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- PDB-6yi1: Crystal structure of human glutaminyl cyclase in complex with Glu... -

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Basic information

Entry
Database: PDB / ID: 6yi1
TitleCrystal structure of human glutaminyl cyclase in complex with Glu(gamma-hydrazide)-Phe-Ala
Components
  • Glu(gamma-hydrazide)-Phe-Ala
  • Glutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / Alpha-Beta Protein / Metalloprotein / Intermediate
Function / homology
Function and homology information


peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / protein modification process / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / zinc ion binding / extracellular region
Similarity search - Function
M28 Zn-Peptidase Glutaminyl Cyclase / Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsKupski, O. / Sautner, V. / Tittmann, K.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)IRTG 1422 Germany
German Federal Ministry for Economic Affairs and EnergyAiF KF2327701SB9 Germany
Alzheimer Forschung Initiative e.V. Germany
CitationJournal: Biochemistry / Year: 2020
Title: Hydrazides Are Potent Transition-State Analogues for Glutaminyl Cyclase Implicated in the Pathogenesis of Alzheimer's Disease.
Authors: Kupski, O. / Funk, L.M. / Sautner, V. / Seifert, F. / Worbs, B. / Ramsbeck, D. / Meyer, F. / Diederichsen, U. / Buchholz, M. / Schilling, S. / Demuth, H.U. / Tittmann, K.
History
DepositionMar 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _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_symmetry / _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.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_symmetry / _struct_conn_type.id
Revision 2.0Mar 15, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _cell.Z_PDB / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _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_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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_num_residues
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 3.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
C: Glu(gamma-hydrazide)-Phe-Ala
D: Glu(gamma-hydrazide)-Phe-Ala
E: Glu(gamma-hydrazide)-Phe-Ala
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,25544
Polymers76,1915
Non-polymers4,06339
Water7,620423
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A: Glutaminyl-peptide cyclotransferase
C: Glu(gamma-hydrazide)-Phe-Ala
D: Glu(gamma-hydrazide)-Phe-Ala
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,16121
Polymers38,2763
Non-polymers1,88518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaminyl-peptide cyclotransferase
E: Glu(gamma-hydrazide)-Phe-Ala
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,09423
Polymers37,9152
Non-polymers2,17921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.380, 120.380, 331.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-401-

SO4

21B-401-

SO4

31A-723-

HOH

41A-731-

HOH

51B-643-

HOH

61B-664-

HOH

71B-673-

HOH

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Components

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Protein / Protein/peptide , 2 types, 5 molecules ABCDE

#1: Protein Glutaminyl-peptide cyclotransferase / / Glutaminyl cyclase / sQC / Glutaminyl-tRNA cyclotransferase / Glutamyl cyclase / EC


Mass: 37553.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase
#2: Protein/peptide Glu(gamma-hydrazide)-Phe-Ala


Mass: 361.419 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Non-polymers , 9 types, 462 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.6M ammonium sulfate, 0.1M MES pH 6.5, 4% (v/v) 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.92→88.279 Å / Num. obs: 70565 / % possible obs: 99.4 % / Redundancy: 5.933 % / Biso Wilson estimate: 26.39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.129 / Χ2: 0.957 / Net I/σ(I): 9.89 / Num. measured all: 418679
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.92-2.025.860.7231.7998570.6820.7999.6
2.02-2.126.1030.552.681480.8210.59899.9
2.12-2.225.9030.4243.3967340.8990.46399.8
2.22-2.325.7210.3264.3556100.9310.35699.7
2.32-2.56.1560.2695.5880350.9550.293100
2.5-2.755.8350.2017.3779380.9740.2299.7
2.75-35.9680.14610.3455290.9840.1699.5
3-3.56.0250.09116.0468710.9950.199.4
3.5-45.8310.0623.9638850.9970.06599.3
4-105.8970.04630.4574220.9980.0598
10-205.4380.02941.794610.9990.03293.3
20-503.2460.02432.946910.02989.6
50-1001.8330.04626.59610.0675

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2940refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AFM
Resolution: 1.92→88.279 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.73
RfactorNum. reflection% reflection
Rfree0.1862 3496 4.95 %
Rwork0.1593 --
obs0.1606 70555 99.43 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 121.67 Å2 / Biso mean: 30.3477 Å2 / Biso min: 5.58 Å2
Refinement stepCycle: final / Resolution: 1.92→88.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 306 428 6032
Biso mean--48.97 36.13 -
Num. residues----658
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-1.94630.29511350.2576263899
1.9463-1.97410.29081470.24062672100
1.9741-2.00360.27721220.22322687100
2.0036-2.03490.2571450.20772632100
2.0349-2.06830.20721250.21162675100
2.0683-2.10390.23291290.20432699100
2.1039-2.14220.2411470.18912672100
2.1422-2.18340.21931390.17912638100
2.1834-2.2280.21821410.17892682100
2.228-2.27640.21491390.16782655100
2.2764-2.32940.17831400.16282654100
2.3294-2.38770.18981420.1612687100
2.3877-2.45220.18271420.15762699100
2.4522-2.52440.22581400.162665100
2.5244-2.60590.18821420.1612694100
2.6059-2.6990.19251400.15782673100
2.699-2.80710.14431410.15452669100
2.8071-2.93480.19841430.14542713100
2.9348-3.08960.15421400.1447267099
3.0896-3.28310.16231420.1425268799
3.2831-3.53670.16551420.1391270899
3.5367-3.89260.16171420.1303268799
3.8926-4.45580.16191440.12682736100
4.4558-5.61370.1551420.1513271699
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)
16.58692.61191.93164.57664.76037.069-0.1953-0.0117-0.37750.23360.0869-0.20520.21260.7923-0.00190.17780.0210.02680.11840.01130.2155-12.1505-27.303120.1342
20.6527-0.06160.09291.01340.19870.9537-0.0128-0.0059-0.02570.0406-0.06790.23390.1115-0.23760.08740.1721-0.03130.01720.2541-0.01490.2265-29.597-8.70124.9082
36.4097-0.2850.15914.7050.45337.80620.06270.13160.936-0.1936-0.09370.4195-0.9569-0.4057-0.06270.23640.05090.00210.21880.01010.3434-27.048610.189823.1072
40.5975-0.2930.0430.68990.07121.27430.01340.0717-0.0322-0.0588-0.03670.01980.0633-0.06860.0130.1461-0.02160.00090.1756-0.00720.1737-18.6269-9.971118.4117
55.43320.8696-2.67041.6892.62397.4045-0.2176-0.09420.4030.2033-0.20920.2011-0.62640.09290.2560.30510.07350.0110.1334-0.04690.3426-27.75723.49965.9126
63.8705-2.7291-1.93382.73552.24715.0534-0.3361-0.438-0.28220.60490.26240.79920.0794-0.39650.12810.46750.01510.19410.37870.09150.3521-27.5172-20.410879.3408
71.9573-1.2788-0.21351.41340.2580.9610.00510.0308-0.14850.0341-0.00930.1610.076-0.14720.00080.1691-0.02280.01890.13510.00830.1733-19.8373-21.097456.2213
82.2325-1.2541-0.30082.86190.07021.44270.0195-0.0881-0.0780.16840.01870.2885-0.0262-0.2297-0.03990.202-0.02810.03930.16470.0180.1684-20.4864-19.104563.7714
91.7502-1.16890.71041.6691-0.1440.54830.0067-0.01480.09880.1257-0.0385-0.03-0.0643-0.06440.01320.2119-0.02470.02420.15110.01380.1981-13.0491-9.815858.1397
103.37760.3633-1.20673.6061-3.35884.44450.0348-0.42160.28280.6391-0.04460.1565-0.5904-0.0442-0.08290.47830.060.05010.2681-0.07820.2355-18.4591-3.527778.7588
112.6547-1.2179-2.63281.23231.29012.7972-0.0813-0.6480.20810.55420.1624-0.4897-0.07090.4836-0.22760.4835-0.0099-0.090.3795-0.05920.296-9.9564-8.75977.7162
122.7227-2.1511.0514.1862-1.08331.377-0.1992-0.19690.12950.41480.125-0.333-0.089-0.04940.10110.2092-0.0169-0.01490.1659-0.01330.1326-7.3591-15.57267.36
133.7373-2.47580.44923.8442-0.58453.9012-0.1916-0.3896-0.30960.71510.35220.6343-0.1971-0.3394-0.11520.3015-0.010.10330.26630.00230.2142-23.5269-12.616375.3403
146.26754.2924-3.04084.5955-2.00516.86650.12850.230.19290.1058-0.0606-0.106-0.26510.15760.00990.17730.01110.01120.1809-0.0020.2112-11.60024.725821.6919
154.1048-0.0054-2.28351.66653.22457.48720.6570.69740.5665-0.27350.17550.3503-0.6513-0.3514-0.75161.18950.0034-0.00530.46660.14350.429-25.1019-9.6239-6.7363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 49 )A33 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 140 )A50 - 140
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 160 )A141 - 160
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 361 )A161 - 361
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 49 )B33 - 49
6X-RAY DIFFRACTION6chain 'B' and (resid 50 through 68 )B50 - 68
7X-RAY DIFFRACTION7chain 'B' and (resid 69 through 140 )B69 - 140
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 198 )B141 - 198
9X-RAY DIFFRACTION9chain 'B' and (resid 199 through 261 )B199 - 261
10X-RAY DIFFRACTION10chain 'B' and (resid 262 through 280 )B262 - 280
11X-RAY DIFFRACTION11chain 'B' and (resid 281 through 307 )B281 - 307
12X-RAY DIFFRACTION12chain 'B' and (resid 308 through 340 )B308 - 340
13X-RAY DIFFRACTION13chain 'B' and (resid 341 through 361 )B341 - 361
14X-RAY DIFFRACTION14chain 'J' and (resid 1 through 9 )J1 - 9
15X-RAY DIFFRACTION15chain 'I' and (resid 1 through 4 )I1 - 4

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