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- PDB-4m1u: The crystal structure of Stx2 and a disaccharide ligand -

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Basic information

Entry
Database: PDB / ID: 4m1u
TitleThe crystal structure of Stx2 and a disaccharide ligand
Components
  • Shiga toxin 2 A-subunit
  • Shiga toxin 2 B subunit
KeywordsHYDROLASE / rRNA N-glycosylase
Function / homology
Function and homology information


hemolysis by symbiont of host erythrocytes / rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, subunit A / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Enterotoxin / Ribosome-inactivating protein conserved site ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, subunit A / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Enterotoxin / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / rRNA N-glycosylase / Shiga toxin 2 B subunit
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsYin, J. / James, M.N.G. / Jacobson, J.M. / Kitov, P.I. / Bundle, D.R. / Mulvey, G. / Armstrong, G.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The crystal structure of shiga toxin type 2 with bound disaccharide guides the design of a heterobifunctional toxin inhibitor.
Authors: Jacobson, J.M. / Yin, J. / Kitov, P.I. / Mulvey, G. / Griener, T.P. / James, M.N. / Armstrong, G. / Bundle, D.R.
History
DepositionAug 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Shiga toxin 2 A-subunit
B: Shiga toxin 2 B subunit
C: Shiga toxin 2 B subunit
D: Shiga toxin 2 B subunit
E: Shiga toxin 2 B subunit
F: Shiga toxin 2 B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,75011
Polymers72,3516
Non-polymers1,3985
Water13,187732
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14230 Å2
ΔGint-4 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.250, 146.250, 60.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Shiga toxin 2 A-subunit / Shiga toxin 2 subunit A / Shiga-like toxin II A subunit encoded by bacteriophage BP-933W


Mass: 33228.215 Da / Num. of mol.: 1 / Fragment: Stx2 subunit A (unp entries 230-319)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria)
Gene: ECs1205, stx 2 A-subunit, stx2 A-subunit, stx2A, Z1464
Production host: Escherichia coli (E. coli) / References: UniProt: Q7DI68, rRNA N-glycosylase
#2: Protein
Shiga toxin 2 B subunit / Shiga toxin 2 subunit B / Shiga toxin 2 / subunit B / Shiga toxin 2v subunit A / Shiga toxin 2v ...Shiga toxin 2 subunit B / Shiga toxin 2 / subunit B / Shiga toxin 2v subunit A / Shiga toxin 2v subunit B / Stx2B / Stx2B protein / Stx2d B subunit / Verocytotoxin 2 subunit B / Verocytotoxin 2 variant B subunit


Mass: 7824.590 Da / Num. of mol.: 5 / Fragment: Stx2 subunit B (unp entries 20-89)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: stx2B, stx2dB, stx2vB, stxB2, stxII, vtx2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q7DJJ2
#3: Polysaccharide 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-4)-methyl beta-D-galactopyranoside


Type: oligosaccharide / Mass: 397.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAca1-4DGalp[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OC][a2112h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Galp]{[(4+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H11NO3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.8 M sodium formate, 50 mM Tris pH 7.0, 2% ethylene glycol, and 1 mM PPS (3-(1-pyridino)-1-propanesulfonate) , VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97949 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2012
RadiationMonochromator: DCM, Si(111) Watercooled first crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. all: 206175 / Num. obs: 104677 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.082 / Net I/σ(I): 8.8
Reflection shellResolution: 1.56→1.65 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 29975 / Rsym value: 0.978 / % possible all: 89.9

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.5.0055refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1R4P
Resolution: 1.56→40 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.301 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19193 5229 5 %RANDOM
Rwork0.17031 ---
obs0.1714 99444 99.59 %-
all-99853 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.56→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4961 0 93 732 5786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225163
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.9526999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3365624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56624.752242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64415861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0391527
X-RAY DIFFRACTIONr_chiral_restr0.0690.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023867
X-RAY DIFFRACTIONr_mcbond_it0.321.53127
X-RAY DIFFRACTIONr_mcangle_it0.61925068
X-RAY DIFFRACTIONr_scbond_it0.94332036
X-RAY DIFFRACTIONr_scangle_it1.5124.51931
LS refinement shellResolution: 1.558→1.598 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 386 -
Rwork0.318 7149 -
obs--97.45 %
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)
12.3598-1.52450.05484.59831.29953.0824-0.0578-0.04730.25270.17180.026-0.1239-0.20830.01880.03190.1002-0.00560.01450.1190.00840.103117.170863.8006-10.9431
20.7293-0.1352-0.12640.5519-0.35831.0169-0.0088-0.02150.0810.0218-0.02040.0026-0.10240.04140.02910.1081-0.003-0.00130.1334-0.00220.13313.517963.7392-2.2833
31.7021-0.62820.51241.33030.08851.3004-0.02870.09350.20760.0071-0.0371-0.0966-0.0462-0.00020.06580.07380.0079-0.01130.09610.03170.1326.940673.5667-13.3197
41.4631-0.63310.04731.3547-0.38480.6605-0.01510.08350.13680.00440.01960.0372-0.0207-0.0667-0.00450.07460.0045-0.01930.12860.0130.0767-0.973668.9234-17.0744
50.4508-0.44360.23820.7529-0.3291.27390.00470.0324-0.022-0.04830.04420.0070.0487-0.0361-0.04890.0923-0.00410.00190.1367-0.00320.10556.137957.7438-11.4172
63.01570.0214-0.87231.04980.51132.7115-0.03560.1457-0.2026-0.1140.0301-0.06550.210.04450.00560.0975-0.00760.00550.12050.00290.10733.031351.7235-12.3145
72.16070.8293-0.09910.61110.4061.1880.0412-0.0805-0.19290.1305-0.006-0.01160.1050.1101-0.03520.08590.01390.01090.13190.00940.1091-0.203351.83387.9262
82.2367-0.40480.12888.5529-0.07151.87980.0504-0.14280.03710.2566-0.05940.2407-0.0276-0.09920.0090.0825-0.00920.01720.162-0.00420.09825.241354.96265.2823
92.15040.04810.37410.6358-0.09780.90940.0488-0.09310.04790.003-0.0469-0.1510.00340.082-0.00190.0960.00050.01190.14390.01420.1119-9.383851.369812.5845
102.3111-1.92652.23832.5531-0.80123.3830.0272-0.1091-0.208-0.01250.04970.29980.0253-0.1965-0.0770.103-0.01540.01410.12860.02030.1131-31.437642.39878.3565
111.04750.72790.23052.08330.59311.3928-0.0488-0.2044-0.0830.20210.0633-0.13970.07740.0052-0.01450.11070.0321-0.01990.12550.02770.0961-19.774136.089525.9732
122.5320.12930.03711.60780.16580.9235-0.0504-0.1541-0.07550.1360.0751-0.05060.13440.0211-0.02480.12350.0228-0.00220.12270.0160.0862-22.038339.338723.7447
134.24640.2842-3.58281.74190.26543.7455-0.0909-0.19950.16430.16760.1391-0.06320.19710.1124-0.04810.09420.0246-0.03180.15190.01130.0763-17.207246.21228.3305
1415.9173-13.71743.387913.881-1.61721.545-0.0587-0.2414-0.8451.20940.20590.77910.7188-0.0604-0.14720.65080.00660.03350.23630.06280.0569-25.582736.647337.6085
152.24162.3722-1.22655.6636-1.62712.8216-0.0247-0.1896-0.10280.2114-0.0072-0.23340.12580.10150.03190.10450.0298-0.02480.14310.010.0853-21.23645.864728.7661
161.78780.2983-0.22512.0995-0.13330.5559-0.0084-0.0841-0.02360.1270.0186-0.1145-0.03180.0411-0.01020.09730.0032-0.00690.1423-0.01550.0575-25.510157.025224.5571
173.13261.78590.62694.33941.43851.44040.005-0.22410.11310.24310.0453-0.2426-0.0720.0502-0.05020.1040.001-0.02120.1374-0.02050.0863-25.155459.372826.5837
182.16840.5116-0.3461.05980.34931.0645-0.05580.0801-0.0919-0.03940.0306-0.04270.06530.00890.02520.11620.002800.11930.00720.0897-25.898954.164618.4777
1910.3614-4.4539-2.6183.17561.32232.2206-0.0530.22330.01170.0541-0.0088-0.00590.0280.01380.06180.1094-0.0105-0.0020.1288-0.00820.1096-25.885764.84718.4051
201.1018-0.1533-1.68790.37430.33482.85530.032-0.06360.14090.00760.0519-0.0819-0.07650.0797-0.0840.09160.0025-0.00330.1359-0.00830.1285-27.327963.974219.426
213.29760.9411-0.57490.9919-0.54232.295-0.02050.03680.1388-0.047-0.02-0.0434-0.0993-0.0020.04060.0968-0.0020.00470.09470.0050.1039-25.992462.85713.1741
223.49851.5735-0.34883.1151-0.70982.53270.0030.03630.2065-0.0764-0.0544-0.0131-0.1650.02970.05150.10510.00730.00160.1270.01080.0928-28.78663.32192.4427
235.84721.68071.42062.38680.43541.4816-0.0077-0.07190.0008-0.0266-0.0280.02180.0277-0.0410.03570.11990.00780.01220.12740.01150.0931-24.329453.75464.9288
247.6661-2.17094.35471.0348-1.44012.79260.05740.2264-0.3022-0.01670.02740.0920.0010.1026-0.08480.08220.00280.0020.16220.01550.114-23.745459.6128-5.5892
253.2413-3.4983-0.18414.4691-0.14240.1927-0.01430.14480.1547-0.0282-0.0448-0.24580.0152-0.01840.05910.1031-0.0045-0.00270.18130.02910.1182-25.548659.8551-4.6811
263.456-1.0449-0.61932.6738-0.28171.05980.0490.23030.0641-0.2866-0.0482-0.19870.18090.0378-0.00080.09950.00080.03660.1393-0.00960.0247-17.804443.9268-8.1779
271.3474-1.88190.20662.6769-0.13220.87430.15220.13010.1122-0.2248-0.1189-0.1530.11950.0799-0.03340.1335-0.03990.02720.20380.01590.0734-23.672446.3301-8.9795
285.0472.1777-3.0212.5263-1.89928.2091-0.01750.4271-0.0871-0.30470.1989-0.07060.231-0.194-0.18140.1258-0.0130.02490.1311-0.02740.0528-24.369741.2353-9.8561
291.79560.04320.08141.3475-0.1470.64850.00510.1633-0.1332-0.19310.0041-0.08570.11950.0093-0.00920.12760.0050.01990.125-0.00580.0964-19.086540.852-1.9732
306.042-0.6822.89672.5709-0.91173.9316-0.09430.6335-0.0077-0.50590.0302-0.07810.02670.21450.06410.1546-0.00730.04850.1479-0.01910.0894-17.737436.3551-6.553
312.3540.64111.33513.9758-2.2476.3368-0.0715-0.0244-0.31260.0755-0.1317-0.30830.20120.15820.20310.07190.04760.02330.0527-0.00150.1854-10.645826.943511.4879
322.33980.2480.89761.64060.07461.8499-0.0380.1319-0.1559-0.11490.0293-0.08830.22620.05820.00880.11170.02120.0230.0911-0.01190.1358-19.321429.46312.873
332.18250.416-0.06221.7085-0.08270.520.0152-0.0004-0.1649-0.0592-0.0464-0.08130.1290.030.03110.11880.01550.01220.10450.01040.1085-19.177832.59918.9471
344.00241.9098-0.42896.5141-1.24762.04330.0417-0.0113-0.5209-0.113-0.0928-0.16110.27840.00940.05110.11780.0365-0.00680.07320.0220.1566-15.360625.560715.6169
352.21031.02771.58921.1130.84643.21820.072-0.0122-0.32050.0223-0.0238-0.25480.37160.137-0.04820.11980.03210.00880.08510.0230.1718-15.73627.177414.5801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2A13 - 62
3X-RAY DIFFRACTION3A63 - 91
4X-RAY DIFFRACTION4A92 - 153
5X-RAY DIFFRACTION5A154 - 182
6X-RAY DIFFRACTION6A183 - 201
7X-RAY DIFFRACTION7A202 - 225
8X-RAY DIFFRACTION8A226 - 259
9X-RAY DIFFRACTION9A260 - 287
10X-RAY DIFFRACTION10A288 - 297
11X-RAY DIFFRACTION11B1 - 23
12X-RAY DIFFRACTION12B24 - 44
13X-RAY DIFFRACTION13B45 - 52
14X-RAY DIFFRACTION14B53 - 58
15X-RAY DIFFRACTION15B59 - 70
16X-RAY DIFFRACTION16C1 - 17
17X-RAY DIFFRACTION17C18 - 27
18X-RAY DIFFRACTION18C28 - 46
19X-RAY DIFFRACTION19C47 - 54
20X-RAY DIFFRACTION20C55 - 70
21X-RAY DIFFRACTION21D1 - 16
22X-RAY DIFFRACTION22D17 - 31
23X-RAY DIFFRACTION23D32 - 46
24X-RAY DIFFRACTION24D47 - 54
25X-RAY DIFFRACTION25D55 - 70
26X-RAY DIFFRACTION26E1 - 14
27X-RAY DIFFRACTION27E15 - 25
28X-RAY DIFFRACTION28E26 - 32
29X-RAY DIFFRACTION29E33 - 55
30X-RAY DIFFRACTION30E56 - 70
31X-RAY DIFFRACTION31F1 - 10
32X-RAY DIFFRACTION32F11 - 25
33X-RAY DIFFRACTION33F26 - 46
34X-RAY DIFFRACTION34F47 - 55
35X-RAY DIFFRACTION35F56 - 70

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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