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- PDB-2h89: Avian Respiratory Complex II with Malonate Bound -

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Basic information

Entry
Database: PDB / ID: 2h89
TitleAvian Respiratory Complex II with Malonate Bound
Components
  • (SUCCINATE DEHYDROGENASE CYTOCHROME B, ...) x 2
  • SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
  • Succinate dehydrogenase Ip subunit
KeywordsOXIDOREDUCTASE / COMPLEX II / MEMBRANE PROTEIN / HEME PROTEIN / IRON SULFUR PROTEIN / CYTOCHROME B / REDOX ENZYME / RESPIRATORY CHAIN / MALONATE / UBIQUINONE
Function / homology
Function and homology information


The tricarboxylic acid cycle / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / succinate metabolic process / 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 ...The tricarboxylic acid cycle / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / succinate metabolic process / 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 / electron transfer activity / mitochondrial inner membrane / heme binding / metal ion binding / membrane
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. / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein 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. / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 3 helical TM bundles of succinate and fumarate reductases / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 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 / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / 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 / Rhinovirus 14, subunit 4 / FAD binding domain / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / FAD/NAD(P)-binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / FAD/NAD(P)-binding domain / 2Fe-2S ferredoxin-like superfamily / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
hexyl beta-D-galactopyranoside / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / : / MALONATE ION / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / IRON/SULFUR CLUSTER / Unknown ligand ...hexyl beta-D-galactopyranoside / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / : / MALONATE 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 / SYNCHROTRON / rigid body refinement of previous / Resolution: 2.4 Å
AuthorsHuang, L.S. / Shen, J.T. / Wang, A.C. / Berry, E.A.
Citation
Journal: Biochim.Biophys.Acta
Title: Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the
Authors: Huang, L.S. / Shen, J.T. / Wang, A.C. / Berry, E.A.
#1: Journal: 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.S. / Sun, G. / Cobessi, D. / Wang, A.C. / Shen, J.T. / Tung, E.Y. / Anderson, V.E. / Berry, E.A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A
Authors: Huang, L.S. / Borders, T.M. / Shen, J.T. / Wang, C.J. / Berry, E.A.
#3: Journal: Cell(Cambridge,Mass.) / Year: 2005
Title: Crystal structure of mitochondrial respiratory membrane protein complex II.
Authors: Sun, F. / Huo, X. / Zhai, Y. / Wang, A. / Xu, J. / Su, D. / Bartlam, M. / Rao, Z.
History
DepositionJun 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 29, 2014Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Jul 29, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_entity_nonpoly.name / _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.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 / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Aug 30, 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 999SEQUENCE SEQUENCE 1-71 OF SUCCINATE DEHYDROGENASE FP SUBUNIT DOES NOT MATCH TO ANY SEQUENCE IN THE ...SEQUENCE SEQUENCE 1-71 OF SUCCINATE DEHYDROGENASE FP SUBUNIT DOES NOT MATCH TO ANY SEQUENCE IN THE DATABASE. THE SEQUENCE OF SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT IS NOT AVAILABLE IN ANY OF THE DATABASE SEQUENCES AT THE TIME OF PROCESSING.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,46455
Polymers123,3064
Non-polymers4,15851
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23260 Å2
ΔGint-138 kcal/mol
Surface area40590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.520, 84.118, 292.212
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 , 2 types, 2 molecules AB

#1: Protein SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT


Mass: 68256.922 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q9YHT2, succinate dehydrogenase

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SUCCINATE DEHYDROGENASE CYTOCHROME B, ... , 2 types, 2 molecules CD

#3: Protein SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT


Mass: 15392.052 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZIS0, succinate dehydrogenase

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Sugars , 1 types, 1 molecules

#12: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H24O6

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Non-polymers , 10 types, 630 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#8: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 40 / Source method: obtained synthetically
#9: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#10: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#11: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#13: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#14: 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
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
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 MALONATE, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA., pH 7.5, ...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 MALONATE, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2004
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.29→60 Å / Num. all: 63148 / Num. obs: 63148 / % possible obs: 78.6 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 52.7 Å2 / Rsym value: 0.158 / Net I/σ(I): 7
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 724 / Rsym value: 0.545 / % possible all: 18.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: rigid body refinement of previous
Starting model: 1YQ3

1yq3


Resolution: 2.4→50.74 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2908 4.9 %RANDOM
Rwork0.226 ---
all0.229 59635 --
obs0.229 59635 86.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.4229 Å2 / ksol: 0.257581 e/Å3
Displacement parametersBiso mean: 59.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.89 Å20 Å20 Å2
2--5.97 Å20 Å2
3----12.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.4→50.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8500 0 222 580 9302
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.131.5
X-RAY DIFFRACTIONc_mcangle_it3.392
X-RAY DIFFRACTIONc_scbond_it3.12
X-RAY DIFFRACTIONc_scangle_it4.272.5
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.366 100 4.5 %
Rwork0.341 2102 -
obs-2202 48.8 %

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