[English] 日本語
Yorodumi
- PDB-1sq3: Crystal structures of a novel open pore ferritin from the hyperth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sq3
TitleCrystal structures of a novel open pore ferritin from the hyperthermophilic Archaeon Archaeoglobus fulgidus.
Componentsferritin
KeywordsMETAL BINDING PROTEIN / Ferroxidase / four helix bundle / iron storage
Function / homology
Function and homology information


ferroxidase activity / : / ferric iron binding / ferrous iron binding / iron ion transport / identical protein binding / cytosol
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ferritin, putative
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJohnson, E. / Cascio, D. / Michael, S. / Schroder, I.
CitationJournal: Structure / Year: 2005
Title: Crystal structures of a tetrahedral open pore ferritin from the hyperthermophilic archaeon Archaeoglobus fulgidus.
Authors: Johnson, E. / Cascio, D. / Sawaya, M.R. / Gingery, M. / Schroder, I.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2013Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ferritin
B: ferritin
C: ferritin
D: ferritin
E: ferritin
F: ferritin
G: ferritin
H: ferritin
I: ferritin
J: ferritin
K: ferritin
L: ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,13248
Polymers249,12212
Non-polymers2,01036
Water9,278515
1
A: ferritin
B: ferritin
C: ferritin
D: ferritin
E: ferritin
F: ferritin
G: ferritin
H: ferritin
I: ferritin
J: ferritin
K: ferritin
L: ferritin
hetero molecules

A: ferritin
B: ferritin
C: ferritin
D: ferritin
E: ferritin
F: ferritin
G: ferritin
H: ferritin
I: ferritin
J: ferritin
K: ferritin
L: ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)502,26496
Polymers498,24324
Non-polymers4,02172
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Unit cell
Length a, b, c (Å)184.502, 190.243, 179.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22E
13A
23G
14A
24J
15A
25K
16B
26C
17B
27F
18B
28H
19B
29I
110B
210L
111C
211A
311C
411A
511C
611A
711C
811A
112C
212B
312C
412B
512C
612B
712C
812B
113C
213D
313C
413D
513C
613D
713C
813D
114C
214E
314C
414E
514C
614E
714C
814E
115C
215F
315C
415F
515C
615F
715C
815F
116C
216G
316C
416G
516C
616G
716C
816G
117C
217H
317C
417H
517C
617H
717C
817H
118C
218I
318C
418I
518C
618I
718C
818I
119C
219J
319C
419J
519C
619J
719C
819J
120C
220K
320C
420K
520C
620K
720C
820K
121C
221L
321C
421L
521C
621L
721C
821L

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILELEULEU4AA4 - 1624 - 162
211ILEILELEULEU4DD4 - 1624 - 162
112ILEILELEULEU4AA4 - 1624 - 162
212ILEILELEULEU4EE4 - 1624 - 162
113ILEILELEULEU4AA4 - 1624 - 162
213ILEILELEULEU4GG4 - 1624 - 162
114ILEILELEULEU4AA4 - 1624 - 162
214ILEILELEULEU4JJ4 - 1624 - 162
115ILEILELEULEU4AA4 - 1624 - 162
215ILEILELEULEU4KK4 - 1624 - 162
116ILEILELEULEU4BB4 - 1624 - 162
216ILEILELEULEU4CC4 - 1624 - 162
117ILEILELEULEU4BB4 - 1624 - 162
217ILEILELEULEU4FF4 - 1624 - 162
118ILEILELEULEU4BB4 - 1624 - 162
218ILEILELEULEU4HH4 - 1624 - 162
119ILEILELEULEU4BB4 - 1624 - 162
219ILEILELEULEU4II4 - 1624 - 162
1110ILEILELEULEU4BB4 - 1624 - 162
2110ILEILELEULEU4LL4 - 1624 - 162
1111ALAALAILEILE1CC18 - 2018 - 20
2111ALAALAILEILE1AA18 - 2018 - 20
3211GLUGLUALAALA1CC51 - 5651 - 56
4211GLUGLUALAALA1AA51 - 5651 - 56
5311HISHISVALVAL1CC95 - 9795 - 97
6311HISHISVALVAL1AA95 - 9795 - 97
7411ALAALAGLUGLU1CC127 - 133127 - 133
8411ALAALAGLUGLU1AA127 - 133127 - 133
1112ALAALAILEILE1CC18 - 2018 - 20
2112ALAALAILEILE1BB18 - 2018 - 20
3212GLUGLUALAALA1CC51 - 5651 - 56
4212GLUGLUALAALA1BB51 - 5651 - 56
5312HISHISVALVAL1CC95 - 9795 - 97
6312HISHISVALVAL1BB95 - 9795 - 97
7412ALAALAGLUGLU1CC127 - 133127 - 133
8412ALAALAGLUGLU1BB127 - 133127 - 133
1113ALAALAILEILE1CC18 - 2018 - 20
2113ALAALAILEILE1DD18 - 2018 - 20
3213GLUGLUALAALA1CC51 - 5651 - 56
4213GLUGLUALAALA1DD51 - 5651 - 56
5313HISHISVALVAL1CC95 - 9795 - 97
6313HISHISVALVAL1DD95 - 9795 - 97
7413ALAALAGLUGLU1CC127 - 133127 - 133
8413ALAALAGLUGLU1DD127 - 133127 - 133
1114ALAALAILEILE1CC18 - 2018 - 20
2114ALAALAILEILE1EE18 - 2018 - 20
3214GLUGLUALAALA1CC51 - 5651 - 56
4214GLUGLUALAALA1EE51 - 5651 - 56
5314HISHISVALVAL1CC95 - 9795 - 97
6314HISHISVALVAL1EE95 - 9795 - 97
7414ALAALAGLUGLU1CC127 - 133127 - 133
8414ALAALAGLUGLU1EE127 - 133127 - 133
1115ALAALAILEILE1CC18 - 2018 - 20
2115ALAALAILEILE1FF18 - 2018 - 20
3215GLUGLUALAALA1CC51 - 5651 - 56
4215GLUGLUALAALA1FF51 - 5651 - 56
5315HISHISVALVAL1CC95 - 9795 - 97
6315HISHISVALVAL1FF95 - 9795 - 97
7415ALAALAGLUGLU1CC127 - 133127 - 133
8415ALAALAGLUGLU1FF127 - 133127 - 133
1116ALAALAILEILE1CC18 - 2018 - 20
2116ALAALAILEILE1GG18 - 2018 - 20
3216GLUGLUALAALA1CC51 - 5651 - 56
4216GLUGLUALAALA1GG51 - 5651 - 56
5316HISHISVALVAL1CC95 - 9795 - 97
6316HISHISVALVAL1GG95 - 9795 - 97
7416ALAALAGLUGLU1CC127 - 133127 - 133
8416ALAALAGLUGLU1GG127 - 133127 - 133
1117ALAALAILEILE1CC18 - 2018 - 20
2117ALAALAILEILE1HH18 - 2018 - 20
3217GLUGLUALAALA1CC51 - 5651 - 56
4217GLUGLUALAALA1HH51 - 5651 - 56
5317HISHISVALVAL1CC95 - 9795 - 97
6317HISHISVALVAL1HH95 - 9795 - 97
7417ALAALAGLUGLU1CC127 - 133127 - 133
8417ALAALAGLUGLU1HH127 - 133127 - 133
1118ALAALAILEILE1CC18 - 2018 - 20
2118ALAALAILEILE1II18 - 2018 - 20
3218GLUGLUALAALA1CC51 - 5651 - 56
4218GLUGLUALAALA1II51 - 5651 - 56
5318HISHISVALVAL1CC95 - 9795 - 97
6318HISHISVALVAL1II95 - 9795 - 97
7418ALAALAGLUGLU1CC127 - 133127 - 133
8418ALAALAGLUGLU1II127 - 133127 - 133
1119ALAALAILEILE1CC18 - 2018 - 20
2119ALAALAILEILE1JJ18 - 2018 - 20
3219GLUGLUALAALA1CC51 - 5651 - 56
4219GLUGLUALAALA1JJ51 - 5651 - 56
5319HISHISVALVAL1CC95 - 9795 - 97
6319HISHISVALVAL1JJ95 - 9795 - 97
7419ALAALAGLUGLU1CC127 - 133127 - 133
8419ALAALAGLUGLU1JJ127 - 133127 - 133
1120ALAALAILEILE1CC18 - 2018 - 20
2120ALAALAILEILE1KK18 - 2018 - 20
3220GLUGLUALAALA1CC51 - 5651 - 56
4220GLUGLUALAALA1KK51 - 5651 - 56
5320HISHISVALVAL1CC95 - 9795 - 97
6320HISHISVALVAL1KK95 - 9795 - 97
7420ALAALAGLUGLU1CC127 - 133127 - 133
8420ALAALAGLUGLU1KK127 - 133127 - 133
1121ALAALAILEILE1CC18 - 2018 - 20
2121ALAALAILEILE1LL18 - 2018 - 20
3221GLUGLUALAALA1CC51 - 5651 - 56
4221GLUGLUALAALA1LL51 - 5651 - 56
5321HISHISVALVAL1CC95 - 9795 - 97
6321HISHISVALVAL1LL95 - 9795 - 97
7421ALAALAGLUGLU1CC127 - 133127 - 133
8421ALAALAGLUGLU1LL127 - 133127 - 133

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

-
Components

#1: Protein
ferritin


Mass: 20760.139 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: Ftn / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 codon plus / References: UniProt: O29424
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 7.5
Details: PEG 400, HEPES, MgCl2, FeSO4 , pH 7.5, MICROBATCH UNDER OIL, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 27, 2003 / Details: osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→80 Å / Num. all: 86172 / Num. obs: 86172 / % possible obs: 99.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 26.43
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 6.67 / Num. unique all: 8527 / Rsym value: 0.394 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1S3Q

1s3q


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.725 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.541 / ESU R Free: 0.273 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21755 4330 5 %RANDOM
Rwork0.17672 ---
all0.17877 86172 --
obs0.17877 81803 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.829 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--0.43 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16113 0 36 515 16664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02116482
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214697
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.94522209
X-RAY DIFFRACTIONr_angle_other_deg1.135334179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16751929
X-RAY DIFFRACTIONr_chiral_restr0.080.22337
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0218243
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023477
X-RAY DIFFRACTIONr_nbd_refined0.2670.34941
X-RAY DIFFRACTIONr_nbd_other0.2790.316658
X-RAY DIFFRACTIONr_nbtor_other0.0880.58986
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2780.51339
X-RAY DIFFRACTIONr_metal_ion_refined0.120.541
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.364
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4710.514
X-RAY DIFFRACTIONr_mcbond_it1.66629690
X-RAY DIFFRACTIONr_mcangle_it2.734315525
X-RAY DIFFRACTIONr_scbond_it2.08826792
X-RAY DIFFRACTIONr_scangle_it3.32136684
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11C284tight positional0.190.05
12C284tight positional0.180.05
13C284tight positional0.070.05
14C284tight positional0.090.05
15C282tight positional0.070.05
16C284tight positional0.080.05
17C284tight positional0.090.05
18C284tight positional0.070.05
19C282tight positional0.070.05
20C282tight positional0.180.05
21C284tight positional0.060.05
1A2520medium positional0.340.5
2A2520medium positional0.330.5
3A2520medium positional0.320.5
4A2518medium positional0.310.5
5A2518medium positional0.330.5
6B2520medium positional0.290.5
7B2518medium positional0.30.5
8B2520medium positional0.370.5
9B2520medium positional0.310.5
10B2520medium positional0.340.5
11C284tight thermal0.30.5
12C284tight thermal0.380.5
13C284tight thermal0.390.5
14C284tight thermal0.370.5
15C282tight thermal0.440.5
16C284tight thermal0.330.5
17C284tight thermal0.440.5
18C284tight thermal0.390.5
19C282tight thermal0.390.5
20C282tight thermal0.450.5
21C284tight thermal0.40.5
1A2520medium thermal0.92
2A2520medium thermal0.952
3A2520medium thermal0.852
4A2518medium thermal0.942
5A2518medium thermal1.032
6B2520medium thermal0.952
7B2518medium thermal1.052
8B2520medium thermal0.952
9B2520medium thermal0.92
10B2520medium thermal1.362
LS refinement shellResolution: 2.7→2.772 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 303
Rwork0.204 5969
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.87210.4090.05842.1469-0.62760.2877-0.02510.4779-0.1947-0.10570.0312-0.06350.0852-0.089-0.00610.226-0.01680.04150.4699-0.10120.131558.60476.81129.314
20.83750.6735-0.19082.1636-0.14920.1179-0.11210.58130.0312-0.02790.07770.09240.0548-0.10680.03430.2082-0.0385-0.02430.6327-0.0390.104333.17581.412126.749
32.499-1.26840.320.68630.01560.22380.06220.28350.5531-0.0293-0.0115-0.2859-0.0727-0.0398-0.05070.2286-0.0451-0.02150.15550.19920.452464.322130.49150.321
41.747-0.94230.64030.60730.19910.4510.17830.46870.2018-0.1567-0.12-0.0629-0.0996-0.0092-0.05830.23070.01210.04670.42870.26240.191659.101114.044130.887
50.71130.3130.59390.58510.46181.39970.00130.27790.02120.0528-0.0206-0.129-0.0120.11280.01930.148-0.00720.03180.23560.03190.233685.32294.346148.583
60.64090.16480.56880.40330.38941.34410.10250.0681-0.16020.0296-0.01080.00110.19630.0457-0.09170.2230.0356-0.0150.1327-0.00550.305384.09572.334162.346
71.07460.1255-0.34910.2249-0.50511.1638-0.08780.3449-0.5103-0.0658-0.0041-0.03750.2495-0.11780.0920.3359-0.11310.06250.1384-0.21790.402317.36445.906158.141
81.39410.2944-1.03630.1927-0.44672.0616-0.25890.0304-0.6221-0.01850.014-0.1160.25330.19490.2450.3150.01770.11770.1118-0.15520.525442.81842.946162.807
91.7067-0.06960.4485-0.0272-0.07470.7315-0.0575-0.3971-0.18410.024-0.0788-0.112-0.0407-0.17590.13630.2839-0.02510.04060.32390.14820.186211.88763.821212.778
101.7054-0.34360.72290.26890.00920.62530.026-0.173-0.44490.0647-0.0129-0.01560.1778-0.0142-0.0130.3066-0.09680.06850.12170.12990.436316.54745.238195.282
110.957-0.4081-0.27370.70760.4160.6681-0.04860.0172-0.27130.06280.00050.06890.0434-0.21590.04810.2253-0.11180.0470.1998-0.04150.2102-9.364.34176.69
120.8423-0.6437-0.46030.81660.60031.0614-0.00330.1507-0.0739-0.087-0.04090.06470.0152-0.08070.04420.213-0.0638-0.01070.2807-0.06550.0855-7.73579.466155.64
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1643 - 164
2X-RAY DIFFRACTION2BB3 - 1643 - 164
3X-RAY DIFFRACTION3CC3 - 1643 - 164
4X-RAY DIFFRACTION4DD3 - 1643 - 164
5X-RAY DIFFRACTION5EE3 - 1643 - 164
6X-RAY DIFFRACTION6FF3 - 1643 - 164
7X-RAY DIFFRACTION7GG3 - 1643 - 164
8X-RAY DIFFRACTION8HH3 - 1643 - 164
9X-RAY DIFFRACTION9II3 - 1643 - 164
10X-RAY DIFFRACTION10JJ3 - 1643 - 164
11X-RAY DIFFRACTION11KK3 - 1643 - 164
12X-RAY DIFFRACTION12LL3 - 1643 - 164

+
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