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- PDB-4niy: Crystal structure of trypsiligase (K60E/N143H/Y151H/D189K trypsin... -

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Basic information

Entry
Database: PDB / ID: 4niy
TitleCrystal structure of trypsiligase (K60E/N143H/Y151H/D189K trypsin) complexed to YRH-ecotin (M84Y/M85R/A86H ecotin)
Components
  • Cationic trypsin
  • Ecotin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Trypsin inhibitor / Serine proteinase / Enzyme design / Activation domain / Peptide ligation / Reverse proteolysis / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / defense response / outer membrane-bounded periplasmic space / endopeptidase activity / serine-type endopeptidase activity / protein homodimerization activity ...trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / defense response / outer membrane-bounded periplasmic space / endopeptidase activity / serine-type endopeptidase activity / protein homodimerization activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. ...Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serine protease 1 / Ecotin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.84 Å
AuthorsSchoepfel, M. / Parthier, C. / Stubbs, M.T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: N-terminal protein modification by substrate-activated reverse proteolysis.
Authors: Liebscher, S. / Schopfel, M. / Aumuller, T. / Sharkhuukhen, A. / Pech, A. / Hoss, E. / Parthier, C. / Jahreis, G. / Stubbs, M.T. / Bordusa, F.
History
DepositionNov 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
B: Cationic trypsin
C: Cationic trypsin
D: Cationic trypsin
E: Ecotin
F: Ecotin
G: Ecotin
H: Ecotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,55713
Polymers158,3328
Non-polymers2265
Water59433
1
A: Cationic trypsin
E: Ecotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6233
Polymers39,5832
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-20 kcal/mol
Surface area17120 Å2
MethodPISA
2
B: Cationic trypsin
F: Ecotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6884
Polymers39,5832
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-59 kcal/mol
Surface area17110 Å2
MethodPISA
3
C: Cationic trypsin
G: Ecotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6233
Polymers39,5832
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-19 kcal/mol
Surface area17180 Å2
MethodPISA
4
D: Cationic trypsin
H: Ecotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6233
Polymers39,5832
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-19 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.241, 78.615, 98.084
Angle α, β, γ (deg.)90.000, 96.620, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESSEQ 20:137 OR RESSEQ 153:184 OR RESSEQ 191:200 OR RESSEQ 202:243 )
21CHAIN B AND (RESSEQ 20:57 OR RESSEQ 59:137 OR RESSEQ...
31CHAIN C AND (RESSEQ 20:137 OR RESSEQ 153:158 OR RESSEQ...
41CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...
12CHAIN F AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...
22CHAIN G AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...
32CHAIN H AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...
42CHAIN E AND (RESSEQ 7:8 OR RESSEQ 10:17 OR RESSEQ...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESSEQ 20:137 OR RESSEQ 153:184 OR RESSEQ 191:200 OR RESSEQ 202:243 )A20 - 137
121CHAIN A AND (RESSEQ 20:137 OR RESSEQ 153:184 OR RESSEQ 191:200 OR RESSEQ 202:243 )A153 - 184
131CHAIN A AND (RESSEQ 20:137 OR RESSEQ 153:184 OR RESSEQ 191:200 OR RESSEQ 202:243 )A191 - 200
141CHAIN A AND (RESSEQ 20:137 OR RESSEQ 153:184 OR RESSEQ 191:200 OR RESSEQ 202:243 )A202 - 243
211CHAIN B AND (RESSEQ 20:57 OR RESSEQ 59:137 OR RESSEQ...B20 - 57
221CHAIN B AND (RESSEQ 20:57 OR RESSEQ 59:137 OR RESSEQ...B59 - 137
231CHAIN B AND (RESSEQ 20:57 OR RESSEQ 59:137 OR RESSEQ...B154 - 184
241CHAIN B AND (RESSEQ 20:57 OR RESSEQ 59:137 OR RESSEQ...B191 - 200
251CHAIN B AND (RESSEQ 20:57 OR RESSEQ 59:137 OR RESSEQ...B202 - 217
261CHAIN B AND (RESSEQ 20:57 OR RESSEQ 59:137 OR RESSEQ...B222 - 243
311CHAIN C AND (RESSEQ 20:137 OR RESSEQ 153:158 OR RESSEQ...C20 - 137
321CHAIN C AND (RESSEQ 20:137 OR RESSEQ 153:158 OR RESSEQ...C153 - 158
331CHAIN C AND (RESSEQ 20:137 OR RESSEQ 153:158 OR RESSEQ...C160 - 184
341CHAIN C AND (RESSEQ 20:137 OR RESSEQ 153:158 OR RESSEQ...C191 - 200
351CHAIN C AND (RESSEQ 20:137 OR RESSEQ 153:158 OR RESSEQ...C202 - 217
361CHAIN C AND (RESSEQ 20:137 OR RESSEQ 153:158 OR RESSEQ...C221 - 243
411CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D20 - 22
421CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D24
431CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D27 - 112
441CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D117 - 136
451CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D153 - 155
461CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D157 - 172
471CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D174 - 184
481CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D191 - 197
491CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D199 - 200
4101CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D202 - 214
4111CHAIN D AND (RESSEQ 20:22 OR RESSEQ 24:24 OR RESSEQ...D221 - 242
112CHAIN F AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...F7 - 17
122CHAIN F AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...F19 - 30
132CHAIN F AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...F32 - 53
142CHAIN F AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...F55 - 85
152CHAIN F AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...F87 - 88
162CHAIN F AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...F92 - 141
212CHAIN G AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...G7 - 17
222CHAIN G AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...G19 - 30
232CHAIN G AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...G32 - 53
242CHAIN G AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...G55 - 88
252CHAIN G AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...G92 - 134
262CHAIN G AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...G136 - 141
312CHAIN H AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...H7 - 17
322CHAIN H AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...H19 - 30
332CHAIN H AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...H32 - 53
342CHAIN H AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...H55 - 84
352CHAIN H AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...H86 - 88
362CHAIN H AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...H92 - 132
372CHAIN H AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...H134
382CHAIN H AND (RESSEQ 7:17 OR RESSEQ 19:30 OR RESSEQ...H136 - 141
412CHAIN E AND (RESSEQ 7:8 OR RESSEQ 10:17 OR RESSEQ...E7 - 8
422CHAIN E AND (RESSEQ 7:8 OR RESSEQ 10:17 OR RESSEQ...E10 - 17
432CHAIN E AND (RESSEQ 7:8 OR RESSEQ 10:17 OR RESSEQ...E19 - 30
442CHAIN E AND (RESSEQ 7:8 OR RESSEQ 10:17 OR RESSEQ...E32 - 53
452CHAIN E AND (RESSEQ 7:8 OR RESSEQ 10:17 OR RESSEQ...E55 - 85
462CHAIN E AND (RESSEQ 7:8 OR RESSEQ 10:17 OR RESSEQ...E87 - 88
472CHAIN E AND (RESSEQ 7:8 OR RESSEQ 10:17 OR RESSEQ...E92 - 136
482CHAIN E AND (RESSEQ 7:8 OR RESSEQ 10:17 OR RESSEQ...E138 - 141

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.866939, -0.497498, -0.03021), (-0.497655, 0.860683, 0.107531), (-0.027496, 0.108257, -0.993743)-53.5229, -14.6342, 20.0779
2given(0.999263, 0.038003, 0.00541), (-0.038351, 0.982435, 0.182624), (0.001626, -0.182697, 0.983168)5.72223, -42.252899, -29.7012
3given(-0.871638, -0.483273, -0.081814), (-0.489677, 0.851248, 0.188665), (-0.021533, 0.20451, -0.978628)-38.7318, -53.5476, 45.858898
4given(-0.844327, -0.525498, -0.104705), (-0.535339, 0.818957, 0.206691), (-0.022867, 0.230568, -0.972788)-36.955601, -56.571602, 45.751099
5given(0.999852, 0.015509, 0.007506), (-0.016427, 0.989473, 0.143781), (-0.005197, -0.143883, 0.989581)5.79988, -41.178299, -30.135201
6given(-0.847869, -0.529031, -0.035277), (-0.529011, 0.839619, 0.123233), (-0.035574, 0.123147, -0.991751)-53.993, -16.9597, 20.1931

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Components

#1: Protein
Cationic trypsin / Beta-trypsin / Alpha-trypsin chain 1 / Alpha-trypsin chain 2


Mass: 23337.330 Da / Num. of mol.: 4 / Fragment: UNP residues 24-246 / Mutation: K60E, N143H, Y151H, D189K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin
#2: Protein
Ecotin


Mass: 16245.554 Da / Num. of mol.: 4 / Fragment: UNP residues 21-162 / Mutation: M84Y, M85R, A86H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eco, eti, b2209, JW2197 / Production host: Escherichia coli (E. coli) / References: UniProt: P23827
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.3 M sodium acetate, 0.1 M Tris/HCl, 10 mM CaCl2, 20% (w/v) polyethyleneglycol 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.84→49.596 Å / Num. obs: 33639 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.68 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.84-3.020.6921.9620471534698.8
3.02-3.220.3923.4919496506999.9
3.22-3.480.2485.4318314475399.9
3.48-3.810.1329.4716847437699.9
3.81-4.260.08413.7115192395599.9
4.26-4.910.05819.3213466352299.8
4.91-60.05919.0811288297299.9
6-8.420.05920.588604230798.9
8.420.03729.254694133998.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→49.596 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7929 / SU ML: 0.38 / σ(F): 2 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 1681 5 %
Rwork0.1917 --
obs0.1948 33622 99.59 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.72 Å2 / Biso mean: 26.9233 Å2 / Biso min: 1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.84→49.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10536 0 5 33 10574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110768
X-RAY DIFFRACTIONf_angle_d1.2314546
X-RAY DIFFRACTIONf_chiral_restr0.0791627
X-RAY DIFFRACTIONf_plane_restr0.0051854
X-RAY DIFFRACTIONf_dihedral_angle_d14.8443919
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1434X-RAY DIFFRACTIONPOSITIONAL0.057
12B1434X-RAY DIFFRACTIONPOSITIONAL0.057
13C1450X-RAY DIFFRACTIONPOSITIONAL0.054
14D1036X-RAY DIFFRACTIONPOSITIONAL0.057
21F1019X-RAY DIFFRACTIONPOSITIONAL0.071
22G1019X-RAY DIFFRACTIONPOSITIONAL0.071
23H999X-RAY DIFFRACTIONPOSITIONAL0.057
24E1011X-RAY DIFFRACTIONPOSITIONAL0.07
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.84-2.92720.371370.30062620275798
2.9272-3.02170.32881380.260426082746100
3.0217-3.12970.26141410.229526722813100
3.1297-3.2550.30651380.224826402778100
3.255-3.40310.29361410.219726742815100
3.4031-3.58250.30741390.205326532792100
3.5825-3.80680.26011400.188526512791100
3.8068-4.10060.21641400.178826742814100
4.1006-4.51310.2171410.159226652806100
4.5131-5.16550.22111410.165326782819100
5.1655-6.50570.24431420.184126922834100
6.5057-49.60370.21091430.1672714285798

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