[English] 日本語
Yorodumi
- PDB-5egc: Structure of the Adeno-Associated Virus Serotype 1 sialic acid complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5egc
TitleStructure of the Adeno-Associated Virus Serotype 1 sialic acid complex
ComponentsCapsid protein
KeywordsVIRUS / Adeno-Associated Virus 1 / single-stranded DNA virus / parvovirus / icosahedral virus / glycan receptor / sialic acid
Function / homology
Function and homology information


T=1 icosahedral viral capsid / structural molecule activity
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Capsid protein
Similarity search - Component
Biological speciesAdeno-associated virus - 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.011 Å
AuthorsHuang, L.Y. / Agbandje-McKenna, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL089221 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: J.Virol. / Year: 2016
Title: Characterization of the Adeno-Associated Virus 1 and 6 Sialic Acid Binding Site.
Authors: Huang, L.Y. / Patel, A. / Ng, R. / Miller, E.B. / Halder, S. / McKenna, R. / Asokan, A. / Agbandje-McKenna, M.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Refinement description
Category: citation / pdbx_audit_support / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _software.classification
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6903
Polymers58,3561
Non-polymers3342
Water181
1
A: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,521,403180
Polymers3,501,38960
Non-polymers20,015120
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 293 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)293,45015
Polymers291,7825
Non-polymers1,66810
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 352 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)352,14018
Polymers350,1396
Non-polymers2,00112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Capsid protein
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 1.76 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,760,70290
Polymers1,750,69430
Non-polymers10,00760
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)455.627, 261.749, 450.980
Angle α, β, γ (deg.)90.000, 111.060, 90.000
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.97569, 0.17885, -0.12662), (-0.17783, 0.3086, -0.93442), (-0.12805, 0.93423, 0.3329)49.46813, 364.43869, 260.57446
3generate(0.93717, 0.10939, -0.33128), (-0.10951, -0.80933, -0.57705), (-0.33124, 0.57707, -0.7465)129.27692, 224.42676, 681.75217
4generate(0.93696, -0.10835, -0.33223), (0.11119, -0.80886, 0.5774), (-0.33129, -0.57793, -0.74582)129.62619, -226.11145, 681.03647
5generate(0.97612, -0.17624, -0.127), (0.17752, 0.3102, 0.93395), (-0.1252, -0.93419, 0.33408)49.54176, -364.83213, 259.54687
6generate(0.74446, -0.00079, 0.66767), (-0.00023, -1, -0.00093), (0.66767, 0.00054, -0.74446)-322.53796, -0.54, 842.72146
7generate(0.64221, -0.75576, 0.12806), (-0.17784, -0.30941, -0.93415), (0.74561, 0.57714, -0.33311)-112.23222, 364.01823, 682.41165
8generate(0.56119, 0.75744, 0.33369), (-0.75783, 0.30811, 0.57512), (0.33281, -0.57563, 0.74692)-211.09127, -364.88034, 160.23299
9generate(0.64116, -0.17638, 0.74686), (-0.75642, -0.30931, 0.57633), (0.12936, -0.93446, -0.33173)-372.60026, -365.59801, 581.12763
10generate(0.50087, -0.86552, 0.00119), (-0.86552, -0.50087, -0.0009), (0.00137, -0.00058, -1)-81.80158, -140.33187, 842.19733
11generate(0.37272, 0.86599, 0.33339), (-0.64643, 0.50007, -0.57624), (-0.66574, -0.00074, 0.74618)-241.68521, 138.05275, -1.35672
12generate(0.47659, -0.10931, 0.8723), (-0.46781, 0.80855, 0.35692), (-0.74432, -0.57818, 0.33421)-452.24095, -225.98854, 159.23793
13generate(0.47602, 0.10838, 0.87273), (0.4673, 0.80951, -0.35542), (-0.745, 0.57701, 0.3347)-452.40978, 225.16276, 159.45905
14generate(0.37378, -0.86593, 0.33234), (0.64595, 0.50016, 0.5767), (-0.66561, -0.00088, 0.7463)-241.85963, -138.67681, -1.28054
15generate(0.49798, 0.86718, 0.00175), (0.86718, -0.49799, 0.00092), (0.00167, 0.00106, -1)-81.57387, 139.05161, 842.18108
16generate(0.64058, 0.17875, 0.7468), (0.75729, -0.30812, -0.57583), (0.12717, 0.9344, -0.33274)-372.49495, 364.24558, 582.17193
17generate(0.56345, -0.75597, 0.3332), (0.75679, 0.31054, -0.57519), (0.33136, 0.57626, 0.74708)-211.34271, 364.24691, 160.5474
18generate(0.63999, 0.75773, 0.12751), (0.17881, -0.30826, 0.93434), (0.74729, -0.57517, -0.33278)-111.51403, -365.24257, 681.89088
19generate(0.37235, -0.64482, -0.6675), (0.86646, 0.49925, 0.00105), (0.33257, -0.57875, 0.74461)179.13885, 139.38726, 161.14941
20generate(-0.1692, 0.64348, 0.74652), (0.64623, -0.49946, 0.577), (0.74415, 0.58006, -0.33133)-503.46589, -139.27821, 681.32822
21generate(-0.14495, -0.46782, 0.87185), (0.46913, -0.80831, -0.35574), (0.87115, 0.35745, 0.33663)-552.69116, 224.6711, 420.58576
22generate(0.4741, 0.46768, -0.746), (0.10966, 0.80931, 0.57706), (0.87362, -0.35539, 0.33241)229.22052, -225.32169, 422.37329
23generate(0.47495, -0.46648, -0.7462), (-0.11239, 0.80885, -0.57718), (0.87281, 0.358, 0.33173)229.023, 225.04274, 422.9391
24generate(-0.14552, 0.4669, 0.87225), (-0.46772, -0.80936, 0.35521), (0.87182, -0.35628, 0.33616)-552.53414, -225.99599, 420.51783
25generate(-0.16807, -0.64375, 0.74655), (-0.64576, -0.50031, -0.5768), (0.74482, -0.57903, -0.33162)-503.84141, 137.8243, 681.01151
26generate(0.37049, 0.64612, -0.66728), (-0.8676, 0.49726, -0.00021), (0.33168, 0.57902, 0.7448)179.45473, -140.29995, 161.42045
27generate(0.33275, -0.35776, -0.87252), (-0.93447, -0.00081, -0.35604), (0.12667, 0.93381, -0.33458)259.17851, -1.59255, 582.7765
28generate(0.33633, -0.93286, 0.12906), (-0.35747, 0.00033, 0.93392), (-0.87126, -0.36024, -0.33336)-162.52101, -451.53212, 419.76972
29generate(0.3335, 0.93405, 0.12782), (0.3582, -0.00013, -0.93364), (-0.87205, 0.35715, -0.33462)-161.45697, 450.57074, 420.53065
30generate(0.33266, 0.35894, -0.87207), (0.9343, 0.00018, 0.35648), (0.12811, -0.93336, -0.33529)259.29522, 0.45127, 582.4427
31generate(1, 0.00031, 0.00228), (-0.00031, 1, 0.00015), (-0.00228, -0.00015, 1)80.07904, 108.84414, -210.74289
32generate(0.97556, 0.18013, -0.12586), (-0.17757, 0.3088, -0.93441), (-0.12945, 0.93391, 0.33324)130.14548, 473.36989, 49.75314
33generate(0.93616, 0.11053, -0.33376), (-0.10991, -0.80972, -0.57643), (-0.33396, 0.57631, -0.74588)211.26678, 333.02852, 470.72603
34generate(0.9365, -0.1087, -0.3334), (0.11139, -0.80929, 0.57676), (-0.33251, -0.57727, -0.74579)211.07398, -116.91256, 470.36414
35generate(0.97607, -0.1771, -0.12621), (0.17709, 0.31047, 0.93394), (-0.12622, -0.93394, 0.3344)130.23371, -255.93699, 48.74155
36generate(0.74523, -0.00022, 0.66681), (0.00018, -1, -0.00054), (0.66681, 0.00052, -0.74523)-240.96736, 108.25817, 632.42303
37generate(0.64313, -0.75508, 0.12747), (-0.17799, -0.3093, -0.93416), (0.74479, 0.5781, -0.33331)-30.74711, 472.9331, 471.89565
38generate(0.56163, 0.75646, 0.33517), (-0.75791, 0.30787, 0.57514), (0.33188, -0.57704, 0.74624)-130.57191, -255.97916, -50.07126
39generate(0.64151, -0.17795, 0.74619), (-0.75628, -0.30964, 0.57634), (0.12849, -0.93405, -0.33322)-291.22985, -256.68829, 371.16986
40generate(0.50029, -0.86586, -0.00098), (-0.86586, -0.50029, -0.00086), (0.00025, 0.00128, -1)0.11938, -31.43287, 631.63267
41generate(0.37148, 0.86601, 0.3347), (-0.64622, 0.50002, -0.57652), (-0.66663, -0.00212, 0.74539)-161.39499, 247.0883, -211.53734
42generate(0.47483, -0.10998, 0.87318), (-0.46835, 0.80842, 0.35651), (-0.74511, -0.57824, 0.33235)-371.81035, -116.9392, -50.5166
43generate(0.47444, 0.11014, 0.87337), (0.46703, 0.80951, -0.35579), (-0.74619, 0.57669, 0.33263)-371.86455, 334.23578, -50.25228
44generate(0.37299, -0.86577, 0.33364), (0.64577, 0.50043, 0.57666), (-0.66622, 0.00036, 0.74575)-161.53878, -29.73215, -211.60385
45generate(0.49721, 0.86763, -8.0E-5), (0.86763, -0.49721, 0.00087), (0.00072, -0.0005, -1)0.2012, 248.04243, 631.59567
46generate(0.64094, 0.17998, 0.74619), (0.75719, -0.3077, -0.57618), (0.1259, 0.93431, -0.3335)-291.1575, 473.33606, 371.84756
47generate(0.56415, -0.75494, 0.33436), (0.75652, 0.31039, -0.57562), (0.33078, 0.57769, 0.74623)-130.69517, 473.34571, -49.64766
48generate(0.64131, 0.75663, 0.12738), (0.1786, -0.30866, 0.93425), (0.7462, -0.5764, -0.33309)-30.20307, -256.2739, 471.42225
49generate(0.37308, -0.64597, -0.66598), (0.86639, 0.49936, 0.00099), (0.33193, -0.57737, 0.74597)259.65543, 248.35401, -49.94381
50generate(-0.16758, 0.6444, 0.7461), (0.64658, -0.49946, 0.5766), (0.74421, 0.57904, -0.33295)-422.01467, -30.14786, 471.64043
51generate(-0.1432, -0.46695, 0.87261), (0.46897, -0.80844, -0.35565), (0.87153, 0.3583, 0.33475)-471.69411, 333.55374, 211.02388
52generate(0.47571, 0.46718, -0.74528), (0.10943, 0.80928, 0.57715), (0.87277, -0.35612, 0.33386)310.21603, -116.44969, 211.20029
53generate(0.47602, -0.46609, -0.74576), (-0.11181, 0.80904, -0.57702), (0.8723, 0.35806, 0.33301)310.098, 333.92716, 211.83165
54generate(-0.14389, 0.46624, 0.87288), (-0.4687, -0.80896, 0.35483), (0.87156, -0.35806, 0.33493)-471.48993, -116.9581, 210.55247
55generate(-0.16733, -0.64466, 0.74593), (-0.64569, -0.50011, -0.57705), (0.74504, -0.5782, -0.33257)-422.3656, 246.86914, 470.98458
56generate(0.3716, 0.64685, -0.66595), (-0.86734, 0.49771, -0.00054), (0.33111, 0.57781, 0.74599)260.0598, -31.21945, -49.61653
57generate(0.33281, -0.35686, -0.87286), (-0.93453, -0.0011, -0.35587), (0.12604, 0.93416, -0.33386)340.36994, 107.22962, 371.97021
58generate(0.33396, -0.93382, 0.12825), (-0.35803, 0.00019, 0.93371), (-0.87194, -0.35774, -0.33427)-81.453, -342.54356, 209.679
59generate(0.33159, 0.93483, 0.12705), (0.35766, 5.0E-5, -0.93385), (-0.873, 0.3551, -0.33434)-80.35858, 559.55812, 209.86035
60generate(0.33261, 0.35769, -0.8726), (0.9343, 0.00089, 0.35649), (0.12829, -0.93384, -0.3339)340.59634, 109.39163, 371.39418

-
Components

#1: Protein Capsid protein


Mass: 58356.480 Da / Num. of mol.: 1 / Fragment: residues 217-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9WBP8
#2: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M HEPES-NaOH pH 7.3, 0.05 M MgCl2, 0.03% NaN3, 1.0 M NaCl, 7% PEG 6K and 25% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 593352 / % possible obs: 61.6 % / Redundancy: 2 % / Biso Wilson estimate: 35.08 Å2 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.123 / Rrim(I) all: 0.205 / Χ2: 2.301 / Net I/av σ(I): 6.849 / Net I/σ(I): 5.1 / Num. measured all: 1170740
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.051.50.468213790.8620.4090.6241.22344.6
3.05-3.111.60.432236690.8770.3740.5751.25349.2
3.11-3.171.60.442256220.5830.3760.5831.30553.5
3.17-3.231.70.377272460.90.3140.4931.60856.6
3.23-3.31.70.327288060.9260.270.4261.48660
3.3-3.381.80.297302430.9230.240.3841.67863
3.38-3.461.90.272307680.90.2140.3482.08264.1
3.46-3.561.90.245310730.9540.1890.3111.90764.7
3.56-3.6620.232311050.9440.1750.2932.19864.6
3.66-3.7820.209311150.9680.1540.2612.20564.7
3.78-3.912.10.201310950.9520.1460.252.59564.7
3.91-4.072.10.171310490.9770.1230.2112.58464.6
4.07-4.262.10.152311180.9820.1090.1882.80264.7
4.26-4.482.10.134311270.9840.0960.1653.15264.6
4.48-4.762.10.126311980.9860.090.1562.88864.7
4.76-5.132.10.121312400.9870.0870.152.55364.8
5.13-5.642.20.118313410.9880.0860.1472.06665.1
5.64-6.462.20.115315800.9880.0850.1441.65765.4
6.46-8.132.20.092316910.9930.0670.1151.68765.5
8.13-502.30.071308870.9910.0540.094.12463.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
AUTOMARdata reduction
RefinementResolution: 3.011→49.923 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 2000 0.34 %
Rwork0.2688 585536 -
obs0.2688 587536 60.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.94 Å2 / Biso mean: 21.8652 Å2 / Biso min: 5.48 Å2
Refinement stepCycle: final / Resolution: 3.011→49.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 22 1 4143
Biso mean--31.7 26.55 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008257220
X-RAY DIFFRACTIONf_angle_d1.065351000
X-RAY DIFFRACTIONf_chiral_restr0.08136600
X-RAY DIFFRACTIONf_plane_restr0.00746500
X-RAY DIFFRACTIONf_dihedral_angle_d17.62791860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0114-3.08670.3937890.366265582664739
3.0867-3.17010.38141120.3616349723508451
3.1701-3.26340.39791390.3491388413898056
3.2634-3.36870.35691410.328420064214761
3.3687-3.4890.32891510.3122439184406964
3.489-3.62870.30641450.2989443304447564
3.6287-3.79380.33291600.2879443154447564
3.7938-3.99370.27231470.2718442354438264
3.9937-4.24380.24921490.2535441274427664
4.2438-4.57130.24551570.2222441134427064
4.5713-5.03090.21531450.2116443944453964
5.0309-5.7580.23551640.218448144497865
5.758-7.25090.21891510.2256454314558265
7.2509-49.93020.20161500.2547434824363262

+
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