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Basic information

Entry
Database: PDB / ID: 3t8w
TitleA bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases
ComponentsM17 leucyl aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / M17-leucyl aminopeptidase / protease / metallo-aminopeptidase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / identical protein binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like ...Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Chem-DGZ / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcGowan, S. / Klemba, M. / Greebaum, D.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases
Authors: Harbut, M.B. / Velmourougane, G. / Dalal, S. / Reiss, G. / Whisstock, J.C. / Onder, O. / Brisson, D. / McGowan, S. / Klemba, M. / Greenbaum, D.C.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
G: M17 leucyl aminopeptidase
H: M17 leucyl aminopeptidase
I: M17 leucyl aminopeptidase
J: M17 leucyl aminopeptidase
K: M17 leucyl aminopeptidase
L: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)730,398124
Polymers704,50812
Non-polymers25,890112
Water86,3824795
1
A: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,36357
Polymers352,2546
Non-polymers12,10951
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39130 Å2
ΔGint-497 kcal/mol
Surface area95220 Å2
MethodPISA
2
G: M17 leucyl aminopeptidase
H: M17 leucyl aminopeptidase
I: M17 leucyl aminopeptidase
J: M17 leucyl aminopeptidase
K: M17 leucyl aminopeptidase
L: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,03567
Polymers352,2546
Non-polymers13,78161
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41860 Å2
ΔGint-595 kcal/mol
Surface area95170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.748, 177.057, 231.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
M17 leucyl aminopeptidase / Pf-LAP


Mass: 58708.973 Da / Num. of mol.: 12 / Fragment: UNP residues 84-605
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IL11

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Non-polymers , 7 types, 4907 molecules

#2: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-DGZ / N-((2R,3S,6S,18S,21S)-2-amino-18-(4-benzoylbenzyl)-21-carbamoyl-3-hydroxy-6-(naphthalen-2-ylmethyl)-4,7,16,19-tetraoxo-1-phenyl-11,14-dioxa-5,8,17,20-tetraazapentacosan-25-yl)hex-5-ynamide


Mass: 1010.183 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C57H67N7O10
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: SO4
#6: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4795 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 40%(v/v) PEG400, 0.1M Tris, 0.2M LiSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→88.64 Å / Num. obs: 477295 / % possible obs: 100 % / Biso Wilson estimate: 17.48 Å2

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→81.32 Å / Cor.coef. Fo:Fc: 0.9545 / Cor.coef. Fo:Fc free: 0.9331 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 23964 5.03 %RANDOM
Rwork0.1637 ---
obs0.1655 476465 --
Displacement parametersBiso max: 236.76 Å2 / Biso mean: 20.4 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-2.1295 Å20 Å20 Å2
2--1.1358 Å20 Å2
3----3.2653 Å2
Refine analyzeLuzzati coordinate error obs: 0.196 Å
Refinement stepCycle: LAST / Resolution: 2→81.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47032 0 1468 4795 53295
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d16170SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes1126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes7114HARMONIC5
X-RAY DIFFRACTIONt_it48440HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion6466SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact61291SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d49376HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg66810HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion17.26
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2318 1769 5.05 %
Rwork0.204 33254 -
all0.2054 35023 -
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)
10.4555-0.0409-0.1340.14380.03250.1854-0.0131-0.08510.03120.02740.0146-0.0178-0.0296-0.0176-0.0015-0.04080.0223-0.01420.0064-0.0373-0.026873.595682.077340.083
20.3941-0.03660.07660.2250.0380.4311-0.0266-0.00430.0397-0.02940.0251-0.10770.02210.06670.0016-0.07860.0010.0246-0.0513-0.03010.027119.38669.175413.9286
30.3839-0.0941-0.08580.320.12840.1719-0.00570.0274-0.0645-0.0461-0.01470.0267-0.0141-0.05750.0204-0.0368-0.0045-0.0072-0.0136-0.016-0.031371.563557.824-8.6197
40.3185-0.1111-0.04290.27540.02410.1298-0.0215-0.0318-0.04210.0090.00680.04270.0324-0.0540.0147-0.0519-0.01630.00660.0213-0.0087-0.032457.388541.441427.1722
50.12590.03430.03160.16720.09270.384-0.0175-0.0055-0.0531-0.01690.0153-0.05690.03550.040.0022-0.04250.01620.0207-0.0264-0.01430.0177105.66431.0246.0791
60.44-0.0020.01690.41220.10850.22930.0173-0.12890.02920.0872-0.0016-0.09730.02190.017-0.0157-0.05780.017-0.02460.0255-0.0083-0.0613101.39754.945453.8534
70.5314-0.0508-0.1460.1716-0.00530.2547-0.0101-0.06950.00810.02180.0252-0.0157-0.0225-0.023-0.0151-0.03930.0191-0.0152-0.02320.0499-0.021276.051482.1077155.793
80.3496-0.03270.09090.19420.07250.4313-0.01650.01910.0267-0.03760.0165-0.10430.04060.08390-0.0624-0.0010.0388-0.04170.05330.0183121.87269.2173129.639
90.277-0.0638-0.10630.33530.24440.3452-0.01360.047-0.0797-0.0412-0.01910.0368-0.0043-0.0450.0327-0.0360.0014-0.0067-0.00890.065-0.042674.102957.8409107.187
100.3188-0.1415-0.10070.30170.03460.1497-0.00760.0047-0.0351-0.01360.00470.06480.0352-0.0670.0028-0.0535-0.018-0.00990.00780.0638-0.016759.935841.4506142.827
110.0810.05380.00030.09920.07480.4722-0.01250.0006-0.0382-0.01550.0233-0.05440.02130.029-0.0108-0.02660.01860.0129-0.02590.04170.0005108.23931.0226121.801
120.54930.02690.00890.3994-0.0010.22560.0105-0.08190.04640.03470.0073-0.0607-0.00010.0239-0.0177-0.04960.0212-0.0217-0.01320.0607-0.0522103.91654.9151169.588
130-0.06210.059500.03740.1684-0.0024-0.0077-0.05860.06770.00530.0038-0.0586-0.0671-0.00290.0061-0.05860.04250.08550.05020.068979.853554.24880.9855
140.0079-0.00590.00450.02230.06910.09780.0154-0.0252-0.01290.03670.0095-0.02420.0046-0.0274-0.0249-0.0153-0.00480.0542-0.06960.06610.039188.015354.412289.8377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|85 - A|603 }A85 - 603
2X-RAY DIFFRACTION2{ B|86 - B|603 }B86 - 603
3X-RAY DIFFRACTION3{ C|86 - C|603 }C86 - 603
4X-RAY DIFFRACTION4{ D|85 - D|603 }D85 - 603
5X-RAY DIFFRACTION5{ E|86 - E|602 }E86 - 602
6X-RAY DIFFRACTION6{ F|86 - F|603 }F86 - 603
7X-RAY DIFFRACTION7{ G|85 - G|603 }G85 - 603
8X-RAY DIFFRACTION8{ H|86 - H|603 }H86 - 603
9X-RAY DIFFRACTION9{ I|86 - I|603 }I86 - 603
10X-RAY DIFFRACTION10{ J|85 - J|603 }J85 - 603
11X-RAY DIFFRACTION11{ K|86 - K|602 }K86 - 602
12X-RAY DIFFRACTION12{ L|86 - L|603 }L86 - 603
13X-RAY DIFFRACTION13{ A|609 - A|610 C|610 - C|614 E|609 - E|611 D|610 - D|611 G|610 - G|613 I|610 - I|614 H|610 - H|612 K|609 - K|609 J|610 - J|612 L|610 - L|610 }A609 - 610
14X-RAY DIFFRACTION13{ A|609 - A|610 C|610 - C|614 E|609 - E|611 D|610 - D|611 G|610 - G|613 I|610 - I|614 H|610 - H|612 K|609 - K|609 J|610 - J|612 L|610 - L|610 }C610 - 614
15X-RAY DIFFRACTION13{ A|609 - A|610 C|610 - C|614 E|609 - E|611 D|610 - D|611 G|610 - G|613 I|610 - I|614 H|610 - H|612 K|609 - K|609 J|610 - J|612 L|610 - L|610 }E609 - 611
16X-RAY DIFFRACTION13{ A|609 - A|610 C|610 - C|614 E|609 - E|611 D|610 - D|611 G|610 - G|613 I|610 - I|614 H|610 - H|612 K|609 - K|609 J|610 - J|612 L|610 - L|610 }D610 - 611
17X-RAY DIFFRACTION13{ A|609 - A|610 C|610 - C|614 E|609 - E|611 D|610 - D|611 G|610 - G|613 I|610 - I|614 H|610 - H|612 K|609 - K|609 J|610 - J|612 L|610 - L|610 }G610 - 613
18X-RAY DIFFRACTION13{ A|609 - A|610 C|610 - C|614 E|609 - E|611 D|610 - D|611 G|610 - G|613 I|610 - I|614 H|610 - H|612 K|609 - K|609 J|610 - J|612 L|610 - L|610 }I610 - 614
19X-RAY DIFFRACTION13{ A|609 - A|610 C|610 - C|614 E|609 - E|611 D|610 - D|611 G|610 - G|613 I|610 - I|614 H|610 - H|612 K|609 - K|609 J|610 - J|612 L|610 - L|610 }H610 - 612
20X-RAY DIFFRACTION13{ A|609 - A|610 C|610 - C|614 E|609 - E|611 D|610 - D|611 G|610 - G|613 I|610 - I|614 H|610 - H|612 K|609 - K|609 J|610 - J|612 L|610 - L|610 }K609
21X-RAY DIFFRACTION13{ A|609 - A|610 C|610 - C|614 E|609 - E|611 D|610 - D|611 G|610 - G|613 I|610 - I|614 H|610 - H|612 K|609 - K|609 J|610 - J|612 L|610 - L|610 }J610 - 612
22X-RAY DIFFRACTION13{ A|609 - A|610 C|610 - C|614 E|609 - E|611 D|610 - D|611 G|610 - G|613 I|610 - I|614 H|610 - H|612 K|609 - K|609 J|610 - J|612 L|610 - L|610 }L610
23X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }A611 - 612
24X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }C615 - 616
25X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }B610
26X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }E612 - 614
27X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }D612 - 615
28X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }G614 - 617
29X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }F610 - 612
30X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }I615 - 617
31X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }H613
32X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }K610 - 613
33X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }J613 - 616
34X-RAY DIFFRACTION14{ A|611 - A|612 C|615 - C|616 B|610 - B|610 E|612 - E|614 D|612 - D|615 G|614 - G|617 F|610 - F|612 I|615 - I|617 H|613 - H|613 K|610 - K|613 J|613 - J|616 L|611 - L|614 }L611 - 614

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