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- PDB-2wqy: Remodelling of carboxin binding to the Q-site of avian respirator... -

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Basic information

Entry
Database: PDB / ID: 2wqy
TitleRemodelling of carboxin binding to the Q-site of avian respiratory complex II
Components(SUCCINATE DEHYDROGENASE ...) x 4
KeywordsOXIDOREDUCTASE / OXALOACETATE NITROPROPIONATE UBIQUINONE / RESPIRATORY CHAIN / COMPLEX II / CYTOCROME B / REDOX ENZYME / HEME PROTEIN / FLAVOPROTEIN / METAL-BINDING / MITOCHONDRION INNER MEMBRANE / IRON SULFUR PROTEIN / TRICARBOXYLIC ACID CYCLE
Function / homology
Function and homology information


The tricarboxylic acid cycle / : / succinate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding ...The tricarboxylic acid cycle / : / succinate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Single helix bin / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit ...Single helix bin / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 3 helical TM bundles of succinate and fumarate reductases / 4Fe-4S dicluster domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / Rhinovirus 14, subunit 4 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 3-Layer(bba) Sandwich / Ubiquitin-like (UB roll) / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / hexyl beta-D-galactopyranoside / Chem-CBE / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / : / OXALOACETATE ION / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine ...AZIDE ION / hexyl beta-D-galactopyranoside / Chem-CBE / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / : / OXALOACETATE ION / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / IRON/SULFUR CLUSTER / Unknown ligand / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRuprecht, J. / Iwata, S. / Cecchini, G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: 3-Nitropropionic Acid is a Suicide Inhibitor of Mitochondrial Respiration that, Upon Oxidation by Complex II, Forms a Covalent Adduct with a Catalytic Base Arginine in the Active Site of the Enzyme.
Authors: Huang, L. / Sun, G. / Cobessi, D. / Wang, A.C. / Shen, J.T. / Tung, E.Y. / Anderson, V.E. / Berry, E.A.
History
DepositionAug 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Non-polymer description ...Database references / Non-polymer description / Other / Version format compliance
Revision 1.2May 20, 2015Group: Non-polymer description
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jul 29, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Dec 20, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Remark 0THIS ENTRY 2WQY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2FBWSF) ...THIS ENTRY 2WQY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2FBWSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 2FBW: L.S.HUANG,G.SUN,D.COBESSI,A.C.WANG,J.T.SHEN,E.Y.TUNG, V.E.ANDERSON,E.A.BERRY
Remark 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ... THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
B: SUCCINATE DEHYDROGENASE IP SUBUNIT
C: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
D: SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT
N: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
O: SUCCINATE DEHYDROGENASE IP SUBUNIT
P: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
Q: SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,433130
Polymers246,6668
Non-polymers7,767122
Water35,9581996
1
A: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
B: SUCCINATE DEHYDROGENASE IP SUBUNIT
C: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
D: SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,23773
Polymers123,3334
Non-polymers3,90469
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15910 Å2
ΔGint-81 kcal/mol
Surface area51890 Å2
MethodPQS
2
N: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
O: SUCCINATE DEHYDROGENASE IP SUBUNIT
P: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
Q: SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,19557
Polymers123,3334
Non-polymers3,86253
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15650 Å2
ΔGint-81.4 kcal/mol
Surface area50890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)118.700, 200.753, 67.631
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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SUCCINATE DEHYDROGENASE ... , 4 types, 8 molecules ANBOCPDQ

#1: Protein SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT


Mass: 68256.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: Q9YHT1, succinate dehydrogenase
#2: Protein SUCCINATE DEHYDROGENASE IP SUBUNIT


Mass: 28685.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: Q9YHT2, succinate dehydrogenase
#3: Protein SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT


Mass: 15419.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VWW3*PLUS, succinate dehydrogenase
#4: Protein SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT


Mass: 10971.604 Da / Num. of mol.: 2 / Fragment: RESIDUES 55-157 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: Q5ZIS0, succinate dehydrogenase

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Sugars , 1 types, 2 molecules

#14: Sugar ChemComp-BHG / hexyl beta-D-galactopyranoside / 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / hexyl beta-D-galactoside / hexyl D-galactoside / hexyl galactoside


Type: D-saccharide / Mass: 264.315 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C12H24O6

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Non-polymers , 13 types, 2116 molecules

#5: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 95 / Source method: obtained synthetically
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#9: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#10: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#12: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#13: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#15: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#16: Chemical ChemComp-CBE / 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE / 5,6-DIHYDRO-2-METHYL-1,4-OXATHIIN-3-CARBOXANILID / CARBOXIN / CBX


Mass: 235.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13NO2S
#17: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1996 / 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: 3.29 Å3/Da / Density % sol: 62.3 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2FBW.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 50 G/L PEG-3350, 25 ML/L ISOPROPANOL, 15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA, CARBOXIN, PH 7.50, VAPOR ...Details: 50 G/L PEG-3350, 25 ML/L ISOPROPANOL, 15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA, CARBOXIN, PH 7.50, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQ3

1yq3


Resolution: 2.1→64.09 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. STRUCTURE IS A REMODELLING OF CARBOXIN BINDING TO THE Q- SITE OF AVIAN COMPLEX II. POSITIONAL AND B-FACTOR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. STRUCTURE IS A REMODELLING OF CARBOXIN BINDING TO THE Q- SITE OF AVIAN COMPLEX II. POSITIONAL AND B-FACTOR REFINEMENT OF CARBOXIN ONLY WAS PERFORMED. THE REST OF THE STRUCTURE IS AS MODELLED IN 2FBW.
RfactorNum. reflection% reflectionSelection details
Rfree0.22283 8009 4.9 %RANDOM
Rwork0.18395 ---
obs0.18585 154202 88.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.499 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-0.4 Å2
2--1.5 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.1→64.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16978 0 516 1996 19490
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 375 -
Rwork0.285 7054 -
obs--54.96 %

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