[English] 日本語
Yorodumi
- PDB-3aeb: Crystal structure of porcine heart mitochondrial complex II bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3aeb
TitleCrystal structure of porcine heart mitochondrial complex II bound with N-(3-Phenoxy-phenyl)-2-trifluoromethyl-benzamide
Components
  • (Succinate dehydrogenase [ubiquinone] ...) x 3
  • Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / respiratory complex II / inhibitors / Electron transport / Iron / Iron-sulfur / Metal-binding / Mitochondrion / Mitochondrion inner membrane / Oxidoreductase / Transit peptide / Transport / Tricarboxylic acid cycle / Heme / Transmembrane / FAD-binding protein / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / 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 ...Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / 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 / 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
Chem-EPH / FE3-S4 CLUSTER / N-(3-phenoxyphenyl)-2-(trifluoromethyl)benzamide / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial ...Chem-EPH / FE3-S4 CLUSTER / N-(3-phenoxyphenyl)-2-(trifluoromethyl)benzamide / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsHarada, S. / Sasaki, T. / Shindo, M. / Kido, Y. / Inaoka, D.K. / Omori, J. / Osanai, A. / Sakamoto, K. / Mao, J. / Matsuoka, S. ...Harada, S. / Sasaki, T. / Shindo, M. / Kido, Y. / Inaoka, D.K. / Omori, J. / Osanai, A. / Sakamoto, K. / Mao, J. / Matsuoka, S. / Inoue, M. / Honma, T. / Tanaka, A. / Kita, K.
CitationJournal: To be Published
Title: Crystal structure of porcine heart mitochondrial complex II bound with N-(3-Phenoxy-phenyl)-2-trifluoromethyl-benzamide
Authors: Harada, S. / Sasaki, T. / Shindo, M. / Kido, Y. / Inaoka, D.K. / Omori, J. / Osanai, A. / Sakamoto, K. / Mao, J. / Matsuoka, S. / Inoue, M. / Honma, T. / Tanaka, A. / Kita, K.
History
DepositionFeb 4, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
B: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
C: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,71312
Polymers123,3184
Non-polymers3,3958
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-50 kcal/mol
Surface area42450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.708, 84.255, 294.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Succinate dehydrogenase [ubiquinone] ... , 3 types, 3 molecules ABD

#1: Protein Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Flavoprotein subunit of complex II / Fp


Mass: 68313.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: Q0QF01, succinate dehydrogenase
#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Iron-sulfur subunit of complex II / Ip


Mass: 28764.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: Q007T0, succinate dehydrogenase
#4: Protein Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate-ubiquinone oxidoreductase cytochrome b small subunit / CybS / Succinate-ubiquinone ...Succinate-ubiquinone oxidoreductase cytochrome b small subunit / CybS / Succinate-ubiquinone reductase membrane anchor subunit / QPs3 / CII-4 / Succinate dehydrogenase complex subunit D


Mass: 10936.758 Da / Num. of mol.: 1 / Fragment: residues 57-159 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: A5GZW8

-
Protein , 1 types, 1 molecules C

#3: Protein Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Succinate-ubiquinone oxidoreductase cytochrome B large subunit / CYBL


Mass: 15304.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: D0VWV4

-
Non-polymers , 8 types, 8 molecules

#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical ChemComp-F7A / N-(3-phenoxyphenyl)-2-(trifluoromethyl)benzamide


Mass: 357.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14F3NO2
#12: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE


Mass: 709.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM

-
Details

Compound detailsTHESE COMPLEX FORMS MITOCHONDRIAL RESPIRATORY COMPLEX II.
Has protein modificationY
Sequence detailsTHE SEQUENCE OF CHAIN D IS REFERRED IN REF 2 IN A5GZW8, UNIPROT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.92 % / Mosaicity: 0.474 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 25mM HEPES-NAOH, 8% PEG 4000, 200mM Sucrose, 100mM NaCl, 10mM CaCl2, 0.5mM EDTA, 3% 1,6-haxanediol, 0.5% n-decyl-beta-D-maltoside, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 33711 / % possible obs: 91.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.087 / Χ2: 0.933 / Net I/σ(I): 18.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.66 / Num. unique all: 3025 / Χ2: 0.719 / % possible all: 84.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.21 Å48.3 Å
Translation3.21 Å48.3 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZOY

1zoy


Resolution: 3→42.43 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.832 / SU B: 32.459 / SU ML: 0.304 / SU R Cruickshank DPI: 0.354 / SU Rfree: 0.421 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1693 5 %RANDOM
Rwork0.215 ---
obs0.217 33632 91.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 140.37 Å2 / Biso mean: 75.021 Å2 / Biso min: 14.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2--0.44 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 3→42.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8480 0 192 0 8672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228882
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.99612064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.41551088
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2823.413375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.035151469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.891559
X-RAY DIFFRACTIONr_chiral_restr0.1280.21309
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216666
X-RAY DIFFRACTIONr_mcbond_it0.1361.55409
X-RAY DIFFRACTIONr_mcangle_it0.25428672
X-RAY DIFFRACTIONr_scbond_it0.28533473
X-RAY DIFFRACTIONr_scangle_it0.4984.53361
LS refinement shellResolution: 3.002→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 114 -
Rwork0.312 2065 -
all-2179 -
obs-2179 83.74 %
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)
11.7797-0.4152-0.51391.1455-0.11973.20540.0039-0.1357-0.083-0.0829-0.05070.0713-0.20990.07530.04680.3658-0.10180.02030.21050.0370.3132-16.688-18.53917.921
22.71130.9328-1.92272.7334-1.10180.69670.5385-0.05410.6010.7892-0.16250.0373-1.26290.0124-0.3761.4448-0.14690.09180.1796-0.04320.5876-18.218.45422.758
31.9834-0.1342-0.67971.53730.01413.07390.0075-0.16070.1228-0.08840.0088-0.1094-0.35150.6207-0.01630.3517-0.15810.03910.32450.06120.2985-4.102-13.50317.774
42.1362-0.3581-0.03610.9693-0.37253.40090.01670.15570.4042-0.2681-0.0786-0.1436-0.76340.5010.06190.5309-0.1870.0760.27090.07310.3273-4.75-6.4684.924
52.7673-0.4753-0.62273.59080.74744.1879-0.018-0.52620.35680.1142-0.0277-0.3472-0.55941.11660.04570.3394-0.3087-0.07030.6135-0.00420.2615-2.525-11.78345.98
61.6642-0.5401-0.75750.6288-0.85864.2025-0.02590.1362-0.0889-0.0097-0.08410.24240.144-0.29480.110.45-0.04970.05960.1796-0.04560.3805-29.208-24.36540.211
76.4171.49983.240210.16474.02785.3006-0.1189-0.3986-0.36911.3163-0.1684-0.08791.76191.17150.28730.74290.19210.23550.46180.20680.2185-11.636-31.17147.281
80.78320.00790.40625.9778-1.82871.443-0.2113-0.1555-0.07530.4149-0.2005-0.37210.02770.29790.41180.7288-0.06790.17110.18440.07820.3867-29.723-28.68572.633
9-0.11847.12271.672912.74040.94618.1950.3922-0.595-0.46131.3766-0.4171-0.8797-1.44580.40670.02491.15850.0650.1930.78290.13140.4963-33.401-28.18194.373
104.00730.47520.02512.5872-1.064614.1810.141-0.09210.00050.4325-0.2583-0.1146-0.59740.19180.11740.6422-0.01390.15090.0558-0.02580.4174-34.631-18.92270.622
112.14551.8605-0.1115.78751.695215.32270.42330.0130.29640.53910.280.1191-1.45410.2392-0.70330.62610.0890.16490.0901-0.03210.409-34.596-11.84666.967
121.14143.0560.02944.08640.115311.0794-0.58360.095-0.461-0.1322-0.23080.6615-0.5059-0.56710.81440.63040.05410.32460.31730.00620.5908-45.454-29.60266.649
1314.3848-1.4428-2.83310.208-0.72625.8432-0.81410.0007-0.65350.01030.1255-0.08540.96240.4360.68870.7118-0.02120.15480.10980.01420.4527-31.606-35.83164.212
1410.3406-0.9339-9.2966.10391.790911.9481-0.3264-0.5711-0.8989-0.2887-0.0695-0.29350.45840.50620.39590.7518-0.00860.26930.04240.12680.4648-35.139-42.54972.341
158.92710.3996-0.1214-6.6902-4.51941.81850.0209-1.03930.02320.7212-0.38160.5091-1.231-1.00640.36071.180.00620.27150.32420.0580.3193-43.899-30.41687.896
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 249
2X-RAY DIFFRACTION2A250 - 340
3X-RAY DIFFRACTION3A341 - 511
4X-RAY DIFFRACTION4A512 - 622
5X-RAY DIFFRACTION5B9 - 105
6X-RAY DIFFRACTION6B106 - 247
7X-RAY DIFFRACTION7C6 - 35
8X-RAY DIFFRACTION8C36 - 65
9X-RAY DIFFRACTION9C66 - 90
10X-RAY DIFFRACTION10C91 - 111
11X-RAY DIFFRACTION11C112 - 143
12X-RAY DIFFRACTION12D35 - 71
13X-RAY DIFFRACTION13D72 - 96
14X-RAY DIFFRACTION14D97 - 120
15X-RAY DIFFRACTION15D121 - 136

+
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