[English] 日本語
Yorodumi
- PDB-6tnp: Crystal structure of the ScFv-5E5 in complex with a Tn glycopeptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tnp
TitleCrystal structure of the ScFv-5E5 in complex with a Tn glycopeptide
Components
  • Heavy chain of our ScFv-5E5
  • Light chain of our ScFv-5E5
KeywordsIMMUNE SYSTEM / Antibody / ScFv / 5E5 / anti-Tn antibody / MUC1 / cancer
Function / homologyChem-NO8
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMacias-Leon, J. / Corzana, F. / Hurtado-Guerrero, R.
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Structural characterization of an unprecedented lectin-like antitumoral anti-MUC1 antibody.
Authors: Macias-Leon, J. / Bermejo, I.A. / Asin, A. / Garcia-Garcia, A. / Companon, I. / Jimenez-Moreno, E. / Coelho, H. / Mangini, V. / Albuquerque, I.S. / Marcelo, F. / Asensio, J.L. / Bernardes, G. ...Authors: Macias-Leon, J. / Bermejo, I.A. / Asin, A. / Garcia-Garcia, A. / Companon, I. / Jimenez-Moreno, E. / Coelho, H. / Mangini, V. / Albuquerque, I.S. / Marcelo, F. / Asensio, J.L. / Bernardes, G.J.L. / Joshi, H.J. / Fiammengo, R. / Blixt, O. / Hurtado-Guerrero, R. / Corzana, F.
History
DepositionDec 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Light chain of our ScFv-5E5
B: Heavy chain of our ScFv-5E5
C: Light chain of our ScFv-5E5
D: Heavy chain of our ScFv-5E5
E: Light chain of our ScFv-5E5
F: Heavy chain of our ScFv-5E5
G: Light chain of our ScFv-5E5
H: Heavy chain of our ScFv-5E5
I: Heavy chain of our ScFv-5E5
J: Light chain of our ScFv-5E5
K: Heavy chain of our ScFv-5E5
L: Light chain of our ScFv-5E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,14117
Polymers152,13112
Non-polymers4,0095
Water1629
1
A: Light chain of our ScFv-5E5
B: Heavy chain of our ScFv-5E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1573
Polymers25,3552
Non-polymers8021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-14 kcal/mol
Surface area10630 Å2
MethodPISA
2
C: Light chain of our ScFv-5E5
D: Heavy chain of our ScFv-5E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1573
Polymers25,3552
Non-polymers8021
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-14 kcal/mol
Surface area10940 Å2
MethodPISA
3
E: Light chain of our ScFv-5E5
F: Heavy chain of our ScFv-5E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1573
Polymers25,3552
Non-polymers8021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-14 kcal/mol
Surface area10480 Å2
MethodPISA
4
G: Light chain of our ScFv-5E5
I: Heavy chain of our ScFv-5E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1573
Polymers25,3552
Non-polymers8021
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-12 kcal/mol
Surface area10600 Å2
MethodPISA
5
H: Heavy chain of our ScFv-5E5
L: Light chain of our ScFv-5E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1573
Polymers25,3552
Non-polymers8021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-13 kcal/mol
Surface area10600 Å2
MethodPISA
6
J: Light chain of our ScFv-5E5
K: Heavy chain of our ScFv-5E5


Theoretical massNumber of molelcules
Total (without water)25,3552
Polymers25,3552
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-8 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.573, 113.195, 151.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14A
24J
15A
25L
16B
26D
17B
27F
18B
28H
19B
29I
110B
210K
111C
211E
112C
212G
113C
213J
114C
214L
115D
215F
116D
216H
117D
217I
118D
218K
119E
219G
120E
220J
121E
221L
122F
222H
123F
223I
124F
224K
125G
225J
126G
226L
127H
227I
128H
228K
129I
229K
130J
230L

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULYSLYSAA2 - 1132 - 113
21LEULEULYSLYSCC2 - 1132 - 113
12LEULEULYSLYSAA2 - 1132 - 113
22LEULEULYSLYSEE2 - 1132 - 113
13LEULEULYSLYSAA2 - 1132 - 113
23LEULEULYSLYSGG2 - 1132 - 113
14LEULEULYSLYSAA2 - 1132 - 113
24LEULEULYSLYSJJ2 - 1132 - 113
15LEULEULYSLYSAA2 - 1132 - 113
25LEULEULYSLYSLL2 - 1132 - 113
16GLNGLNSERSERBB1 - 1151 - 115
26GLNGLNSERSERDD1 - 1151 - 115
17GLNGLNSERSERBB1 - 1151 - 115
27GLNGLNSERSERFF1 - 1151 - 115
18GLNGLNSERSERBB1 - 1151 - 115
28GLNGLNSERSERHH1 - 1151 - 115
19GLNGLNSERSERBB1 - 1151 - 115
29GLNGLNSERSERII1 - 1151 - 115
110GLNGLNSERSERBB1 - 1151 - 115
210GLNGLNSERSERKK1 - 1151 - 115
111LEULEULYSLYSCC2 - 1132 - 113
211LEULEULYSLYSEE2 - 1132 - 113
112LEULEULYSLYSCC2 - 1132 - 113
212LEULEULYSLYSGG2 - 1132 - 113
113LEULEULYSLYSCC2 - 1132 - 113
213LEULEULYSLYSJJ2 - 1132 - 113
114LEULEULYSLYSCC2 - 1132 - 113
214LEULEULYSLYSLL2 - 1132 - 113
115GLNGLNSERSERDD1 - 1151 - 115
215GLNGLNSERSERFF1 - 1151 - 115
116GLNGLNSERSERDD1 - 1151 - 115
216GLNGLNSERSERHH1 - 1151 - 115
117GLNGLNSERSERDD1 - 1151 - 115
217GLNGLNSERSERII1 - 1151 - 115
118GLNGLNSERSERDD1 - 1151 - 115
218GLNGLNSERSERKK1 - 1151 - 115
119LEULEULYSLYSEE2 - 1132 - 113
219LEULEULYSLYSGG2 - 1132 - 113
120LEULEULYSLYSEE2 - 1132 - 113
220LEULEULYSLYSJJ2 - 1132 - 113
121LEULEULYSLYSEE2 - 1132 - 113
221LEULEULYSLYSLL2 - 1132 - 113
122GLNGLNSERSERFF1 - 1151 - 115
222GLNGLNSERSERHH1 - 1151 - 115
123GLNGLNSERSERFF1 - 1151 - 115
223GLNGLNSERSERII1 - 1151 - 115
124GLNGLNSERSERFF1 - 1151 - 115
224GLNGLNSERSERKK1 - 1151 - 115
125LEULEULYSLYSGG2 - 1132 - 113
225LEULEULYSLYSJJ2 - 1132 - 113
126LEULEULYSLYSGG2 - 1132 - 113
226LEULEULYSLYSLL2 - 1132 - 113
127GLNGLNSERSERHH1 - 1151 - 115
227GLNGLNSERSERII1 - 1151 - 115
128GLNGLNSERSERHH1 - 1151 - 115
228GLNGLNSERSERKK1 - 1151 - 115
129GLNGLNSERSERII1 - 1151 - 115
229GLNGLNSERSERKK1 - 1151 - 115
130LEULEULYSLYSJJ2 - 1132 - 113
230LEULEULYSLYSLL2 - 1132 - 113

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

-
Components

#1: Antibody
Light chain of our ScFv-5E5


Mass: 12409.874 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody
Heavy chain of our ScFv-5E5


Mass: 12945.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-NO8 / (2~{S})-~{N}-[2-[[(2~{S})-1-[[(2~{S},3~{R})-3-[(2~{S},3~{R},4~{R},5~{R},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-1-[[(2~{S})-1-[(2~{S})-2-aminocarbonylpyrrolidin-1-yl]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-oxidanylidene-ethyl]-1-[(2~{S})-2-azanylpropanoyl]pyrrolidine-2-carboxamide


Mass: 801.842 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C33H55N9O14 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Ammonium chloride HEPES Glycerol ethoxylate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 30356 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.993 / Rpim(I) all: 0.072 / Net I/σ(I): 7.7
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4370 / CC1/2: 0.503 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YD5
Resolution: 3→19.9 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 50.594 / SU ML: 0.394 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25097 1243 4.1 %RANDOM
Rwork0.20281 ---
obs0.20479 29041 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.163 Å2
Baniso -1Baniso -2Baniso -3
1--4.62 Å20 Å20 Å2
2--7.86 Å20 Å2
3----3.25 Å2
Refinement stepCycle: 1 / Resolution: 3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10450 0 198 9 10657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01310906
X-RAY DIFFRACTIONr_bond_other_d0.0030.0189688
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.66914803
X-RAY DIFFRACTIONr_angle_other_deg1.3381.6122683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.51651326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5224.619459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.32151798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3191518
X-RAY DIFFRACTIONr_chiral_restr0.0770.21472
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211930
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022178
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_it3.5855.6425355
X-RAY DIFFRACTIONr_mcbond_other3.5845.6425354
X-RAY DIFFRACTIONr_mcangle_it5.8168.4546664
X-RAY DIFFRACTIONr_mcangle_other5.8168.4546665
X-RAY DIFFRACTIONr_scbond_it3.5825.9325551
X-RAY DIFFRACTIONr_scbond_other3.5825.9335552
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8718.7578140
X-RAY DIFFRACTIONr_long_range_B_refined8.86462.5511153
X-RAY DIFFRACTIONr_long_range_B_other8.86462.55611154
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)
11A33930.04
12C33930.04
21A33830.05
22E33830.05
31A33070.11
32G33070.11
41A33800.06
42J33800.06
51A33460.07
52L33460.07
61B34520.1
62D34520.1
71B34950.09
72F34950.09
81B34560.11
82H34560.11
91B33210.09
92I33210.09
101B29910.07
102K29910.07
111C34070.04
112E34070.04
121C33030.11
122G33030.11
131C34020.06
132J34020.06
141C33610.07
142L33610.07
151D34620.1
152F34620.1
161D34850.1
162H34850.1
171D32410.1
172I32410.1
181D29490.09
182K29490.09
191E32950.1
192G32950.1
201E34050.05
202J34050.05
211E33720.07
212L33720.07
221F34700.1
222H34700.1
231F33060.09
232I33060.09
241F29560.08
242K29560.08
251G33180.1
252J33180.1
261G32950.1
262L32950.1
271H32550.1
272I32550.1
281H29380.09
282K29380.09
291I29680.08
292K29680.08
301J33590.08
302L33590.08
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 87 -
Rwork0.325 2118 -
obs--99.91 %
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)
11.57870.14970.91750.60780.89372.0656-0.0431-0.07540.0211-0.04190.1327-0.18660.0924-0.2201-0.08960.4746-0.01950.02080.455-0.03770.418313.8814-15.365520.586
22.80560.2720.0480.065-0.09562.1115-0.2055-0.20690.163-0.1101-0.0286-0.02960.1401-0.49930.23410.2558-0.0010.0180.8124-0.00280.3008-7.0307-12.532726.3133
32.7049-0.6708-0.27380.3087-0.25930.8649-0.0667-0.07120.1344-0.07480.1216-0.0290.1711-0.066-0.05490.41770.0317-0.00710.4809-0.14350.464237.068-18.028828.4858
41.1596-1.03540.0041.4283-0.25992.39330.0065-0.43280.0147-0.186-0.01780.2853-0.27070.78960.01140.2841-0.07760.00740.7315-0.27570.384952.988-9.293540.493
51.00230.60990.80910.43740.7894.3028-0.1540.223-0.1748-0.02590.12930.0052-0.1190.55840.02470.38130.0288-0.02260.4897-0.00590.513444.3846-10.5234-18.3024
61.59820.28580.24030.8238-0.36393.63310.0212-0.24450.23450.1593-0.09470.0541-0.27790.38770.07350.4501-0.1489-0.18340.4125-0.05350.411142.89125.2301-2.9831
70.5943-0.578-0.59491.893-0.42162.3047-0.16810.29250.3347-0.11590.6263-0.45560.5511-0.9069-0.45830.5269-0.4097-0.0110.8190.02450.278653.072834.707113.0156
80.54160.4648-0.33581.8257-0.14063.2275-0.01340.2955-0.05820.29740.0509-0.26660.1002-0.3145-0.03750.4652-0.0358-0.08290.379-0.06750.41215.934-23.9773-13.7689
92.2132.42170.00513.3489-1.38123.0946-0.18690.0539-0.1205-0.52720.1114-0.31241.0162-0.03020.07550.8175-0.0420.03170.1946-0.14480.474962.748419.687425.8644
101.52141.6662-0.88242.4308-0.05153.04630.1557-0.2496-0.1241-0.4194-0.5876-0.1356-0.7746-0.79040.43190.8130.3719-0.01560.5028-0.14320.23785.106116.192231.9799
114.6673-0.92560.36720.4483-0.15823.1760.4676-0.1268-0.0089-0.42910.2155-0.3049-0.9342-0.161-0.68311.0215-0.22510.63520.1365-0.19050.557523.267813.392418.5561
121.55150.08510.65171.9876-1.00580.9017-0.1747-0.04650.24580.18290.0818-0.1494-0.058-0.18230.09290.54770.0936-0.09360.5061-0.05680.370312.3749-3.2677-6.6983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 113
2X-RAY DIFFRACTION2B1 - 201
3X-RAY DIFFRACTION3C2 - 113
4X-RAY DIFFRACTION4D1 - 201
5X-RAY DIFFRACTION5E2 - 113
6X-RAY DIFFRACTION6F1 - 201
7X-RAY DIFFRACTION7G2 - 113
8X-RAY DIFFRACTION8H1 - 201
9X-RAY DIFFRACTION9I1 - 201
10X-RAY DIFFRACTION10J2 - 113
11X-RAY DIFFRACTION11K1 - 115
12X-RAY DIFFRACTION12L2 - 113

+
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://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