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- PDB-4rav: Crystal structure of scFvC4 in complex with the first 17 AA of hu... -

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Basic information

Entry
Database: PDB / ID: 4rav
TitleCrystal structure of scFvC4 in complex with the first 17 AA of huntingtin
Components
  • Huntingtin
  • Single-chain Fv, VLSingle-chain variable fragment
  • single-chain Fv, VHSingle-chain variable fragment
KeywordsIMMUNE SYSTEM/Apoptosis / immunoglobulin fold / immunity / 1-17 residues of huntingtin / IMMUNE SYSTEM-Apoptosis complex
Function / homology
Function and homology information


regulation of cAMP-dependent protein kinase activity / regulation of phosphoprotein phosphatase activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / microtubule-based transport / vocal learning / regulation of CAMKK-AMPK signaling cascade / positive regulation of mitophagy / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly ...regulation of cAMP-dependent protein kinase activity / regulation of phosphoprotein phosphatase activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / microtubule-based transport / vocal learning / regulation of CAMKK-AMPK signaling cascade / positive regulation of mitophagy / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly / presynaptic cytosol / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / positive regulation of aggrephagy / postsynaptic cytosol / positive regulation of lipophagy / dynein intermediate chain binding / beta-tubulin binding / Golgi organization / establishment of mitotic spindle orientation / dynactin binding / Regulation of MECP2 expression and activity / autophagosome / inclusion body / heat shock protein binding / centriole / negative regulation of extrinsic apoptotic signaling pathway / protein destabilization / cytoplasmic vesicle membrane / kinase binding / p53 binding / late endosome / transmembrane transporter binding / early endosome / positive regulation of apoptotic process / axon / apoptotic process / dendrite / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT ...Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT / Armadillo-like helical / Armadillo-type fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDe Genst, E. / Chirgadze, D.Y. / Dobson, C.M.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure of a single-chain fv bound to the 17 N-terminal residues of huntingtin provides insights into pathogenic amyloid formation and suppression.
Authors: De Genst, E. / Chirgadze, D.Y. / Klein, F.A. / Butler, D.C. / Matak-Vinkovic, D. / Trottier, Y. / Huston, J.S. / Messer, A. / Dobson, C.M.
History
DepositionSep 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Single-chain Fv, VL
A: single-chain Fv, VH
D: Single-chain Fv, VL
C: single-chain Fv, VH
E: Huntingtin
F: Huntingtin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,67710
Polymers55,2936
Non-polymers3844
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-90 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.313, 35.933, 110.946
Angle α, β, γ (deg.)90.00, 120.72, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Single-chain Fv, VL / Single-chain variable fragment


Mass: 12267.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody single-chain Fv, VH / Single-chain variable fragment


Mass: 13401.765 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide Huntingtin / / Huntington disease protein / HD protein


Mass: 1977.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42858
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium sulphate, 25% PEG 4000 and 0.1 M sodium acetate buffer at pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07169 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07169 Å / Relative weight: 1
ReflectionResolution: 2.5→47.69 Å / Num. all: 18107 / Num. obs: 18107 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.5-2.64197.8
7.91-47.69198.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIXmodel building
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→44.236 Å / SU ML: 0.31 / σ(F): 1.44 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 907 5.01 %
Rwork0.1796 --
obs0.182 18092 98.95 %
all-18092 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→44.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 20 32 3606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033648
X-RAY DIFFRACTIONf_angle_d0.7184948
X-RAY DIFFRACTIONf_dihedral_angle_d10.8221236
X-RAY DIFFRACTIONf_chiral_restr0.028540
X-RAY DIFFRACTIONf_plane_restr0.003636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65660.30781500.2672780X-RAY DIFFRACTION98
2.6566-2.86170.30861480.23562829X-RAY DIFFRACTION99
2.8617-3.14960.27671480.21982833X-RAY DIFFRACTION99
3.1496-3.60520.2471510.20122860X-RAY DIFFRACTION99
3.6052-4.54150.2061530.15192896X-RAY DIFFRACTION99
4.5415-44.24260.17421570.14582987X-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)
10.04520.0148-0.0410.0043-0.01210.03920.00950.0598-0.1424-0.0045-0.00540.10270.1158-0.03920.02040.48630.0124-0.00050.1636-0.00420.350733.555-13.997381.4928
20.10840.29020.15081.28770.77050.7319-0.00210.19030.01660.3348-0.49280.32840.70410.5691-0.55880.37440.1661-0.07270.50290.06110.243641.6065-9.833584.3901
30.02120.0218-0.0290.043-0.03170.033-0.09620.1393-0.0238-0.0557-0.04430.1521-0.361-0.0330.00010.26640.0267-0.07130.27660.04380.405434.88881.368780.1819
40.2832-0.2675-0.48983.08170.9080.989-0.09630.1240.15170.5854-0.34630.05670.04061.0841-0.26250.2435-0.0882-0.11170.48980.06440.258645.97-2.385183.619
50.0097-0.00680.00090.0141-0.00750.00340.02890.03330.114-0.1286-0.03990.032-0.2388-0.015700.6065-0.0831-0.07920.4011-0.0860.462135.77224.032593.13
60.03350.00720.02320.02920.05860.0956-0.2224-0.06310.3179-0.0793-0.04430.25660.00080.0160.00020.37590.0421-0.0360.13560.02240.349534.2039-4.323482.118
70.29110.1668-0.01290.0975-0.0058-00.4470.07560.04550.2643-0.41040.1970.35090.41110.0080.42050.0807-0.06020.39120.05570.313838.5416-11.494971.5173
80.00680.0018-0.00470.03580.01010.0033-0.01-0.14-0.0503-0.1728-0.0732-0.01160.0356-0.0591-0.02970.4572-0.02920.01360.3194-0.16090.375930.4176-2.390593.609
90.08290.1261-0.03850.2771-0.170.1578-0.17550.0268-0.03630.1064-0.15380.0117-0.0795-0.0009-0.15370.5442-0.0697-0.15580.208-0.08460.578930.21110.691667.5967
100.1496-0.06890.05160.0574-0.03240.0306-0.48640.04170.0542-0.18980.0118-0.07940.1141-0.093-0.15380.366-0.11430.02120.33780.03830.681714.0646-4.138561.4478
110.01140.0208-0.01470.0069-0.00710.0231-0.1292-0.07250.15270.13860.032-0.13590.03210.09520.00810.28220.018-0.07110.1398-0.05470.458126.46985.565460.7901
120.14270.0045-0.02760.0006-0.00320.0044-0.09390.06490.01160.0347-0.0719-0.0865-0.06370.1685-0.15780.3756-0.5381-0.00190.78870.44350.255440.79748.623761.8383
130.1993-0.04530.10520.049-0.10310.2027-0.0473-0.282-0.1112-0.00220.0602-0.06360.0009-0.1347-0.01680.3723-0.25030.03180.3650.1320.320127.9407-4.130570.3764
140.00670.00510.0095-0.00530.00570.01210.18090.2323-0.35680.0666-0.11750.03520.31460.133-0.00030.29680.0165-0.03030.24070.0160.36333.196-6.266365.7572
150.5243-0.7049-0.79320.94811.06611.1943-0.12290.25250.04920.177-0.10630.25080.39120.401-0.13110.30870.0602-0.02230.68140.01750.379439.2337-3.684755.891
160.17110.05910.19620.02840.10260.30320.11740.1380.0278-0.05210.1560.05140.06450.31410.21370.3065-0.0139-0.04570.09550.03080.366229.4499-6.109757.9248
170.14050.0481-0.060.03950.05890.375-0.0230.0168-0.0207-0.0818-0.00170.2183-0.05270.1112-0.01460.2944-0.3297-0.01430.03810.05480.402229.86574.527156.9208
180.00850.002-0.0010.00470.01690.0605-0.0553-0.1173-0.1462-0.0513-0.0933-0.1670.0894-0.0682-0.03230.4681-0.17870.04780.32650.05480.437819.2919-10.122862.9117
190.01150.0838-0.02610.4722-0.14170.0452-0.0470.01-0.08930.0001-0.02380.2003-0.23280.0647-0.10960.2166-0.2341-0.017-0.07770.02830.420429.54790.739268.8531
200.03120.00680.01420.07260.02340.0135-0.1250.00740.2035-0.0004-0.18570.1257-0.10130.4108-0.00070.3393-0.13-0.05090.51970.03920.474637.92452.146770.5896
210.0731-0.08840.07570.104-0.09180.0834-0.2529-0.04010.11290.073-0.1177-0.06350.0027-0.0904-0.0120.2153-0.05660.06120.4624-0.07160.308814.2232-4.15567.6541
220.00250.0037-0.00130.09410.06580.0531-0.00050.07740.2659-0.08590.1518-0.1864-0.0805-0.0630.02450.55130.0619-0.0390.24010.06910.435973.092521.050973.1313
230.04240.01570.06960.0868-0.01470.1178-0.1283-0.12030.16580.3512-0.18560.0308-0.18050.0783-0.00360.50690.1089-0.00580.2727-0.04370.327173.534412.836986.3847
240.0535-0.0178-0.05480.01120.0020.0873-0.41710.00520.14630.042-0.27330.0295-0.1515-0.2215-0.53230.54570.3141-0.03510.982-0.03540.418558.146720.541272.1451
250.02860.081-0.04010.2425-0.11270.20720.0049-0.08140.2787-0.0466-0.1639-0.05490.5174-0.0345-0.04120.2080.0473-0.01370.35590.0350.267870.94615.192273.433
260.19470.10460.09330.701-0.05480.0664-0.0385-0.2657-0.10950.4756-0.247-0.0845-0.0692-1.0061-0.01670.41550.00740.04190.5948-0.03450.332162.13218.881380.8043
270.0051-0.0063-0.00520.00610.00410.00490.0872-0.0143-0.0135-0.1375-0.03290.03850.1664-0.03250.00010.61880.0161-0.02350.25240.03630.384675.29712.722885.6131
280.0094-0.00610.0036-0.00010.00010.01030.09610.0842-0.16750.1954-0.11810.01420.08160.03680.00020.38960.0316-0.04750.384-0.00470.343672.236610.997874.8774
290.1570.02040.03211.1529-0.16420.1016-0.1212-0.09380.28320.2368-0.2793-0.0855-0.1043-0.2264-0.18050.28030.17230.01120.5939-0.08010.314869.361215.176272.5705
300.03790.0368-0.0580.0212-0.04670.13280.13320.15690.1006-0.2344-0.1287-0.13860.157-0.03670.05870.4079-0.19950.1170.58890.06190.508977.62754.90353.8469
310.002-0.0019-0.0010.00660.00950.00980.28990.0973-0.27650.0294-0.03230.06610.2910.0224-00.4736-0.16620.09770.5594-0.0430.442771.85141.289952.4718
320.002-0.00230.00450.00230.0007-0.0056-0.06280.07170.02160.00620.0007-0.02240.073-0.064-0.20940.2433-0.532-0.01561.01920.05110.291659.152-2.419458.6098
330.11930.0867-0.02510.04660.01640.1439-0.0472-0.0830.11230.02250.08080.04630.085-0.0360.05460.2916-0.13610.0030.3271-0.0160.318473.23211.346661.6492
340.01140.0032-0.00930.0066-0.01550.02020.04810.08580.2202-0.07720.0806-0.2095-0.1302-0.1779-0.00030.3518-0.04020.01610.57480.03160.365566.803312.999259.295
350.3649-0.26350.14390.4259-0.44410.5445-0.11890.05330.05270.1109-0.15530.011-0.1553-0.0486-0.11230.3779-0.0990.01111.05460.06330.362157.8039.912752.4138
360.1330.01280.05460.01980.0350.0812-0.0154-0.07150.05930.08870.0431-0.0798-0.1142-0.06190.00120.66720.03760.03960.25640.08680.61769.303719.885952.1003
370.1132-0.0150.05420.0027-0.00590.0744-0.01960.1257-0.0622-0.1557-0.0306-0.03230.1086-0.1528-0.03760.3413-0.20890.0230.7107-0.02630.392465.5636.989149.6145
380.1158-0.06810.02460.0455-0.00880.0024-0.13160.04580.0247-0.047-0.1594-0.190.3394-0.0805-0.10340.4755-0.21380.05970.4599-0.00650.290967.32832.06750.072
390.00320.0082-0.00490.0092-0.01520.0077-0.15810.04910.2594-0.00440.1013-0.2272-0.0062-0.0176-0.00020.4715-0.1962-0.02250.65140.08840.386678.468117.746151.7256
400.0451-0.00460.0224-0.0065-0.00930.04580.0611-0.06520.1672-0.0299-0.0783-0.19610.1802-0.14140.0757-0.4049-0.63780.23270.2410.1740.231771.6926.345661.0118
410.0452-0.04570.01410.11460.01450.00810.1009-0.0804-0.0260.0915-0.086-0.11390.1788-0.29980.03760.3012-0.16830.02020.55710.00650.399465.31174.026665.7965
420.1766-0.0222-0.12820.0060.01220.0936-0.26010.0974-0.00030.0253-0.14290.0561-0.03750.076-0.07160.2635-0.137-0.00680.4568-0.09580.440584.009111.331754.8121
430.0965-0.0092-0.02190.00010.00160.0049-0.064-0.03280.0480.0092-0.08930.00730.05520.1079-0.15040.26130.44060.05481.31810.14480.461244.3399-10.600959.3027
440.0213-0.0514-0.00590.2676-0.07410.08920.03050.024-0.00810.02450.2877-0.10380.11940.2441-0.05810.291-0.033-0.08641.33560.1030.460148.50413.851862.2739
450.32-0.06-0.00680.02480.13691.2051-0.2876-0.00840.0593-0.006-0.18410.0536-0.0186-0.1507-0.03390.41050.2131-0.01791.62540.0130.54154.167716.506157.394
460.02930.0292-0.02140.0142-0.00510.0063-0.1572-0.077-0.0579-0.04890.09460.1148-0.064-0.026600.4408-0.03020.0021.30680.10790.457951.58412.146861.5213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 128 through 135 )
2X-RAY DIFFRACTION2chain 'B' and (resid 136 through 162 )
3X-RAY DIFFRACTION3chain 'B' and (resid 163 through 177 )
4X-RAY DIFFRACTION4chain 'B' and (resid 178 through 204 )
5X-RAY DIFFRACTION5chain 'B' and (resid 205 through 212 )
6X-RAY DIFFRACTION6chain 'B' and (resid 213 through 218 )
7X-RAY DIFFRACTION7chain 'B' and (resid 219 through 230 )
8X-RAY DIFFRACTION8chain 'B' and (resid 231 through 237 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 7 )
10X-RAY DIFFRACTION10chain 'A' and (resid 8 through 17 )
11X-RAY DIFFRACTION11chain 'A' and (resid 18 through 25 )
12X-RAY DIFFRACTION12chain 'A' and (resid 26 through 33 )
13X-RAY DIFFRACTION13chain 'A' and (resid 34 through 44 )
14X-RAY DIFFRACTION14chain 'A' and (resid 45 through 51 )
15X-RAY DIFFRACTION15chain 'A' and (resid 52 through 60 )
16X-RAY DIFFRACTION16chain 'A' and (resid 61 through 73 )
17X-RAY DIFFRACTION17chain 'A' and (resid 74 through 83 )
18X-RAY DIFFRACTION18chain 'A' and (resid 84 through 91 )
19X-RAY DIFFRACTION19chain 'A' and (resid 92 through 98 )
20X-RAY DIFFRACTION20chain 'A' and (resid 99 through 108 )
21X-RAY DIFFRACTION21chain 'A' and (resid 109 through 117 )
22X-RAY DIFFRACTION22chain 'D' and (resid 127 through 135 )
23X-RAY DIFFRACTION23chain 'D' and (resid 136 through 150 )
24X-RAY DIFFRACTION24chain 'D' and (resid 151 through 162 )
25X-RAY DIFFRACTION25chain 'D' and (resid 163 through 177 )
26X-RAY DIFFRACTION26chain 'D' and (resid 178 through 204 )
27X-RAY DIFFRACTION27chain 'D' and (resid 205 through 212 )
28X-RAY DIFFRACTION28chain 'D' and (resid 213 through 218 )
29X-RAY DIFFRACTION29chain 'D' and (resid 219 through 236 )
30X-RAY DIFFRACTION30chain 'C' and (resid 2 through 17 )
31X-RAY DIFFRACTION31chain 'C' and (resid 18 through 25 )
32X-RAY DIFFRACTION32chain 'C' and (resid 26 through 33 )
33X-RAY DIFFRACTION33chain 'C' and (resid 34 through 44 )
34X-RAY DIFFRACTION34chain 'C' and (resid 45 through 51 )
35X-RAY DIFFRACTION35chain 'C' and (resid 52 through 60 )
36X-RAY DIFFRACTION36chain 'C' and (resid 61 through 67 )
37X-RAY DIFFRACTION37chain 'C' and (resid 68 through 73 )
38X-RAY DIFFRACTION38chain 'C' and (resid 74 through 83 )
39X-RAY DIFFRACTION39chain 'C' and (resid 84 through 91 )
40X-RAY DIFFRACTION40chain 'C' and (resid 92 through 98 )
41X-RAY DIFFRACTION41chain 'C' and (resid 99 through 108 )
42X-RAY DIFFRACTION42chain 'C' and (resid 109 through 115 )
43X-RAY DIFFRACTION43chain 'E' and (resid 4 through 11 )
44X-RAY DIFFRACTION44chain 'E' and (resid 12 through 18 )
45X-RAY DIFFRACTION45chain 'F' and (resid 4 through 11 )
46X-RAY DIFFRACTION46chain 'F' and (resid 12 through 18 )

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