RAY DIFFRACTION96
4.8829-5.00490.27371930.21714096X-RAY DIFFRACTION96
5.0049-5.14010.24922120.21074061X-RAY DIFFRACTION96
5.1401-5.29120.27292300.22264036X-RAY DIFFRACTION96
5.2912-5.46180.26792220.22934034X-RAY DIFFRACTION96
5.4618-5.65670.24222050.22624079X-RAY DIFFRACTION96
5.6567-5.88290.26882220.21994087X-RAY DIFFRACTION97
5.8829-6.15010.24562090.21554059X-RAY DIFFRACTION96
6.1501-6.47370.26811990.22744079X-RAY DIFFRACTION96
6.4737-6.87830.27362130.20274071X-RAY DIFFRACTION96
6.8783-7.40780.25822150.19154072X-RAY DIFFRACTION96
7.4078-8.15030.20732140.17424057X-RAY DIFFRACTION96
8.1503-9.32290.1672180.15034048X-RAY DIFFRACTION95
9.3229-11.72020.16232240.13993854X-RAY DIFFRACTION91
11.7202-49.56150.24011690.20833579X-RAY DIFFRACTION82
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.807-0.0254-0.02043.2641-0.1360.7276-0.191-0.60590.19980.4620.11770.0175-0.1947-0.19740.07260.99670.1010.01390.7716-0.16510.537514.29363.580991.7482
22.01661.2566-0.62961.7953-0.43771.0029-0.0246-0.0670.40190.3087-0.0015-0.1622-0.5912-0.16510.0230.96570.099-0.05030.4971-0.11240.791734.466231.369570.0728
33.34890.05-0.62991.45070.62411.9348-0.1010.25580.6165-0.1388-0.05430.1967-0.71380.26440.15960.8618-0.09530.01760.59210.16530.765662.231925.789741.0145
42.7191.03840.53553.7145-0.07491.1292-0.04110.3860.0735-0.09370.2334-0.002-0.16630.3438-0.21561.02660.0260.15310.85160.05710.543276.7743-9.157926.5005
54.29310.2470.40472.734-0.87760.86740.0410.508-0.7114-0.09040.0629-0.29810.49590.2456-0.08430.92050.12290.02470.6936-0.15260.627767.1797-47.029237.2882
63.2238-0.2003-0.33081.10650.06512.14740.1059-0.1595-1.0740.02580.00320.1590.3003-0.0151-0.08541.0116-0.0531-0.0160.4790.10880.909440.5785-59.260365.3868
72.1441-0.2619-0.83241.82850.92492.2545-0.0554-0.66-0.46790.4853-0.00280.17730.1985-0.38120.08340.8956-0.06560.07240.83790.16650.550916.9819-36.817989.6339
81.3856-0.1287-0.15533.5621-0.40493.2607-0.12950.58730.0625-0.25530.1037-0.1518-0.21410.20920.01860.7435-0.00660.14540.9160.12750.53751.97712.19385.847
93.1768-0.2853-1.02131.7197-0.35694.6095-0.0030.05260.6558-0.19070.0066-0.0031-0.53330.17020.02790.80450.05540.06010.50480.14490.756731.677130.587626.5725
103.21430.3043-0.73121.1484-0.65031.6475-0.0177-0.04930.5978-0.12050.00820.0893-0.3386-0.253-0.03910.93410.1508-0.03560.5779-0.05830.76043.907825.875855.8916
110.846-0.63530.18325.05990.92731.0148-0.0529-0.0506-0.07440.15320.07030.14510.0353-0.4177-0.0370.5839-0.01340.14860.85290.06310.5839-10.4426-8.627471.5525
124.068-0.2522-1.09671.98780.48012.13470.0408-0.1891-0.50760.00850.09860.22460.109-0.1593-0.08660.9573-0.13370.03750.7220.05850.7155-0.7563-46.811162.0517
133.31090.2437-0.80452.79090.0683.12850.07450.3719-1.0219-0.25280.0285-0.11190.45340.0627-0.08960.9631-0.0034-0.05640.5854-0.14190.831525.8859-59.822734.3602
141.62351.10790.051.6697-0.97121.5517-0.1330.8634-0.4239-0.37190.0871-0.19260.130.10030.07930.99330.09260.11090.9694-0.17620.637949.4082-38.05929.4158
156.6479-3.0606-0.22888.09742.99594.79770.1478-1.7828-0.06181.25910.1199-0.6255-0.4853-1.6231-0.22081.3413-0.02440.08511.3637-0.0280.569122.4341-13.9463111.3366
165.47241.86452.156410.0037-2.89365.3789-0.227-0.81340.42870.7223-0.0036-0.5134-0.9816-0.05390.27541.1380.09260.03050.8313-0.38750.746735.470726.950597.1483
177.3771.1527-1.26465.5183-0.6794.2916-0.6866-0.24540.94210.04710.6317-0.6277-0.28910.66130.05570.7885-0.0528-0.03290.6141-0.07371.270265.531237.943665.4247
183.6953-2.372-0.27088.87214.98433.8691-0.43150.56520.17810.65490.4035-0.5747-0.42190.9835-0.06750.8099-0.07890.18521.07160.06180.884890.287510.417640.0356
199.284-1.28060.44783.4751-1.47994.5585-0.60290.2902-0.17250.78190.3405-1.1504-1.21660.69640.05621.01720.1180.0930.9666-0.05490.997891.2828-34.399539.8561
209.16534.9898-0.58063.8093-1.5375.92860.7439-0.7293-1.73280.2225-0.7363-0.70810.90490.77260.01271.11270.1176-0.07450.54090.10491.266367.6731-62.946965.0505
216.0561-0.2527-1.97947.5528-1.8416.5102-0.0453-0.8047-0.70280.20950.2029-0.37720.5469-0.005-0.11931.448-0.1017-0.12850.95820.28970.923737.194-53.806896.845
227.23844.46811.47498.87220.74015.7392-0.08671.36420.0921-1.23780.08360.3627-0.51750.85-0.00911.00770.2020.10781.1873-0.02170.545443.8444-15.8504-13.1532
235.991-2.40732.68855.7718-1.4212.388-0.39971.5671.1051-0.14810.2610.09-1.01850.19960.23551.4477-0.05660.04061.16150.46360.988630.73225.3294-0.3578
248.7089-1.0723-0.21476.78911.25378.9037-0.58060.66131.733-0.19160.12010.2096-0.5963-0.61810.48160.97440.1243-0.04810.76150.20550.99160.530237.08931.0765
259.34961.18261.96728.5899-3.65088.476-0.5079-0.17540.7962-0.0430.3119-0.1087-0.1814-0.8810.28840.85950.16450.07630.96860.00450.8011-24.100610.41957.4061
268.70892.4699-0.03356.4281-1.28144.03080.9874-1.0131-0.72820.376-0.7330.52111.2505-0.5782-0.33841.1205-0.188-0.00170.9801-0.00950.9103-24.9304-34.360159.0591
279.2029-4.1446-2.59819.23150.76425.49380.49140.5958-1.6335-0.3569-0.21140.44270.8859-0.4819-0.25041.1533-0.0824-0.21950.6326-0.08441.119-1.2319-63.618934.7782
283.0286-0.0267-2.37035.29012.28036.51840.30860.9317-0.1527-0.72970.4447-0.11660.5180.4218-0.71571.28970.06490.06381.0638-0.18570.67229.2111-55.25772.8073
293.5776-0.28673.31997.32332.34497.7461-0.5244-0.5091.05930.54560.0831-0.87470.01541.56540.40091.7676-0.2721-0.44122.51340.16551.5650.0135-13.4702128.643
308.5196-0.88892.76614.9841-1.51194.61690.5460.3973-0.17050.7138-0.3721-0.9136-0.16720.0823-0.2372.1250.01-0.71061.67570.09962.590161.452519.117114.2369
318.78462.1647-4.88898.21652.02973.9241-0.2792-0.84870.49881.56070.26870.59670.58760.1639-0.04861.72480.2042-0.39691.4262-0.39592.065887.454629.653686.5838
327.9832.25565.19517.95180.61694.295-0.0923-1.0456-0.41050.31360.825-0.30330.57770.3411-0.80091.4320.3638-0.05721.8688-0.18371.4566106.66317.463967.5358
334.3192-1.1235-3.10645.4152-0.75877.24670.4861-1.89130.80010.8897-0.58290.7556-0.999-0.76480.17651.4921-0.0595-0.20961.8742-0.06411.7793107.345-31.763766.9726
349.9040.54720.78846.50874.13585.02730.3246-0.8325-0.48350.8923-0.1184-0.21250.38390.5233-0.19081.9715-0.3277-0.26421.56540.27661.429888.674-53.578987.5484
358.22370.25822.27834.5918-3.0587.2763-1.4206-0.20652.8594-0.30570.296-1.3498-1.5596-0.19721.11582.1938-0.4581-0.62311.64730.09242.299662.2431-46.0882114.4618
369.04553.13391.61038.1249-3.79073.9474-0.130.3770.53960.6665-0.4363-0.8973-0.0938-0.09680.74952.02020.204-0.46642.6116-0.48491.987716.1714-15.8915-30.3845
374.4134.35472.10664.93335.08219.95340.19641.14110.0686-0.70320.38220.1658-0.2091.3086-0.62631.7353-0.0746-0.64642.0039-0.1392.62824.796817.6921-17.64
384.06480.9759-1.00474.71370.44374.02580.10030.2932-0.2253-0.59640.4053-0.0112.4738-0.9674-0.51061.938-0.2053-0.48791.71710.73472.3923-21.410528.31710.0233
396.4647-1.9892.17674.87730.75345.1973-0.32241.15150.0711-1.54980.93020.72940.6458-1.3279-0.70471.6677-0.3985-0.10462.23190.34961.5166-40.47416.645729.9205
409.0162-1.8634-0.34394.48222.05824.24740.52282.30990.1882-0.5732-0.2202-0.2324-0.41380.6227-0.39521.5212-0.0974-0.11.9095-0.04731.5819-41.0353-32.487531.9169
416.5493-0.3436-1.35855.1938-0.66872.61860.26030.342-0.7149-0.4482-0.0494-0.27790.4391-0.1347-0.16892.0090.2796-0.35831.8757-0.44781.4865-22.0953-54.579611.9065
427.5507-0.87723.58476.06472.51888.0368-1.5971.78862.9212-0.16540.13180.1205-2.63531.13721.33971.9770.171-0.76492.0945-0.08112.52314.2431-47.609-14.8058
434.26492.33724.4884.0844.2865.2015-0.2367-0.02940.0457-0.46670.0058-0.00370.0333-2.03460.40222.0297-0.29060.28782.4405-0.06011.6874125.0191-5.5791101.3959
447.86660.85080.48175.5982-1.04566.9141-0.00380.5980.3133-0.36110.49330.5377-0.29730.5216-0.48642.0756-0.227-0.00182.17420.13831.9491122.8913-28.4286104.7143
453.14012.9309-2.40627.43783.69458.0201-1.57740.26690.0615-0.85160.20352.5695-0.1722-1.52461.34531.8056-0.0367-0.28011.8840.3022.2282108.2797-38.3786118.5836
469.4115-1.1948-4.74867.30981.26874.7312-0.16370.70161.7866-0.58510.7187-0.0851-1.71950.1934-0.66412.4952-0.3285-0.11212.40780.52361.821593.4758-29.2256133.6066
478.4868-3.59113.66446.74244.53727.9570.6510.755-0.2761-1.7177-0.5570.3708-1.3021-0.3535-0.13552.6691-0.0499-0.0472.27770.37171.312289.1884-6.9007137.7445
487.4542-2.78183.35338.129-8.16488.1268-0.1338-1.7092-0.0657-0.47430.11720.39730.5512-1.6290.22922.92550.0679-0.12422.362-0.44211.918398.827711.1367127.1794
493.34541.0893-2.1958.3829-3.90236.1042-0.624-0.2037-1.29230.29731.28940.8896-0.0571-0.8947-0.61912.4437-0.08820.04262.11870.05671.7842115.862912.7937111.4282
504.47521.84841.5376.3693-3.79438.1522-0.01-1.37450.17971.1874-0.262-0.00561.07272.25410.12232.02960.7010.13722.6109-0.10961.414-58.7983-7.4457-3.3242
515.8568-2.99510.32128.3928-4.957.10330.3888-0.3379-0.28670.91970.47130.1964-0.161-0.1312-0.78342.13650.272-0.06742.1077-0.1231.7432-56.6854-30.3992-5.635
529.1595-3.3948-3.32759.5402-1.59113.70630.1261-0.6051.9585-0.5461-0.9509-0.9672-0.13130.22011.12521.88520.0915-0.53671.7257-0.07442.1603-41.9348-41.0341-19.1212
535.17763.5375-3.39764.71612.10127.410.138-1.92131.4550.82770.18830.3628-0.0230.5763-0.29892.22110.4376-0.17091.8046-0.22072.2019-27.1823-32.5074-34.6577
542.01687.12781.5514.87051.1827.94511.2736-0.5984-1.31221.26-0.2858-1.9664-1.02210.9673-0.99922.4542-0.13010.17172.3506-0.25352.3171-23.2765-10.6843-39.4751
556.46450.434-0.77693.49175.17766.10221.1578-0.4916-0.75472.2492-0.6324-0.5496-0.21170.1602-0.45792.68170.0131-0.13561.91080.23651.8433-33.18328.148-30.376
568.32950.6748-4.02385.99653.90764.13820.2951-0.1149-1.1252-0.07550.7198-0.7921-0.63711.0307-12.7490.5941-0.16122.1811-0.01992.0102-49.826410.2507-14.3199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2:136 OR RESID 411:602)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 2:136 OR RESID 411:602)
3X-RAY DIFFRACTION3CHAIN C AND (RESID 2:136 OR RESID 411:602)
4X-RAY DIFFRACTION4CHAIN D AND (RESID 2:136 OR RESID 411:602)
5X-RAY DIFFRACTION5CHAIN E AND (RESID 2:136 OR RESID 411:602)
6X-RAY DIFFRACTION6CHAIN F AND (RESID 2:136 OR RESID 411:602)
7X-RAY DIFFRACTION7CHAIN G AND (RESID 2:136 OR RESID 411:602)
8X-RAY DIFFRACTION8CHAIN H AND (RESID 2:136 OR RESID 411:602)
9X-RAY DIFFRACTION9CHAIN I AND (RESID 2:136 OR RESID 411:602)
10X-RAY DIFFRACTION10CHAIN J AND (RESID 2:136 OR RESID 411:602)
11X-RAY DIFFRACTION11CHAIN K AND (RESID 2:136 OR RESID 411:602)
12X-RAY DIFFRACTION12CHAIN L AND (RESID 2:136 OR RESID 411:602)
13X-RAY DIFFRACTION13CHAIN M AND (RESID 2:136 OR RESID 411:602)
14X-RAY DIFFRACTION14CHAIN N AND (RESID 2:136 OR RESID 411:602)
15X-RAY DIFFRACTION15CHAIN A AND (RESID 137:192 OR RESID 375:410)
16X-RAY DIFFRACTION16CHAIN B AND (RESID 137:192 OR RESID 375:410)
17X-RAY DIFFRACTION17CHAIN C AND (RESID 137:192 OR RESID 375:410)
18X-RAY DIFFRACTION18CHAIN D AND (RESID 137:192 OR RESID 375:410)
19X-RAY DIFFRACTION19CHAIN E AND (RESID 137:192 OR RESID 375:410)
20X-RAY DIFFRACTION20CHAIN F AND (RESID 137:192 OR RESID 375:410)
21X-RAY DIFFRACTION21CHAIN G AND (RESID 137:192 OR RESID 375:410)
22X-RAY DIFFRACTION22CHAIN H AND (RESID 137:192 OR RESID 375:410)
23X-RAY DIFFRACTION23CHAIN I AND (RESID 137:192 OR RESID 375:410)
24X-RAY DIFFRACTION24CHAIN J AND (RESID 137:192 OR RESID 375:410)
25X-RAY DIFFRACTION25CHAIN K AND (RESID 137:192 OR RESID 375:410)
26X-RAY DIFFRACTION26CHAIN L AND (RESID 137:192 OR RESID 375:410)
27X-RAY DIFFRACTION27CHAIN M AND (RESID 137:192 OR RESID 375:410)
28X-RAY DIFFRACTION28CHAIN N AND (RESID 137:192 OR RESID 375:410)
29X-RAY DIFFRACTION29CHAIN A AND RESID 193:374
30X-RAY DIFFRACTION30CHAIN B AND RESID 193:374
31X-RAY DIFFRACTION31CHAIN C AND RESID 193:374
32X-RAY DIFFRACTION32CHAIN D AND RESID 193:374
33X-RAY DIFFRACTION33CHAIN E AND RESID 193:374
34X-RAY DIFFRACTION34CHAIN F AND RESID 193:374
35X-RAY DIFFRACTION35CHAIN G AND RESID 193:374
36X-RAY DIFFRACTION36CHAIN H AND RESID 193:374
37X-RAY DIFFRACTION37CHAIN I AND RESID 193:374
38X-RAY DIFFRACTION38CHAIN J AND RESID 193:374
39X-RAY DIFFRACTION39CHAIN K AND RESID 193:374
40X-RAY DIFFRACTION40CHAIN L AND RESID 193:374
41X-RAY DIFFRACTION41CHAIN M AND RESID 193:374
42X-RAY DIFFRACTION42CHAIN N AND RESID 193:374
43X-RAY DIFFRACTION43CHAIN O
44X-RAY DIFFRACTION44CHAIN P
45X-RAY DIFFRACTION45CHAIN Q
46X-RAY DIFFRACTION46CHAIN R
47X-RAY DIFFRACTION47CHAIN S
48X-RAY DIFFRACTION48CHAIN T
49X-RAY DIFFRACTION49CHAIN U
50X-RAY DIFFRACTION50CHAIN V
51X-RAY DIFFRACTION51CHAIN W
52X-RAY DIFFRACTION52CHAIN X
53X-RAY DIFFRACTION53CHAIN Y
54X-RAY DIFFRACTION54CHAIN Z
55X-RAY DIFFRACTION55CHAIN a
56X-RAY DIFFRACTION56CHAIN b

+
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://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