[English] 日本語
Yorodumi
- PDB-3inu: Crystal structure of an unbound KZ52 neutralizing anti-Ebolavirus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3inu
TitleCrystal structure of an unbound KZ52 neutralizing anti-Ebolavirus antibody.
Components
  • KZ52 antibody fragment heavy chain
  • KZ52 antibody fragment light chain
KeywordsIMMUNE SYSTEM / antibody fragment (Fab) / immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLee, J.E. / Fusco, M.L. / Abelson, D.M. / Hessell, A.J. / Burton, D.R. / Saphire, E.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Techniques and tactics used in determining the structure of the trimeric ebolavirus glycoprotein.
Authors: Lee, J.E. / Fusco, M.L. / Abelson, D.M. / Hessell, A.J. / Burton, D.R. / Saphire, E.O.
History
DepositionAug 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.version
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: KZ52 antibody fragment heavy chain
L: KZ52 antibody fragment light chain
M: KZ52 antibody fragment heavy chain
N: KZ52 antibody fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,97216
Polymers95,8354
Non-polymers1,13712
Water1,36976
1
H: KZ52 antibody fragment heavy chain
L: KZ52 antibody fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4868
Polymers47,9182
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-85 kcal/mol
Surface area19480 Å2
MethodPISA
2
M: KZ52 antibody fragment heavy chain
N: KZ52 antibody fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4868
Polymers47,9182
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-84 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.520, 129.520, 184.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Antibody KZ52 antibody fragment heavy chain


Mass: 24020.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody KZ52 antibody fragment light chain


Mass: 23896.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.68 Å3/Da / Density % sol: 73.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5 and 12% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 2.5→47.96 Å / Num. obs: 114050 / % possible obs: 99 % / Redundancy: 6.99 % / Rmerge(I) obs: 0.118 / Χ2: 0.86 / Net I/σ(I): 7.5 / Scaling rejects: 48200
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.41 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2 / Num. measured all: 42658 / Num. unique all: 6117 / Χ2: 0.99 / % possible all: 98.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.464 / Packing: 0.269
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral98.9 0

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
CNSrefinement
d*TREK9.6Ddata scaling
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N0X
Resolution: 2.5→47.955 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.252 5622 4.93 %random
Rwork0.203 ---
obs0.205 114050 94.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.866 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 181.98 Å2 / Biso mean: 66.853 Å2 / Biso min: 29.53 Å2
Baniso -1Baniso -2Baniso -3
1-2.274 Å2-0 Å2-0 Å2
2--2.274 Å2-0 Å2
3----4.547 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 64 76 6846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086917
X-RAY DIFFRACTIONf_angle_d1.2029397
X-RAY DIFFRACTIONf_chiral_restr0.0771055
X-RAY DIFFRACTIONf_plane_restr0.0051195
X-RAY DIFFRACTIONf_dihedral_angle_d19.222425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5280.4251610.3953310347186
2.528-2.5580.4451660.3713347351389
2.558-2.5890.3771770.3663433361089
2.589-2.6220.3852130.343371358490
2.622-2.6570.3941840.3413496368091
2.657-2.6930.3682080.3233473368192
2.693-2.7310.3461650.3193409357491
2.731-2.7720.3592160.313499371592
2.772-2.8160.2991710.2843553372492
2.816-2.8620.3331620.2853541370393
2.862-2.9110.311850.2783543372894
2.911-2.9640.2821830.2643553373693
2.964-3.0210.3191550.2633669382495
3.021-3.0830.3212270.2473560378795
3.083-3.150.2781740.2263699387396
3.15-3.2230.2791970.2213638383596
3.223-3.3030.2731590.2233711387097
3.303-3.3930.2492170.2143667388497
3.393-3.4930.2182090.1943663387297
3.493-3.6050.2391850.1943758394398
3.605-3.7340.2422000.1923717391798
3.734-3.8830.2262030.183744394798
3.883-4.060.2461550.1673767392298
4.06-4.2740.1922240.1453691391598
4.274-4.5420.1831800.1323766394698
4.542-4.8920.2011910.133741393299
4.892-5.3840.1541960.1293796399299
5.384-6.1610.2091810.1543769395099
6.161-7.7570.2981620.193840400299
7.757-47.9630.2152160.1933704392098
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)
10.0968-0.6426-0.6271.0691-1.39122.0243-0.09160.11890.07580.1252-0.1907-0.4374-0.2216-0.32160.30110.40010.0214-0.01460.44480.11160.5896-71.153768.1996-141.7549
21.63810.4533-0.25042.1887-3.09389.3712-0.4638-0.06460.05360.3162-0.5081-0.867-1.0114-0.44540.80860.35780.02880.00180.40020.02690.5033-76.964770.8707-141.7761
30.9498-0.8653-0.06250.4512.47593.81440.18210.2739-0.16630.1656-0.16670.270.0213-0.3395-0.0290.28110.09080.01680.46790.05520.4063-83.949763.5172-146.9785
40.7562-1.32011.55520.44461.88252.7616-0.1777-0.3940.042-0.0432-0.05240.0065-0.3168-0.31450.23020.31410.1204-0.01660.42390.03520.4428-83.268468.524-139.2046
50.918-2.27160.86940.84941.0544-0.29350.39660.51010.0246-0.2509-0.26410.29020.7164-0.0181-0.0830.36390.06740.0180.57330.03480.478-78.365161.982-146.7585
6-0.9768-0.2649-3.10462.13391.64881.03350.19390.2387-0.2957-0.3552-0.2349-0.2365-0.0189-0.3130.08280.40410.0442-0.02690.65010.03940.4127-81.540464.9449-154.2048
7-0.7792-0.01870.47931.3135-0.43261.5079-0.08350.2305-0.18810.10540.1216-0.2312-0.10170.5623-0.10750.3834-0.03560.01960.6174-0.07250.494-55.944155.6813-130.8766
80.9024-0.85180.09351.9693-1.26221.82810.38960.11990.3502-0.0238-0.0554-0.3113-0.49130.3541-0.22660.3471-0.11870.05820.5513-0.0410.4722-50.720156.695-138.0699
90.4109-2.76851.06251.5777-0.51462.39210.21320.41710.3084-0.0182-0.1575-0.4222-0.17560.583-0.02340.4008-0.12540.05430.5708-0.03170.4627-49.690856.3536-139.3927
106.1234-2.7906-1.72270.0241-1.36562.00850.6427-0.29491.2139-0.0049-0.188-0.2809-0.56180.4169-0.36570.5757-0.226-0.0030.6591-0.10410.7608-49.178163.1476-132.4428
110.4542-0.18951.37331.6070.61563.6501-0.6301-0.14840.18560.31740.54890.36840.6115-0.0654-0.0970.31020.1248-0.0520.6761-0.0890.5741-74.409443.9518-156.909
12-0.11070.77641.89382.02330.94371.28590.73150.0998-0.4719-0.5493-0.45390.69770.15730.0952-0.24570.49810.163-0.14240.8647-0.07910.6383-82.287148.8373-164.531
131.8594-0.05531.01272.5140.60982.09720.17650.42450.41370.1327-0.3026-0.1790.36760.09480.14580.33020.1312-0.03590.70460.02460.3669-73.789956.5307-157.7605
140.3901-3.0669-0.31352.42151.68531.95770.6030.74480.2064-0.5193-0.6226-0.1656-0.10770.36020.05190.38280.18830.01890.8679-0.03320.3459-72.291553.0412-164.3935
152.2989-2.03890.85010.2050.77712.9674-0.20510.3593-1.14710.1961-0.17260.46280.0131-0.46580.33810.36620.09270.04060.57960.04180.5821-80.046551.7126-154.7787
160.8404-0.03590.9581.21962.13032.85420.24690.1244-0.0879-0.15470.3931-0.6094-0.28240.8952-0.620.25130.0405-0.00010.7113-0.07920.4314-46.2944.9781-143.6191
170.0837-0.51410.08911.86990.65742.1176-0.25060.05380.26860.1250.13250.39350.33820.30720.03850.18340.03520.04080.5428-0.01950.3056-48.871742.3615-138.2598
185.5406-1.65630.99983.2467-2.17873.4866-0.6047-0.63090.41090.24090.2488-0.40080.4073-0.94120.25690.4778-0.03810.04590.8274-0.03610.5366-49.782936.4119-130.7724
190.32720.0813-0.9240.69280.06262.20610.0697-0.24490.02250.02030.0860.2327-0.3756-0.9219-0.29340.26510.14850.03950.71410.02730.4263-52.203446.2711-142.3095
20-0.23740.92342.13641.91980.28743.08030.3681-0.0013-0.24040.31310.4852-0.67120.43770.4231-0.50160.4640.0848-0.09750.8902-0.07840.5407-41.603837.0762-135.386
212.89181.17770.92770.16320.40552.6268-0.42760.0273-0.3299-0.0380.04910.07120.0030.52090.29970.4223-0.0268-0.03970.4616-0.00930.4952-33.880634.5273-173.0496
222.15061.10922.34530.89050.13871.897-0.23330.6074-0.2963-0.09650.13070.1428-0.01120.1620.04640.3784-0.09460.01970.4275-0.04830.4407-32.418838.2986-184.1863
232.39032.86191.67881.767-0.78224.7331-0.17310.01670.29790.0652-0.0183-0.0729-0.4110.21740.16330.3474-0.0358-0.04110.37970.00730.4071-31.071444.8907-176.9535
240.7481.5512.97554.79381.3031.6321-0.1895-0.44830.5909-0.3680.20280.7869-0.2493-0.58850.06010.3042-0.042-0.07660.3861-0.07890.3466-40.622140.8001-173.8582
252.71421.39570.36861.08830.0592-0.21860.25890.4428-0.2060.5642-0.2993-0.555-0.2750.46760.0370.5468-0.1456-0.06520.71180.06340.5582-32.220444.4449-192.0644
261.9003-0.42651.52620.4306-1.64292.67690.2411-0.605-0.5597-0.16530.2760.00750.13240.0329-0.39280.4046-0.0546-0.14280.37080.1240.5383-46.829128.5759-166.2665
276.22531.91363.0373.9727-0.00510.9948-0.7610.87720.08620.25230.8799-0.3538-0.19240.3379-0.04441.4602-0.0958-0.46111.49130.44471.3626-70.529311.4959-171.1925
282.5231-4.1119-0.0873-0.2007-0.71322.78941.2604-0.5838-0.76540.1054-0.0105-0.37510.78380.6917-0.54020.40550.0523-0.25750.25030.21430.2567-54.848722.816-167.3
298.2635-0.79652.21150.2475-0.74092.64210.6624-0.1894-1.3965-0.57720.22460.47640.456-0.0047-0.8630.5680.0057-0.27360.34460.06990.6767-55.716221.3301-171.8281
303.10921.59650.26190.3192.81150.64370.7784-0.0961-1.79170.26130.0357-0.78291.01130.1798-0.75450.9883-0.0225-0.40790.48050.12551.058-50.579113.6168-167.9748
31-0.42421.36341.48780.98141.97122.6727-0.0926-0.3915-0.1355-0.66350.0641-0.0138-0.8492-0.0587-0.02230.5805-0.0949-0.0870.40690.06690.688-50.667652.882-187.2308
321.53020.6028-1.58451.45-3.35832.60520.18570.17230.61560.38950.02710.8568-0.5238-0.4664-0.11570.6132-0.061-0.08220.56070.06030.5853-60.098542.9339-193.9231
334.2514-2.07721.51380.7450.06441.0507-0.02540.48480.3698-0.1767-0.1024-0.1168-0.15350.27070.10830.4056-0.1356-0.0340.50760.05740.4106-43.521845.461-194.208
342.85150.62540.45510.2053-0.43620.2144-0.19591.21150.0411-0.41160.00470.1205-0.04230.05150.11080.558-0.1472-0.10580.78570.06220.531-49.047542.4741-199.7869
354.45521.59051.96322.87551.29582.46960.27430.3089-1.0235-0.1130.1679-0.9910.4550.1899-0.37670.4343-0.0381-0.04890.4252-0.00270.4182-54.534336.822-192.3799
364.05272.44730.93662.5964-0.31152.34470.3097-0.86570.87960.1796-0.45480.6382-0.437-0.03070.09760.3915-0.0553-0.05970.4136-0.0020.5329-46.529447.7901-187.6881
373.9705-0.75540.61540.12470.1327-0.60970.4323-1.3281-0.92590.0377-0.3312-0.0730.1478-0.1695-0.10940.4883-0.3083-0.20830.84240.37470.5942-66.130621.7587-168.3299
383.61820.56622.92492.20130.15811.8420.4229-0.7793-0.14490.1963-0.39-0.1764-0.206-0.1715-0.04840.4337-0.1307-0.04110.5018-0.00590.4021-68.5528.913-172.9278
39-0.2454-2.6524-0.48742.1414-0.9632.36750.2865-1.3251-0.62680.6694-0.05730.2496-1.0803-0.1189-0.18310.6237-0.4469-0.11121.23790.30370.4905-70.578724.5241-160.1013
402.5905-1.73671.0680.4269-1.02275.5732-0.3269-0.4407-1.6207-0.0277-0.49130.0043-0.9015-1.27010.44020.259-0.2391-0.00910.55680.39460.7368-77.716521.7707-169.3687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain H and resid 1:13H1 - 13
2X-RAY DIFFRACTION2chain H and resid 14:29H14 - 29
3X-RAY DIFFRACTION3chain H and resid 30:62H30 - 62
4X-RAY DIFFRACTION4chain H and resid 63:83H63 - 83
5X-RAY DIFFRACTION5chain H and resid 84:98H84 - 98
6X-RAY DIFFRACTION6chain H and resid 99:107H99 - 107
7X-RAY DIFFRACTION7chain H and resid 108:129H108 - 129
8X-RAY DIFFRACTION8chain H and resid 130:165H130 - 165
9X-RAY DIFFRACTION9chain H and resid 166:212H166 - 212
10X-RAY DIFFRACTION10chain H and resid 213:228H213 - 228
11X-RAY DIFFRACTION11chain L and resid 1:15L1 - 15
12X-RAY DIFFRACTION12chain L and resid 16:29L16 - 29
13X-RAY DIFFRACTION13chain L and resid 30:47L30 - 47
14X-RAY DIFFRACTION14chain L and resid 48:89L48 - 89
15X-RAY DIFFRACTION15chain L and resid 90:105L90 - 105
16X-RAY DIFFRACTION16chain L and resid 106:124L106 - 124
17X-RAY DIFFRACTION17chain L and resid 125:149L125 - 149
18X-RAY DIFFRACTION18chain L and resid 150:162L150 - 162
19X-RAY DIFFRACTION19chain L and resid 163:184L163 - 184
20X-RAY DIFFRACTION20chain L and resid 185:211L185 - 211
21X-RAY DIFFRACTION21chain M and resid 1:22M1 - 22
22X-RAY DIFFRACTION22chain M and resid 23:41M23 - 41
23X-RAY DIFFRACTION23chain M and resid 42:83M42 - 83
24X-RAY DIFFRACTION24chain M and resid 84:93M84 - 93
25X-RAY DIFFRACTION25chain M and resid 94:102M94 - 102
26X-RAY DIFFRACTION26chain M and resid 103:126M103 - 126
27X-RAY DIFFRACTION27chain M and resid 127:132M127 - 132
28X-RAY DIFFRACTION28chain M and resid 133:152M133 - 152
29X-RAY DIFFRACTION29chain M and resid 153:196M153 - 196
30X-RAY DIFFRACTION30chain M and resid 197:227M197 - 227
31X-RAY DIFFRACTION31chain N and resid 1:8N1 - 8
32X-RAY DIFFRACTION32chain N and resid 9:25N9 - 25
33X-RAY DIFFRACTION33chain N and resid 26:50N26 - 50
34X-RAY DIFFRACTION34chain N and resid 51:74N51 - 74
35X-RAY DIFFRACTION35chain N and resid 75:89N75 - 89
36X-RAY DIFFRACTION36chain N and resid 90:105N90 - 105
37X-RAY DIFFRACTION37chain N and resid 106:133N106 - 133
38X-RAY DIFFRACTION38chain N and resid 134:172N134 - 172
39X-RAY DIFFRACTION39chain N and resid 173:197N173 - 197
40X-RAY DIFFRACTION40chain N and resid 198:210N198 - 210

+
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