[English] 日本語
Yorodumi
- PDB-3zwg: Crystal structure of the pore-forming toxin FraC from Actinia fra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zwg
TitleCrystal structure of the pore-forming toxin FraC from Actinia fragacea (form 2)
ComponentsFRAGACEATOXIN C
KeywordsTOXIN / ION TRANSPORT / MEMBRANE PROTEIN / ACTINOPORINS
Function / homology
Function and homology information


nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / channel activity / pore complex / monoatomic cation transport / toxin activity / lipid binding / extracellular region / identical protein binding
Similarity search - Function
Sea anemone actinoporin-like / Sea anemone cytotoxic protein / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta
Similarity search - Domain/homology
DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesACTINIA FRAGACEA (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å
AuthorsMechaly, A.E. / Bellomio, A. / Morante, K. / Gonzalez-Manas, J.M. / Guerin, D.M.A.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Pores of the Toxin Frac Assemble Into 2D Hexagonal Clusters in Both Crystal Structures and Model Membranes.
Authors: Mechaly, A.E. / Bellomio, A. / Morante, K. / Agirre, J. / Gil-Carton, D. / Valle, M. / Gonzalez-Manas, J.M. / Guerin, D.M.A.
History
DepositionJul 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FRAGACEATOXIN C
B: FRAGACEATOXIN C
C: FRAGACEATOXIN C
D: FRAGACEATOXIN C
E: FRAGACEATOXIN C
F: FRAGACEATOXIN C
G: FRAGACEATOXIN C
H: FRAGACEATOXIN C
I: FRAGACEATOXIN C
J: FRAGACEATOXIN C
K: FRAGACEATOXIN C
L: FRAGACEATOXIN C
M: FRAGACEATOXIN C
N: FRAGACEATOXIN C
O: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)296,19515
Polymers296,19515
Non-polymers00
Water00
1
A: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
O: FRAGACEATOXIN C


Theoretical massNumber of molelcules
Total (without water)19,7461
Polymers19,7461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.770, 118.770, 431.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number149
Space group name H-MP312
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:179 )
211CHAIN B AND (RESSEQ 2:179 )
311CHAIN C AND (RESSEQ 2:179 )
411CHAIN D AND (RESSEQ 2:179 )
511CHAIN E AND (RESSEQ 2:179 )
611CHAIN F AND (RESSEQ 2:179 )
711CHAIN G AND (RESSEQ 2:179 )
811CHAIN H AND (RESSEQ 2:179 )
911CHAIN I AND (RESSEQ 2:179 )
1011CHAIN J AND (RESSEQ 2:179 )
1111CHAIN K AND (RESSEQ 2:179 )
1211CHAIN L AND (RESSEQ 2:179 )
1311CHAIN M AND (RESSEQ 2:179 )
1411CHAIN N AND (RESSEQ 2:179 )
1511CHAIN O AND (RESSEQ 2:179 )

-
Components

#1: Protein
FRAGACEATOXIN C / FRAC


Mass: 19746.303 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) ACTINIA FRAGACEA (sea anemone) / References: UniProt: B9W5G6

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.77 % / Description: NONE
Crystal growDetails: 4M SODIUM FORMATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→66.14 Å / Num. obs: 68444 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 42.58 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3→58.969 Å / SU ML: 0.8 / σ(F): 0 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2501 3455 5.1 %
Rwork0.2041 --
obs0.2065 68219 96.74 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.984 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.289 Å20 Å20 Å2
2--6.289 Å20 Å2
3----12.578 Å2
Refinement stepCycle: LAST / Resolution: 3→58.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20835 0 0 0 20835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921360
X-RAY DIFFRACTIONf_angle_d1.20728920
X-RAY DIFFRACTIONf_dihedral_angle_d12.5157530
X-RAY DIFFRACTIONf_chiral_restr0.0873015
X-RAY DIFFRACTIONf_plane_restr0.0053705
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1389X-RAY DIFFRACTIONPOSITIONAL
12B1389X-RAY DIFFRACTIONPOSITIONAL0.049
13C1389X-RAY DIFFRACTIONPOSITIONAL0.046
14D1389X-RAY DIFFRACTIONPOSITIONAL0.054
15E1389X-RAY DIFFRACTIONPOSITIONAL0.053
16F1389X-RAY DIFFRACTIONPOSITIONAL0.052
17G1389X-RAY DIFFRACTIONPOSITIONAL0.049
18H1389X-RAY DIFFRACTIONPOSITIONAL0.054
19I1389X-RAY DIFFRACTIONPOSITIONAL0.05
110J1389X-RAY DIFFRACTIONPOSITIONAL0.047
111K1389X-RAY DIFFRACTIONPOSITIONAL0.048
112L1389X-RAY DIFFRACTIONPOSITIONAL0.048
113M1389X-RAY DIFFRACTIONPOSITIONAL0.05
114N1389X-RAY DIFFRACTIONPOSITIONAL0.052
115O1389X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04110.37821470.27982625X-RAY DIFFRACTION98
3.0411-3.08460.36631450.29642547X-RAY DIFFRACTION98
3.0846-3.13060.31091280.26012632X-RAY DIFFRACTION98
3.1306-3.17950.31531480.24042581X-RAY DIFFRACTION98
3.1795-3.23160.36091200.2332574X-RAY DIFFRACTION98
3.2316-3.28730.28921330.23142618X-RAY DIFFRACTION98
3.2873-3.34710.24211310.21082589X-RAY DIFFRACTION98
3.3471-3.41150.25831570.2022570X-RAY DIFFRACTION97
3.4115-3.48110.23941230.19332638X-RAY DIFFRACTION98
3.4811-3.55680.25111430.18772584X-RAY DIFFRACTION98
3.5568-3.63950.27081330.19522586X-RAY DIFFRACTION98
3.6395-3.73050.25531460.21842655X-RAY DIFFRACTION98
3.7305-3.83140.23751540.19142570X-RAY DIFFRACTION98
3.8314-3.94410.25661440.18042599X-RAY DIFFRACTION98
3.9441-4.07140.22581480.18332593X-RAY DIFFRACTION98
4.0714-4.21690.2291480.18522592X-RAY DIFFRACTION98
4.2169-4.38560.22961510.18142631X-RAY DIFFRACTION98
4.3856-4.58520.21371310.16312585X-RAY DIFFRACTION97
4.5852-4.82680.15711450.15992562X-RAY DIFFRACTION96
4.8268-5.1290.21961380.17682591X-RAY DIFFRACTION96
5.129-5.52480.24481230.19442556X-RAY DIFFRACTION95
5.5248-6.08030.25741160.20482538X-RAY DIFFRACTION93
6.0803-6.95890.26791310.22652437X-RAY DIFFRACTION90
6.9589-8.76290.23441360.21432722X-RAY DIFFRACTION99
8.7629-58.97990.2491360.24542589X-RAY DIFFRACTION91
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)
10.314-0.1049-0.19940.90670.86791.43370.03590.0434-0.0503-0.00890.0932-0.22170.03820.1867-0.2385-0.03970.0728-0.05730.0404-0.12570.093-13.970225.6453201.1408
20.7493-0.09160.07280.13840.00120.18160.01580.2256-0.0445-0.09880.08230.07930.0025-0.02840.2244-0.41170.1256-0.1971-0.07130.09180.0313-24.100432.7295194.6582
30.84670.1298-0.44090.0534-0.0240.29070.05710.10790.1507-0.04170.02020.1546-0.0497-0.0937-0.0516-0.06820.1031-0.0241-0.00010.10190.2179-30.560742.3871194.9997
40.8703-0.0366-0.30010.25370.16620.5473-0.02340.12130.17730.0029-0.05240.0708-0.0385-0.0377-0.1157-0.18460.0066-0.09450.10320.07670.1575-18.018742.8423198.7783
52.94710.47511.74090.68790.2753.62760.08450.0524-0.614-0.02510.02630.03770.4769-0.2108-0.14110.1005-0.0906-0.06460.0780.01450.15643.072230.8123206.2791
63.19262.8292.37432.58482.78447.72420.17650.0426-0.71170.19890.0223-0.67440.5710.6972-0.20930.08060.0325-0.00550.1010.01390.21937.193626.88196.6908
70.6224-0.2067-0.08070.22570.06410.21030.06610.18290.0631-0.0956-0.09920.1124-0.0162-0.04790.0255-0.42780.1304-0.00650.03330.03160.08922.258140.6572194.6121
80.6403-0.0407-0.23980.02130.01850.10130.00380.0580.1711-0.0127-0.01290.0071-0.0453-0.0392-0.1552-0.0092-0.05230.03440.02530.14850.21843.838952.1741194.6243
90.70880.387-0.43820.4532-0.20190.57170.01670.1270.1696-0.060.01760.0276-0.0594-0.0968-0.08370.0342-0.03370.11440.06410.15770.202415.254647.7773195.4437
101.5341-0.281-0.14620.80050.45440.7847-0.0393-0.00230.02620.02060.0267-0.12280.01310.1119-0.1684-0.04250.02570.01440.07850.03710.099912.197341.4538201.0145
111.75030.48411.04540.49420.76381.92480.05050.0236-0.3159-0.01650.05030.05060.178-0.0841-0.16020.048-0.0846-0.08190.06660.080.172222.193418.3232201.2143
120.85050.086-0.05130.4598-0.00570.4069-0.02790.1799-0.0266-0.155-0.00410.03970.0163-0.02920.1235-0.1848-0.03110.1117-0.08450.05980.046527.657829.2715194.5101
130.4703-0.3795-0.13241.28770.35510.1720.0109-0.0190.1182-0.0001-0.004-0.0937-0.021-0.0105-0.08910.0253-0.00280.0379-0.0210.01670.215535.857336.6024197.819
141.1223-0.82090.11581.0711-0.19240.9650.01730.08290.1709-0.0718-0.027-0.1707-0.11860.10440.01910.0843-0.11240.10180.12530.07850.141339.698432.4224190.4974
150.41570.08250.08330.99730.21320.5042-0.0578-0.0019-0.0151-0.0403-0.0129-0.04290.01150.0186-0.10940.0018-0.0035-0.0019-0.03220.06270.170237.310423.7879201.1553
161.26250.0001-2.30432.7078-2.79167.08660.00030.1935-0.1082-0.03920.01710.62020.173-0.5108-0.02290.3674-0.3125-0.07750.470.01180.296718.007723.0538143.3944
170.44570.25950.03320.48680.10140.54410.101-0.1506-0.06160.2384-0.05320.0096-0.06690.08830.09760.599-0.5359-0.13860.4062-0.2269-0.267128.861627.9163151.0405
180.5961-0.0912-0.06091.36430.8351.2265-0.060.05820.0536-0.04850.0783-0.095-0.10680.1727-0.070.4662-0.39660.04890.4342-0.23520.183136.836936.7263150.9525
190.8710.14770.09320.93610.60472.3031-0.0593-0.08440.0660.0044-0.0398-0.0441-0.24070.118-0.0460.6836-0.31140.03160.4281-0.04240.059724.523839.062147.0295
202.532-1.24151.54672.3482-3.71938.86220.02730.0821-0.7147-0.12440.20460.39810.7614-0.5006-0.22880.6431-0.2063-0.01390.3007-0.0210.2628-1.102729.3921143.4603
210.8416-0.085-0.05760.55910.23461.33630.0214-0.3470.01550.2973-0.00040.0010.01760.03610.01160.8273-0.28060.10040.3115-0.2492-0.27754.123540.1089151.0617
221.2526-0.0708-0.98180.41420.48591.69620.0284-0.13690.2313-0.1257-0.03590.022-0.42350.1159-0.05550.9552-0.1250.06670.3714-0.22680.36664.618951.983150.9199
230.87310.2138-0.4251.49980.32312.5640.0027-0.15090.14160.1134-0.130.0305-0.2924-0.0773-0.00860.7263-0.12690.06940.3279-0.23910.1531-6.33945.8855147.0156
245.84614.74184.03684.09323.87554.25240.06780.0944-0.52880.18050.1073-0.31770.73670.645-0.21580.5110.14560.00390.5028-0.13840.1806-18.362224.6721139.2847
253.4212-1.48953.09538.8201-1.10194.95910.43790.1619-1.2497-0.1073-0.03990.1041.214-0.2364-0.39640.51560.19760.04290.39090.07490.4405-20.853218.6486147.9267
260.83080.1336-0.38851.07410.20321.848-0.0308-0.44160.03730.24260.00220.026-0.1128-0.066-0.0240.53960.31360.13860.517-0.1573-0.0757-22.446633.3287151.0543
270.58150.8583-0.5652.9597-0.9441.95860.16680.06510.2619-0.0553-0.05840.3417-0.2947-0.2112-0.13760.58240.31140.11710.5679-0.14820.3194-29.502242.1602147.8368
282.42340.6811-0.68872.98572.24422.59790.1883-0.07250.36290.0052-0.19510.2897-0.2476-0.16-0.01550.48540.31770.10680.605-0.14160.2602-33.863738.64155.2227
291.4808-0.3749-1.19571.8146-0.20522.5748-0.01550.04520.0181-0.0142-0.09520.0851-0.163-0.26960.01160.40950.20430.0430.6236-0.08820.1254-33.1329.7795144.4992
301.1837-0.1082-1.45762.75373.77896.6418-0.155-0.0935-0.30250.16390.2058-0.33220.37830.4114-0.06240.43590.24890.00450.2346-0.06130.1736-9.998127.7211115.8297
310.9662-0.0183-0.00510.7937-0.35771.68110.05840.25950.0118-0.16470.04550.05360.0251-0.07420.02740.52870.239-0.02970.1570.2436-0.2594-18.785635.842108.3028
321.89230.2602-0.9831.67250.17220.57120.08820.23940.3107-0.1888-0.00280.2134-0.3188-0.2406-0.09750.56590.270.06510.24220.16860.3066-23.57946.7127108.5362
330.75370.58710.75871.6399-0.77854.44280.26180.41050.2574-0.4109-0.25570.0919-0.56-0.2025-0.12670.60580.13550.08910.24970.08150.21-11.547548.9273109.3628
344.0682-1.3268-2.29642.25530.96042.92530.0843-0.06090.1411-0.1840.0169-0.1601-0.31550.0495-0.20130.43330.08660.01160.1689-0.11350.0501-10.827341.8654114.8418
351.96891.16041.77713.30713.49834.27640.14950.0083-0.67220.45350.07550.00120.84680.1941-0.26320.4698-0.06330.00870.2171-0.07760.206710.042527.6057115.8487
361.2544-0.2012-0.25380.8689-0.151.10670.10140.3030.0043-0.26950.0180.0741-0.093-0.04890.02230.6042-0.19290.05270.18420.0057-0.10718.569339.469108.3077
372.3314-0.3157-1.01370.28620.57311.8280.1187-0.01870.29280.0737-0.0872-0.0687-0.4399-0.0013-0.09930.6333-0.16150.06320.14620.00410.185311.933850.8635108.524
381.88530.2877-0.61281.5053-0.10122.2354-0.07680.08010.1335-0.1113-0.1612-0.1148-0.25890.11470.05040.3722-0.13090.01250.23250.06910.090520.326741.5426112.4002
393.2154-0.4512.41380.58950.41952.90760.17880.0839-0.53970.03010.01840.43470.673-0.2321-0.20590.4773-0.269-0.07210.34610.03220.246825.581914.6234115.8049
401.2866-0.2964-0.14091.41310.13052.31060.13810.41430.0307-0.462-0.07940.00950.0664-0.00130.0210.4266-0.22520.11980.51440.0823-0.091832.040524.7205108.305
410.19640.15740.14472.74610.87711.50730.0391-0.12860.04380.02820.0059-0.2166-0.16710.2888-0.0890.2962-0.26660.07510.485-0.04440.126741.395930.9368111.7611
423.6575-1.2982-0.80593.8806-3.40574.23530.14290.02710.4276-0.1232-0.1976-0.6262-0.40520.34430.08480.6148-0.27050.17290.80930.0090.389744.617726.296104.4116
431.68680.0417-0.64372.58510.96182.8852-0.134-0.1089-0.0224-0.0201-0.0878-0.1755-0.0120.3512-0.00740.3611-0.08190.09530.492-0.00960.082640.981118.0162115.0053
440.81380.89-1.71642.6147-1.84984.20180.0674-0.067-0.14880.21370.15640.59950.1382-0.6798-0.28270.2042-0.1614-0.0240.27240.16870.242520.811220.90156.9375
451.55380.0641-0.21641.20230.46762.2112-0.0246-0.3907-0.13270.3590.1089-0.10970.1304-0.037-0.0310.22520.0818-0.02810.1818-0.030.00432.175724.637964.4718
462.2475-1.3104-1.57372.07821.31123.57950.0094-0.26050.25210.03460.2014-0.3884-0.10860.47-0.22170.2527-0.0132-0.08140.1725-0.13480.267741.055132.530264.2401
471.8306-0.30230.17961.4441-0.11341.6969-0.0752-0.18650.22210.12290.0316-0.1204-0.24150.09020.01720.09760.0094-0.05620.1311-0.04610.108429.041436.148660.3584
480.7292-0.0129-0.37712.3404-1.99762.4547-0.0654-0.035-0.5255-0.13910.13030.22010.5403-0.3435-0.04940.3671-0.1674-0.0440.13590.07920.27442.395529.233556.9991
491.2670.1505-0.21730.92790.18341.44930.0642-0.4917-0.06510.2442-0.063-0.02120.1355-0.0320.00450.18-0.1133-0.03990.1219-0.0587-0.15628.733639.452264.4361
501.4415-0.2106-0.99820.55680.24041.85980.0858-0.10790.19510.108-0.0103-0.0882-0.32780.1144-0.10640.1887-0.0337-0.01740.0678-0.14140.283210.489251.200564.0998
511.83280.3280.21181.53980.25731.56720.0102-0.19060.28410.1448-0.03950.0857-0.1947-0.0308-0.02440.2381-0.09350.00990.1319-0.10250.0441-1.057146.243560.284
521.9249-0.75461.0841.6602-2.78314.68680.1945-0.0373-0.5105-0.1391-0.0263-0.11470.89380.0483-0.21610.3240.0736-0.15550.1099-0.0250.1715-17.160323.955457.0807
530.96610.2991-0.30451.09060.15361.5070.2396-0.38790.00730.3897-0.1083-0.06020.13930.06650.0490.209-0.11160.03350.157-0.1315-0.2149-18.750335.906564.4702
541.50381.0941-1.14010.802-0.71622.77210.0949-0.06950.27410.0730.01630.1703-0.3315-0.0361-0.12710.1627-0.02090.08020.1002-0.03860.1432-24.854346.092364.0851
551.0232-0.34720.31140.27770.59163.1310.0382-0.20440.19880.2236-0.07780.1217-0.283-0.06220.02190.194-0.03890.12140.2328-0.1350.3082-33.603737.544163.3059
561.1630.6390.52272.2476-0.78712.42790.01110.00070.0096-0.03660.00840.08940.0576-0.0372-0.05610.1762-0.1579-0.08230.1797-0.01630.0247-28.230232.811557.915
570.75260.634-0.46861.93082.18385.0647-0.0097-0.0097-0.2623-0.00260.0946-0.38110.32780.3534-0.1080.25410.2009-0.04910.1273-0.03440.1656-6.786528.081629.3541
581.2641-0.0754-0.43481.0396-0.47912.22360.00380.2557-0.0672-0.2532-0.0580.1250.1834-0.0821-0.07090.26840.0908-0.05940.09550.1077-0.0172-14.480437.139521.6967
591.85920.135-0.70560.9375-0.75151.876-0.02280.120.37280.08550.06950.093-0.3041-0.1411-0.02660.34410.0822-0.03250.13630.11730.2097-17.85148.526821.7643
600.08980.01060.4731.3982-0.84443.07630.09030.12340.1007-0.20250.01680.0835-0.2164-0.228-0.12740.20790.0930.06890.22680.19090.0998-5.647949.219722.5904
612.6372-1.4133-0.32622.20180.56683.3655-0.0293-0.05730.1150.048-0.0486-0.09290.02940.1463-0.02120.10550.0738-0.05140.18340.06340.0154-5.818742.198328.1593
625.1886-3.64473.72542.5687-2.78556.25610.3089-0.1161-0.7037-0.417-0.02390.16390.8415-0.2852-0.3570.4227-0.0344-0.10810.19950.10610.210911.398828.147833.4508
635.32493.85454.45666.43222.85356.5840.38480.0062-0.71340.2807-0.0461-0.54930.91960.1212-0.29440.2436-0.05250.05120.0707-0.02850.169714.463823.284123.888
641.0356-0.0602-0.39091.0317-0.23541.6368-0.02240.256-0.0614-0.34120.030.05360.0798-0.10710.00040.19450.00830.08410.02570.2298-0.166413.051937.833321.7363
652.4987-2.689-1.21053.37551.95642.66090.0162-0.16920.28330.06410.0275-0.2766-0.26330.1028-0.11990.3308-0.06520.04140.11260.04590.17117.255248.044824.9004
661.9764-0.44230.33311.2655-1.73093.2101-0.01580.14330.17510.0608-0.0358-0.0597-0.22790.04440.04850.2478-0.05850.06510.0460.05-0.008322.472245.871617.5495
671.1878-0.19030.07662.4309-0.12641.6778-0.06010.04420.0317-0.046-0.0857-0.1576-0.060.1092-0.0010.24480.09020.06190.09020.08450.064124.178437.166328.2943
684.17530.42483.55041.50681.16873.78620.22510.0521-0.47260.0843-0.13890.36450.7478-0.1021-0.14860.311-0.06280.02130.2058-0.00090.171227.005211.580929.3689
691.18180.2959-0.24591.29880.43382.07260.00650.36940.0422-0.35460.03620.0232-0.1343-0.0584-0.01520.29230.13430.13570.22780.1115-0.137534.508920.818221.7216
700.6529-0.6273-0.52521.69481.0784.20280.00890.01940.0981-0.050.1436-0.1919-0.33010.2753-0.21250.19630.04180.18120.39260.06590.275945.076126.255521.8174
710.6153-0.0955-0.10320.3356-0.58082.5767-0.02510.30890.1546-0.20380.1269-0.1981-0.13960.2996-0.08430.1575-0.00350.11420.23870.00810.15948.009814.388622.6701
722.09330.05891.08954.06981.20092.98740.0856-0.0108-0.0806-0.0167-0.0105-0.16590.09330.0235-0.14740.29450.11560.05450.14980.08460.140941.064613.258728.2159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:26)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 27:115)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 116:137)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 138:179)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 2:15)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 16:26)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 27:115)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 116:137)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 138:155)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 156:179)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 2:26)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 27:115)
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 116:129)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 130:147)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 148:179)
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 2:24)
17X-RAY DIFFRACTION17CHAIN D AND (RESSEQ 25:115)
18X-RAY DIFFRACTION18CHAIN D AND (RESSEQ 116:137)
19X-RAY DIFFRACTION19CHAIN D AND (RESSEQ 138:179)
20X-RAY DIFFRACTION20CHAIN E AND (RESSEQ 2:24)
21X-RAY DIFFRACTION21CHAIN E AND (RESSEQ 25:115)
22X-RAY DIFFRACTION22CHAIN E AND (RESSEQ 116:137)
23X-RAY DIFFRACTION23CHAIN E AND (RESSEQ 138:179)
24X-RAY DIFFRACTION24CHAIN F AND (RESSEQ 2:15)
25X-RAY DIFFRACTION25CHAIN F AND (RESSEQ 16:24)
26X-RAY DIFFRACTION26CHAIN F AND (RESSEQ 25:115)
27X-RAY DIFFRACTION27CHAIN F AND (RESSEQ 116:129)
28X-RAY DIFFRACTION28CHAIN F AND (RESSEQ 130:147)
29X-RAY DIFFRACTION29CHAIN F AND (RESSEQ 148:179)
30X-RAY DIFFRACTION30CHAIN G AND (RESSEQ 2:24)
31X-RAY DIFFRACTION31CHAIN G AND (RESSEQ 25:115)
32X-RAY DIFFRACTION32CHAIN G AND (RESSEQ 116:137)
33X-RAY DIFFRACTION33CHAIN G AND (RESSEQ 138:155)
34X-RAY DIFFRACTION34CHAIN G AND (RESSEQ 156:179)
35X-RAY DIFFRACTION35CHAIN H AND (RESSEQ 2:24)
36X-RAY DIFFRACTION36CHAIN H AND (RESSEQ 25:115)
37X-RAY DIFFRACTION37CHAIN H AND (RESSEQ 116:137)
38X-RAY DIFFRACTION38CHAIN H AND (RESSEQ 138:179)
39X-RAY DIFFRACTION39CHAIN I AND (RESSEQ 2:24)
40X-RAY DIFFRACTION40CHAIN I AND (RESSEQ 25:115)
41X-RAY DIFFRACTION41CHAIN I AND (RESSEQ 116:129)
42X-RAY DIFFRACTION42CHAIN I AND (RESSEQ 130:147)
43X-RAY DIFFRACTION43CHAIN I AND (RESSEQ 148:179)
44X-RAY DIFFRACTION44CHAIN J AND (RESSEQ 2:24)
45X-RAY DIFFRACTION45CHAIN J AND (RESSEQ 25:115)
46X-RAY DIFFRACTION46CHAIN J AND (RESSEQ 116:137)
47X-RAY DIFFRACTION47CHAIN J AND (RESSEQ 138:179)
48X-RAY DIFFRACTION48CHAIN K AND (RESSEQ 2:24)
49X-RAY DIFFRACTION49CHAIN K AND (RESSEQ 25:115)
50X-RAY DIFFRACTION50CHAIN K AND (RESSEQ 116:137)
51X-RAY DIFFRACTION51CHAIN K AND (RESSEQ 138:179)
52X-RAY DIFFRACTION52CHAIN L AND (RESSEQ 2:24)
53X-RAY DIFFRACTION53CHAIN L AND (RESSEQ 25:115)
54X-RAY DIFFRACTION54CHAIN L AND (RESSEQ 116:137)
55X-RAY DIFFRACTION55CHAIN L AND (RESSEQ 138:155)
56X-RAY DIFFRACTION56CHAIN L AND (RESSEQ 156:179)
57X-RAY DIFFRACTION57CHAIN M AND (RESSEQ 2:24)
58X-RAY DIFFRACTION58CHAIN M AND (RESSEQ 25:115)
59X-RAY DIFFRACTION59CHAIN M AND (RESSEQ 116:137)
60X-RAY DIFFRACTION60CHAIN M AND (RESSEQ 138:155)
61X-RAY DIFFRACTION61CHAIN M AND (RESSEQ 156:179)
62X-RAY DIFFRACTION62CHAIN N AND (RESSEQ 2:15)
63X-RAY DIFFRACTION63CHAIN N AND (RESSEQ 16:26)
64X-RAY DIFFRACTION64CHAIN N AND (RESSEQ 27:115)
65X-RAY DIFFRACTION65CHAIN N AND (RESSEQ 116:129)
66X-RAY DIFFRACTION66CHAIN N AND (RESSEQ 130:147)
67X-RAY DIFFRACTION67CHAIN N AND (RESSEQ 148:179)
68X-RAY DIFFRACTION68CHAIN O AND (RESSEQ 2:24)
69X-RAY DIFFRACTION69CHAIN O AND (RESSEQ 25:115)
70X-RAY DIFFRACTION70CHAIN O AND (RESSEQ 116:137)
71X-RAY DIFFRACTION71CHAIN O AND (RESSEQ 138:155)
72X-RAY DIFFRACTION72CHAIN O AND (RESSEQ 156:179)

+
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