[English] 日本語
Yorodumi
- PDB-6elu: Structure of Serum Resistance Associated protein from T. b. rhode... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6elu
TitleStructure of Serum Resistance Associated protein from T. b. rhodesiense
Components
  • G10_3 Light chain
  • G10_3 heavy chain
  • Serum resistance associated; VSG protein
KeywordsANTITOXIN / Tryanosome / innate immune evasion / sleeping sickness / apolipoprotein LI / SRA / trypanolytic factor.
Function / homology
Function and homology information


evasion of host immune response / plasma membrane
Similarity search - Function
Trypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serum resistance associated; VSG protein
Similarity search - Component
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZoll, S. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/P001424/1 United Kingdom
CitationJournal: Nat Microbiol / Year: 2018
Title: The structure of serum resistance-associated protein and its implications for human African trypanosomiasis.
Authors: Zoll, S. / Lane-Serff, H. / Mehmood, S. / Schneider, J. / Robinson, C.V. / Carrington, M. / Higgins, M.K.
History
DepositionSep 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serum resistance associated; VSG protein
B: G10_3 heavy chain
C: G10_3 Light chain
D: Serum resistance associated; VSG protein
E: G10_3 heavy chain
F: G10_3 Light chain
G: Serum resistance associated; VSG protein
H: G10_3 heavy chain
I: G10_3 Light chain
J: Serum resistance associated; VSG protein
K: G10_3 heavy chain
L: G10_3 Light chain


Theoretical massNumber of molelcules
Total (without water)292,14812
Polymers292,14812
Non-polymers00
Water10,449580
1
A: Serum resistance associated; VSG protein
B: G10_3 heavy chain
C: G10_3 Light chain


Theoretical massNumber of molelcules
Total (without water)73,0373
Polymers73,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Serum resistance associated; VSG protein
E: G10_3 heavy chain
F: G10_3 Light chain


Theoretical massNumber of molelcules
Total (without water)73,0373
Polymers73,0373
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Serum resistance associated; VSG protein
H: G10_3 heavy chain
I: G10_3 Light chain


Theoretical massNumber of molelcules
Total (without water)73,0373
Polymers73,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Serum resistance associated; VSG protein
K: G10_3 heavy chain
L: G10_3 Light chain


Theoretical massNumber of molelcules
Total (without water)73,0373
Polymers73,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.600, 103.550, 150.640
Angle α, β, γ (deg.)90.00, 114.58, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Serum resistance associated; VSG protein


Mass: 24399.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei rhodesiense (eukaryote)
Gene: SRA / Production host: Escherichia coli (E. coli) / Strain (production host): T7 shuffle / References: UniProt: Q8T309
#2: Antibody
G10_3 heavy chain


Mass: 24693.635 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody
G10_3 Light chain


Mass: 23944.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dehydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 100 mM tris(base)/Bicine pH 8.5, ...Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dehydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 100 mM tris(base)/Bicine pH 8.5, 20% (v/v) PEG 500 MME, 10 % (w/v) PEG 20,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→48.431 Å / Num. obs: 310049 / % possible obs: 99.4 % / Redundancy: 3.4 % / Net I/σ(I): 9.5

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.431 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.66
RfactorNum. reflection% reflection
Rfree0.2204 7914 5 %
Rwork0.1905 --
obs0.192 158272 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18573 0 0 580 19153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718966
X-RAY DIFFRACTIONf_angle_d1.00225843
X-RAY DIFFRACTIONf_dihedral_angle_d7.60811433
X-RAY DIFFRACTIONf_chiral_restr0.0563005
X-RAY DIFFRACTIONf_plane_restr0.0063307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.36962610.34444974X-RAY DIFFRACTION100
2.3261-2.35350.34042650.32575030X-RAY DIFFRACTION100
2.3535-2.38220.32112610.31584961X-RAY DIFFRACTION100
2.3822-2.41240.34922640.30235018X-RAY DIFFRACTION100
2.4124-2.44410.33082610.29634946X-RAY DIFFRACTION100
2.4441-2.47760.32452620.28354982X-RAY DIFFRACTION100
2.4776-2.5130.28412640.27555023X-RAY DIFFRACTION100
2.513-2.55050.30922630.27114989X-RAY DIFFRACTION100
2.5505-2.59030.29492630.26214995X-RAY DIFFRACTION100
2.5903-2.63280.30852610.25734968X-RAY DIFFRACTION100
2.6328-2.67820.29132620.2544983X-RAY DIFFRACTION100
2.6782-2.72690.28722680.24215073X-RAY DIFFRACTION100
2.7269-2.77930.25482600.22474949X-RAY DIFFRACTION100
2.7793-2.8360.26052630.21755002X-RAY DIFFRACTION100
2.836-2.89770.25612640.2195020X-RAY DIFFRACTION100
2.8977-2.96510.2722630.22014995X-RAY DIFFRACTION100
2.9651-3.03920.27832640.22195014X-RAY DIFFRACTION100
3.0392-3.12140.27462630.22944993X-RAY DIFFRACTION100
3.1214-3.21320.26462630.21734997X-RAY DIFFRACTION100
3.2132-3.31690.25982620.20634983X-RAY DIFFRACTION100
3.3169-3.43540.23672650.20035038X-RAY DIFFRACTION100
3.4354-3.5730.22662660.18845048X-RAY DIFFRACTION100
3.573-3.73550.20892630.1774995X-RAY DIFFRACTION100
3.7355-3.93240.20352630.15985003X-RAY DIFFRACTION100
3.9324-4.17860.16142650.1555038X-RAY DIFFRACTION100
4.1786-4.5010.16182660.13625043X-RAY DIFFRACTION100
4.501-4.95360.17632650.12935043X-RAY DIFFRACTION100
4.9536-5.66940.17032650.14315029X-RAY DIFFRACTION100
5.6694-7.13920.16862670.16735076X-RAY DIFFRACTION100
7.1392-48.44180.17412720.16645150X-RAY DIFFRACTION99
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)
10.02830.00330.03560.00760.036-0.01210.18740.01170.08480.11640.10640.0161-0.12240.049100.4485-0.1083-0.04030.9371-0.32131.0115133.741333.3475122.6668
2-0.0040.00440.0120.0022-0.0009-0.00670.1080.02340.05040.00650.04040.0035-0.0328-0.027500.8806-0.05910.00110.9326-0.17990.9479125.486840.274116.2138
30.01150.01110.00670.00720.00480.00150.0805-0.00980.03380.01550.0364-0.0292-0.01920.056300.5417-0.0654-0.07060.8073-0.16570.7739134.310311.8073105.5124
40.01130.03830.04070.0355-0.03240.0248-0.0849-0.14510.06530.11630.1683-0.14340.3670.123900.43370.054-0.05660.2415-0.03450.3635115.0412-7.691101.8223
5-0.04440.0259-0.02270.0521-0.0008-0.00230.25950.2132-0.10450.1227-0.0047-0.09710.07250.0462-00.5672-0.14740.0263-1.2782-0.06570.27597.8784-20.659776.5779
6-0.0095-0.00770.00390.0264-0.00320.00360.0395-0.11330.0817-0.0972-0.0677-0.0184-0.02710.0325-00.5645-0.03190.06260.2863-0.06410.4746110.299115.394992.2454
70.0094-0.00480.01310.0068-0.01520.01110.1244-0.03420.0616-0.19220.0455-0.0151-0.06440.1351-00.4701-0.14970.10120.1364-0.13670.3849114.92618.876986.5998
80.0188-0.06930.00650.03580.00910.02140.014-0.24540.00060.02180.1054-0.02870.0102-0.007100.425-0.22250.0604-0.4273-0.02190.279998.7826-4.479582.6496
9-0.0007-0.0257-0.00470.031-0.0211-0.01180.03530.02970.05590.1335-0.00760.0332-0.0498-0.4585-00.3627-0.25190.2145-1.02710.41740.154985.3223-10.03273.4512
100.0122-0.00260.0133-0.00340.00740.00020.0992-0.02480.13990.0032-0.0020.05780.0520.0374-00.9013-0.1365-0.38751.0321-0.09260.907175.94256.619360.9951
110.0037-00.0106-00.00390.00550.0466-0.02270.07230.0031-0.02910.06870.11310.036400.887-0.1772-0.26481.0579-0.18160.9258170.873811.434872.0715
120.00040.00040-0.0019-0.0002-0.0002-0.0056-0.00270.0003-0.0078-0.0010.02110.0135-0.012401.43870.05380.00191.4059-0.01181.3888174.3926-10.900263.7689
130.00530.00160.0037-0.00210.00390.0004-0.02640.0048-0.0224-0.0147-0.03770.00360.04030.0002-00.7715-0.1755-0.24080.9005-0.10780.883161.11489.999168.2979
140.00020.00020.00020.00010.00020.0031-0.0029-0.00390.0036-0.0021-0.00130.0041-0.0011-0.003-01.20610.02250.01751.2404-0.05611.1964143.547321.04979.9459
150.00130.00060.004-0.001-0.00010.00050.02410.0137-0.00050.02810.0146-0.05660.00970.0186-00.706-0.1475-0.18070.8108-0.08440.8309153.422417.609164.205
160.03350.0265-0.00220.0394-0.06150.03620.13330.04110.2384-0.0576-0.0849-0.2403-0.0351-0.0152-00.3573-0.0330.02010.2816-0.05060.3695133.267417.67249.518
17-0.00230.00720.00040.0010.00550.0025-0.0065-0.0085-0.0431-0.0045-0.01430.0662-0.0133-0.0265-00.37140.0009-0.00540.15290.04930.381192.29662.992547.1065
180.0278-0.0070.02010.0303-0.01040.0096-0.01690.09890.01650.01760.03670.1105-0.09790.054100.36710.07710.03450.16190.04070.2294103.04989.823447.4272
190.0035-0.00280.00830.0025-0.00320.0053-0.0707-0.0032-0.03680.1062-0.0823-0.03310.10230.0306-00.40110.0605-0.06050.4590.00770.4621138.1132-5.218559.7912
200.00180.005200.0098-0.00320.00640.0213-0.0540.01390.0822-0.04030.0058-0.02870.097-00.31760.0081-0.090.38410.00360.2915133.22641.459364.6994
210.0013-0.00870.00110.02960.0040.00460.02670.01370.00640.14550.0592-0.03660.16780.1455-00.25810.0398-0.0490.2386-0.03570.2449127.6227-2.496959.2305
220.0046-0.0257-0.00360.04710.02230.0344-0.11450.29570.0160.0829-0.04530.0257-0.0343-0.1265-00.32380.18680.0060.155-0.08760.2115100.6817-5.874942.8945
230.008-0.00170.0129-0.0003-0.00180.01160.1759-0.01280.04050.1336-0.06420.02140.01970.043100.73050.1256-0.18011.10.07860.8163135.8328-41.178363.7673
240.00050.00130.0004-0.00060.001-0.0003-0.0058-0.0075-0.00780.017-0.0033-0.00580.00160.0027-01.3439-0.04980.08361.41630.00851.4277125.5524-27.974376.2601
250.00840.00050.0101-0.0055-0.00010.00410.018-0.02670.0215-0.014-0.0041-0.10120.0072-0.00700.56050.0963-0.11960.76270.01520.5655135.4012-37.1347.0464
26-0.00080.00210.00550.00250.00360.0058-0.03210.0222-0.011-0.0297-0.0116-0.04210.01780.0123-00.55930.1736-0.14040.5984-0.01070.5343131.0466-44.178441.578
270.02150.00830.01910.0626-0.01260.0259-0.21390.09290.0294-0.0240.1973-0.03620.30960.10700.31850.18240.03830.3211-0.07890.2775112.496-46.831925.2559
28-0.0017-0.0032-0.0020.0003-0.00020.0028-0.04430.01750.02820.0101-0.03420.01080.016-0.0098-00.2909-0.005-0.01750.46260.0260.252689.6595-25.2674-4.8324
290.02160.00180.03020.01180.00890.01220.06760.30560.01960.1111-0.06620.04420.13230.0453-00.228-0.01550.00470.3958-0.02190.179396.6402-33.571.7324
300.0008-0.0094-0.01680.00030.00290.0046-0.0082-0.04860.0756-0.05150.039-0.0044-0.00110.0198-00.32210.03450.01680.2733-0.04620.2956107.2951-21.686334.5346
310.0059-0.01270.00440.02050.020.00240.02620.02770.1467-0.0023-0.0354-0.1703-0.06690.067700.27860.0628-0.09840.2794-0.10230.3011117.3703-27.081233.5855
320.0166-0.0059-0.0010.01320.02420.0145-0.01980.05650.07910.04380.0156-0.04840.03660.03900.31360.0617-0.02260.2831-0.02950.2883111.9183-28.410631.2504
330.0081-0.03230.01310.00380.0132-0.00540.04890.2049-0.01530.13330.05860.0137-0.1605-0.1312-00.11660.013-0.00250.3253-0.02440.240192.2585-23.60468.1179
340.0053-0.003-0.00530.0124-0.00590.0064-0.08690.04280.00220.1158-0.03640.0384-0.01-0.0153-00.2341-0.01560.02330.3921-0.010.303384.8551-20.98399.7568
350.0003-0.00130.00040.0027-0.0020.0025-0.0381-0.0009-0.00090.0388-0.0166-0.05560.0159-0.049100.247-0.01230.0090.3359-0.00190.25294.756-23.071714.2181
360.0055-0.00940.00620.0030.00410.00180.01160.0558-0.04460.00150.01430.1074-0.0636-0.1023-00.18180.0254-0.02520.4137-0.00470.325279.9067-22.21873.7265
370.0740.00050.05240.12850.0486-0.0024-0.22680.2674-0.0469-1.1820.0402-0.5020.00660.0634-0-0.80130.6252-0.37980.61230.31220.2687173.9531-17.397513.0316
380.0010.00180.00080.00050.0116-0.00380.0065-0.0099-0.0054-0.0785-0.03860.00340.07270.018-00.78830.01860.13680.9063-0.01740.8033172.4758-23.7205-2.0985
390.0058-0.00690.00430.0008-0.00490.0048-0.07680.0667-0.09110.1791-0.1504-0.0441-0.04980.071600.26540.1301-0.08020.5749-0.04080.499155.7661-11.134122.9548
400.03480.00850.00380.06910.01440.00240.03470.1351-0.02410.10250.05630.2205-0.07070.234700.2497-0.00140.0370.51320.07270.2505136.90116.978613.7841
410.0034-0.00490.00310.0031-0.0038-0.0028-0.01240.03950.0391-0.0204-0.0412-0.02810.0107-0.003700.3782-0.0550.04720.57940.20810.729895.29675.79911.2991
420.014-0.01080.01120.01620.01060.00730.05790.01690.0810.07740.02870.0735-0.06090.035600.25780.04050.07130.36370.15670.4804106.54258.14726.6985
430.0034-0.0032-0.00270.00120.00190.00320.04780.0039-0.0333-0.05430.05540.0416-0.02320.046400.2959-0.02950.0540.5443-0.04120.4099131.5475-15.1316-1.5838
440.00770.00630.00080.00370.0060.0069-0.00030.1096-0.0122-0.02750.11830.0319-0.05280.0697-00.17990.05470.02030.4646-0.0940.2891138.2433-11.89067.0593
450.03710.090.00110.0631-0.00120.0635-0.12090.2379-0.0179-0.09360.2126-0.02170.0020.112200.21640.00390.00110.4228-0.02550.3416125.6606-9.79224.3585
46-0.0226-0.018-0.01030.01930.0339-0.0002-0.10890.1920.181-0.13370.15390.00570.18390.03730-0.20160.127-0.48580.52530.46550.0109103.55151.2112-9.3137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 159 )
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 254 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 127 )
5X-RAY DIFFRACTION5chain 'B' and (resid 128 through 222 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 36 )
7X-RAY DIFFRACTION7chain 'C' and (resid 37 through 94 )
8X-RAY DIFFRACTION8chain 'C' and (resid 95 through 132 )
9X-RAY DIFFRACTION9chain 'C' and (resid 133 through 217 )
10X-RAY DIFFRACTION10chain 'D' and (resid 46 through 80 )
11X-RAY DIFFRACTION11chain 'D' and (resid 81 through 115 )
12X-RAY DIFFRACTION12chain 'D' and (resid 116 through 175 )
13X-RAY DIFFRACTION13chain 'D' and (resid 176 through 205 )
14X-RAY DIFFRACTION14chain 'D' and (resid 206 through 213 )
15X-RAY DIFFRACTION15chain 'D' and (resid 214 through 252 )
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 127 )
17X-RAY DIFFRACTION17chain 'E' and (resid 128 through 142 )
18X-RAY DIFFRACTION18chain 'E' and (resid 143 through 222 )
19X-RAY DIFFRACTION19chain 'F' and (resid 1 through 36 )
20X-RAY DIFFRACTION20chain 'F' and (resid 37 through 79 )
21X-RAY DIFFRACTION21chain 'F' and (resid 80 through 117 )
22X-RAY DIFFRACTION22chain 'F' and (resid 118 through 217 )
23X-RAY DIFFRACTION23chain 'G' and (resid 46 through 120 )
24X-RAY DIFFRACTION24chain 'G' and (resid 121 through 174 )
25X-RAY DIFFRACTION25chain 'G' and (resid 175 through 213 )
26X-RAY DIFFRACTION26chain 'G' and (resid 214 through 252 )
27X-RAY DIFFRACTION27chain 'H' and (resid 1 through 127 )
28X-RAY DIFFRACTION28chain 'H' and (resid 128 through 142 )
29X-RAY DIFFRACTION29chain 'H' and (resid 143 through 222 )
30X-RAY DIFFRACTION30chain 'I' and (resid 1 through 25 )
31X-RAY DIFFRACTION31chain 'I' and (resid 26 through 79 )
32X-RAY DIFFRACTION32chain 'I' and (resid 80 through 105 )
33X-RAY DIFFRACTION33chain 'I' and (resid 106 through 132 )
34X-RAY DIFFRACTION34chain 'I' and (resid 133 through 159 )
35X-RAY DIFFRACTION35chain 'I' and (resid 160 through 178 )
36X-RAY DIFFRACTION36chain 'I' and (resid 179 through 217 )
37X-RAY DIFFRACTION37chain 'J' and (resid 45 through 119 )
38X-RAY DIFFRACTION38chain 'J' and (resid 120 through 183 )
39X-RAY DIFFRACTION39chain 'J' and (resid 184 through 252 )
40X-RAY DIFFRACTION40chain 'K' and (resid 1 through 127 )
41X-RAY DIFFRACTION41chain 'K' and (resid 128 through 142 )
42X-RAY DIFFRACTION42chain 'K' and (resid 143 through 222 )
43X-RAY DIFFRACTION43chain 'L' and (resid 1 through 18 )
44X-RAY DIFFRACTION44chain 'L' and (resid 19 through 52 )
45X-RAY DIFFRACTION45chain 'L' and (resid 53 through 132 )
46X-RAY DIFFRACTION46chain 'L' and (resid 133 through 217 )

+
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