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- PDB-5n4c: Prolyl oligopeptidase B from Galerina marginata bound to 35mer hy... -

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Basic information

Entry
Database: PDB / ID: 5n4c
TitleProlyl oligopeptidase B from Galerina marginata bound to 35mer hydrolysis and macrocyclization substrate - S577A mutant
Components
  • Alpha-amanitin proprotein
  • Prolyl oligopeptidase
KeywordsHYDROLASE / amanitin biosynthesis / prolyl oligopeptidase / macrocyclase / peptidase / beta-propeller / closed form
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / toxin activity / serine-type endopeptidase activity / proteolysis / cytosol
Similarity search - Function
Amanitin/phalloidin toxin / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Amanitin/phalloidin toxin / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-amanitin proprotein 1 / Alpha-amanitin proprotein 1 / Dual function macrocyclase-peptidase POPB
Similarity search - Component
Biological speciesGalerina marginata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsCzekster, C.M. / McMahon, S.A. / Ludewig, H. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council339367 NCB-TNT United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates.
Authors: Czekster, C.M. / Ludewig, H. / McMahon, S.A. / Naismith, J.H.
History
DepositionFeb 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl oligopeptidase
E: Alpha-amanitin proprotein
B: Prolyl oligopeptidase
C: Prolyl oligopeptidase
D: Prolyl oligopeptidase
F: Alpha-amanitin proprotein
G: Alpha-amanitin proprotein
H: Alpha-amanitin proprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,9369
Polymers342,8448
Non-polymers921
Water21,5461196
1
A: Prolyl oligopeptidase
E: Alpha-amanitin proprotein


Theoretical massNumber of molelcules
Total (without water)85,7112
Polymers85,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-21 kcal/mol
Surface area30540 Å2
MethodPISA
2
B: Prolyl oligopeptidase
F: Alpha-amanitin proprotein


Theoretical massNumber of molelcules
Total (without water)85,7112
Polymers85,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-22 kcal/mol
Surface area30040 Å2
MethodPISA
3
C: Prolyl oligopeptidase
G: Alpha-amanitin proprotein


Theoretical massNumber of molelcules
Total (without water)85,7112
Polymers85,7112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-24 kcal/mol
Surface area30250 Å2
MethodPISA
4
D: Prolyl oligopeptidase
H: Alpha-amanitin proprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8033
Polymers85,7112
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-24 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.797, 142.562, 116.356
Angle α, β, γ (deg.)90.00, 90.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14E
24F
15E
25G
16E
26H
17B
27C
18B
28D
19C
29D
110F
210G
111F
211H
112G
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRPGLUGLUAA6 - 7256 - 725
21TRPTRPGLUGLUBC6 - 7256 - 725
12TRPTRPLYSLYSAA6 - 7276 - 727
22TRPTRPLYSLYSCD6 - 7276 - 727
13ALAALAGLUGLUAA7 - 7257 - 725
23ALAALAGLUGLUDE7 - 7257 - 725
14ASPASPCYSCYSEB3 - 353 - 35
24ASPASPCYSCYSFF3 - 353 - 35
15ASPASPCYSCYSEB3 - 353 - 35
25ASPASPCYSCYSGG3 - 353 - 35
16ASPASPCYSCYSEB3 - 353 - 35
26ASPASPCYSCYSHH3 - 353 - 35
17TRPTRPLEULEUBC6 - 7266 - 726
27TRPTRPLEULEUCD6 - 7266 - 726
18ALAALAGLUGLUBC7 - 7257 - 725
28ALAALAGLUGLUDE7 - 7257 - 725
19ALAALAGLUGLUCD7 - 7257 - 725
29ALAALAGLUGLUDE7 - 7257 - 725
110ASPASPCYSCYSFF3 - 353 - 35
210ASPASPCYSCYSGG3 - 353 - 35
111ASPASPCYSCYSFF3 - 353 - 35
211ASPASPCYSCYSHH3 - 353 - 35
112ASPASPCYSCYSGG3 - 353 - 35
212ASPASPCYSCYSHH3 - 353 - 35

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Prolyl oligopeptidase


Mass: 81860.602 Da / Num. of mol.: 4 / Mutation: S577A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galerina marginata (fungus) / Gene: POPB / Plasmid: pJ414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H2E7Q8
#2: Protein/peptide
Alpha-amanitin proprotein


Mass: 3850.276 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Galerina marginata (fungus) / References: UniProt: H2E7Q5, UniProt: A0A067SLB9*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1196 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 28% PEG6000, 100 mM Bicine pH 8.7, 64 mM Sodium Potassium Phosphate, 12.5mM Hexammine cobalt chloride, crystals cryoprotected with 12% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.19→90.14 Å / Num. obs: 163136 / % possible obs: 96.77 % / Redundancy: 2 % / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→90.14 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 14.657 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.226 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24944 7959 4.9 %RANDOM
Rwork0.21391 ---
obs0.21562 155177 96.77 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 32.215 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20.11 Å2
2---3.17 Å20 Å2
3---1.14 Å2
Refinement stepCycle: 1 / Resolution: 2.19→90.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23876 0 6 1196 25078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01924561
X-RAY DIFFRACTIONr_bond_other_d0.0020.0222570
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.93733376
X-RAY DIFFRACTIONr_angle_other_deg0.961352005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12453010
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05324.2171188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.302153897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.67215122
X-RAY DIFFRACTIONr_chiral_restr0.090.23526
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02128178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025892
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1181.28512052
X-RAY DIFFRACTIONr_mcbond_other1.1181.28512051
X-RAY DIFFRACTIONr_mcangle_it1.8791.92115046
X-RAY DIFFRACTIONr_mcangle_other1.8791.92115047
X-RAY DIFFRACTIONr_scbond_it1.4141.41412509
X-RAY DIFFRACTIONr_scbond_other1.4141.41412509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2932.05818327
X-RAY DIFFRACTIONr_long_range_B_refined4.77215.0126032
X-RAY DIFFRACTIONr_long_range_B_other4.77215.00926032
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A455220.06
12B455220.06
21A455920.06
22C455920.06
31A453960.06
32D453960.06
41E14560.08
42F14560.08
51E15360.09
52G15360.09
61E15380.07
62H15380.07
71B455780.07
72C455780.07
81B454200.06
82D454200.06
91C454600.06
92D454600.06
101F14700.08
102G14700.08
111F15020.04
112H15020.04
121G16200.07
122H16200.07
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 612 -
Rwork0.3 11265 -
obs--95.91 %
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)
10.5422-0.0795-0.26171.4446-0.90311.6074-0.0467-0.1296-0.1590.0226-0.0669-0.20670.20790.27870.11360.07880.0143-0.04440.4341-0.01030.143450.8066.32746.379
21.23190.0762-0.04110.56220.1050.99550.0476-0.12040.1186-0.00920.0022-0.0494-0.12250.0321-0.04990.03480.01680.01730.2886-0.00990.091634.49441.84445.828
30.9108-0.1622-0.04890.805-0.38241.7749-0.0028-0.0401-0.03980.0780.06270.00410-0.0293-0.05990.01790.0034-0.02630.3004-0.00360.070335.90710.98739.465
41.87941.15420.78765.33661.63461.5165-0.02360.0324-0.0954-0.01840.0289-0.033-0.07350.0103-0.00530.07330.0184-0.00320.33110.00860.094150.8715.91232.583
51.0136-0.0560.17991.44660.25970.72720.0486-0.05060.025-0.0060.0450.2107-0.0628-0.1186-0.09370.017-0.01350.0260.35040.03960.084412.0745.479-17.114
61.39110.02990.15140.718-0.15950.99820.0633-0.1849-0.17390.0157-0.00350.08270.0338-0.0451-0.05990.00590.0056-0.01630.2880.01110.11228.79227.303-10.371
71.1133-0.09910.05770.71730.17811.49370.0098-0.03520.1640.07020.0750.049-0.10950.0278-0.08480.028-0.0060.04130.26430.00560.103425.60357.389-18.619
82.73970.79590.14824.54950.45760.42280.0152-0.14890.05680.24140.04070.03130.01270.0186-0.05590.08790.0265-0.00170.33420.01070.12589.92151.682-22.751
90.99470.30010.30331.3622-0.46570.611-0.00120.1140.0066-0.05620.0166-0.2192-0.02510.1248-0.01540.02220.04330.02350.3739-0.04830.0995-0.82351.57225.732
101.21560.07290.28160.70830.27190.95710.09460.1565-0.22420.04610.013-0.11450.09710.0901-0.10770.02420.0122-0.04140.3029-0.03390.1136-16.86226.60622.116
111.02070.3774-0.0860.855-0.27041.484-0.01850.06140.0195-0.0450.0274-0.02570.05060.0107-0.0090.00590.01720.00840.2541-0.01420.0606-14.33756.81229.146
123.3807-3.5249-0.8639.40421.44731.40430.0379-0.10930.14670.09630.0907-0.18020.01120.0355-0.12870.0409-0.0133-0.01470.2451-0.00360.10540.67153.77538.929
130.75320.1035-0.03291.37940.24330.83890.05710.0797-0.0508-0.0713-0.00080.15510.1173-0.0688-0.05630.03420.0136-0.0340.40480.02260.0607-38.95720.47484.514
141.1031-0.08170.00270.7264-0.09780.98770.03580.12990.1115-0.0364-0.02120.0401-0.0485-0.0222-0.01460.0082-0.01480.00850.30610.02530.0699-22.97341.97979.424
151.04810.22570.14470.79120.21661.60250.03670.0701-0.0821-0.10960.02390.02910.10010.0531-0.06060.03290.0181-0.02510.28730.00760.0617-25.47611.85687.846
162.5087-1.27641.14667.6658-2.17142.12620.02390.1384-0.0326-0.2352-0.00180.16330.06970.0368-0.02210.0149-0.01620.01260.2989-0.01070.1127-41.00717.47691.673
172.02670.79622.13337.00062.4492.6478-0.25540.0530.4527-0.3863-0.0613-0.0953-0.33050.06580.31670.44650.07680.05020.56780.04230.40136.5832747.199
181.795-4.42281.941213.5853-3.00523.27790.34460.19650.2884-0.7924-0.4537-0.96090.45630.27710.10910.2922-0.03480.08280.5699-0.04620.37941.4523.90335.891
196.4742-1.8993-3.314610.93147.38558.4127-0.41570.0283-0.0840.86840.08260.24410.5954-0.17840.33320.09460.03710.02090.2680.0450.094539.93639.33337.914
204.2464-3.03542.032914.40242.98743.2699-0.1589-0.0652-0.8734-0.21790.5463-0.01190.22310.2456-0.38740.341-0.00050.14150.4904-0.03630.408526.12540.457-8.322
212.84722.3306-3.878913.82063.20168.70980.09760.2648-0.0960.5126-0.40550.44950.0445-0.66090.30790.2598-0.0767-0.03570.58760.01760.537620.20143.744-19.973
222.4821-2.47924.04067.6332-5.07347.1458-0.1807-0.03010.14650.4984-0.1076-0.0613-0.54180.28140.28830.2022-0.0544-0.02080.31890.00150.181621.3929.236-20.64
231.09141.14231.276316.5768-1.83032.17920.2299-0.027-0.0690.160.00530.57290.4152-0.1226-0.23530.3567-0.04710.03190.48630.00510.2485-15.30940.90918.558
243.3687-5.0846-0.473514.9041-2.76985.3659-0.2230.041-0.3563-0.31630.1635-0.31260.3027-0.1640.05950.2327-0.0240.01520.5693-0.00440.5161-9.6642.41630.07
257.44172.62054.2446.84865.62177.2319-0.1144-0.0380.1596-0.5447-0.14470.137-0.4112-0.25940.25910.13250.0345-0.05350.2630.00790.1553-10.51828.76431.082
2611.4979-2.9041-6.00160.73971.52673.15290.0292-0.31120.4188-0.05660.1236-0.0831-0.09180.225-0.15280.5202-0.0947-0.16840.56280.05930.2169-24.90227.69676.674
275.6958-2.63381.076212.72493.06011.3702-0.2001-0.50080.3747-1.27990.17930.4425-0.5341-0.14490.02080.37520.03470.11920.63280.05280.654-30.54626.25288.053
284.93185.2419-2.673810.5207-8.36927.8593-0.31220.0651-0.1811-0.36530.0582-0.4780.245-0.20920.2540.12390.02170.02010.31490.02480.1956-29.75640.06289.028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 82
2X-RAY DIFFRACTION2A83 - 450
3X-RAY DIFFRACTION3A451 - 696
4X-RAY DIFFRACTION4A697 - 727
5X-RAY DIFFRACTION5B6 - 133
6X-RAY DIFFRACTION6B134 - 449
7X-RAY DIFFRACTION7B450 - 693
8X-RAY DIFFRACTION8B694 - 726
9X-RAY DIFFRACTION9C6 - 108
10X-RAY DIFFRACTION10C109 - 451
11X-RAY DIFFRACTION11C452 - 700
12X-RAY DIFFRACTION12C701 - 728
13X-RAY DIFFRACTION13D7 - 117
14X-RAY DIFFRACTION14D118 - 448
15X-RAY DIFFRACTION15D449 - 693
16X-RAY DIFFRACTION16D694 - 726
17X-RAY DIFFRACTION17E3 - 18
18X-RAY DIFFRACTION18E19 - 25
19X-RAY DIFFRACTION19E26 - 35
20X-RAY DIFFRACTION20F2 - 11
21X-RAY DIFFRACTION21F12 - 25
22X-RAY DIFFRACTION22F26 - 35
23X-RAY DIFFRACTION23G3 - 11
24X-RAY DIFFRACTION24G12 - 25
25X-RAY DIFFRACTION25G26 - 35
26X-RAY DIFFRACTION26H3 - 11
27X-RAY DIFFRACTION27H12 - 25
28X-RAY DIFFRACTION28H26 - 35

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