[English] 日本語
Yorodumi
- PDB-3p4p: Crystal structure of Menaquinol:fumarate oxidoreductase in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p4p
TitleCrystal structure of Menaquinol:fumarate oxidoreductase in complex with fumarate
Components(Fumarate reductase ...) x 4
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


: / fumarate reductase (quinol) / : / fermentation / succinate dehydrogenase activity / anaerobic electron transport chain / fumarate metabolic process / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic respiration ...: / fumarate reductase (quinol) / : / fermentation / succinate dehydrogenase activity / anaerobic electron transport chain / fumarate metabolic process / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / bacterial-type flagellum assembly / tricarboxylic acid cycle / FAD binding / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA damage response / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Fumarate reductase, subunit C / Fumarate reductase subunit C / Fumarate reductase, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain ...Fumarate reductase, subunit C / Fumarate reductase subunit C / Fumarate reductase, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 4Fe-4S dicluster domain / 4Fe-4S dicluster domain / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, 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 / 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 / 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
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FUMARIC ACID / IRON/SULFUR CLUSTER / : / : / Fumarate reductase flavoprotein subunit / Fumarate reductase flavoprotein subunit / Fumarate reductase subunit C ...FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FUMARIC ACID / IRON/SULFUR CLUSTER / : / : / Fumarate reductase flavoprotein subunit / Fumarate reductase flavoprotein subunit / Fumarate reductase subunit C / Fumarate reductase subunit D / Fumarate reductase iron-sulfur subunit / Fumarate reductase iron-sulfur subunit
Similarity search - Component
Biological speciesEscherichia coli 042 (bacteria)
Escherichia coli 536 (bacteria)
Escherichia coli DH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsTomasiak, T.M. / Archuleta, T.L. / Andr ll, J. / Luna-Ch vez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankowskaya, V. / Stern, H.A. ...Tomasiak, T.M. / Archuleta, T.L. / Andr ll, J. / Luna-Ch vez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankowskaya, V. / Stern, H.A. / Johnston, J.N. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase.
Authors: Tomasiak, T.M. / Archuleta, T.L. / Andrell, J. / Luna-Chavez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankovskaya, V. / Stern, H.A. / Johnston, J.N. / Maklashina, E. / ...Authors: Tomasiak, T.M. / Archuleta, T.L. / Andrell, J. / Luna-Chavez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankovskaya, V. / Stern, H.A. / Johnston, J.N. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Non-polymer description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur protein
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase iron-sulfur protein
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,36817
Polymers237,0348
Non-polymers3,3349
Water1,42379
1
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur protein
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,2429
Polymers118,5174
Non-polymers1,7255
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17230 Å2
ΔGint-151 kcal/mol
Surface area39700 Å2
MethodPISA
2
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase iron-sulfur protein
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1268
Polymers118,5174
Non-polymers1,6094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17090 Å2
ΔGint-154 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.317, 137.633, 270.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Fumarate reductase ... , 4 types, 8 molecules AMBNCODP

#1: Protein Fumarate reductase flavoprotein subunit


Mass: 63477.707 Da / Num. of mol.: 2 / Fragment: UNP residues 1-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 042 (bacteria) / Strain: 042 / EAEC / Gene: frdA, EC042_4630 / Production host: Escherichia coli (E. coli)
References: UniProt: D3GV56, UniProt: P00363*PLUS, succinate dehydrogenase
#2: Protein Fumarate reductase iron-sulfur protein


Mass: 27021.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 536 (bacteria) / Strain: 536 / UPEC / Gene: ECP_4399 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0T9N6, UniProt: P0AC47*PLUS, succinate dehydrogenase
#3: Protein Fumarate reductase subunit C


Mass: 14898.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: frdC, EcDH1_3838 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QU46, UniProt: P0A8Q0*PLUS
#4: Protein Fumarate reductase subunit D


Mass: 13118.870 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: frdD, EcDH1_3839 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QU47, UniProt: P0A8Q3*PLUS

-
Non-polymers , 6 types, 88 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.8
Details: 12.5% PEG 5000 mme, 85mM MgAc, 100mM Citrate pH 5.8, 0.1% w/v DTT, 0.1mM EDTA, 5mM fumarate, vapor diffusion, temperature 298K, VAPOR DIFFUSION

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→90.76 Å / Num. obs: 84789

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→38.92 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.896 / SU B: 31.801 / SU ML: 0.298
RfactorNum. reflection% reflection
Rfree0.272 1408 1.7 %
Rwork0.249 --
obs0.249 84764 100 %
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 104.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16642 0 152 79 16873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02217423
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.97523676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15952130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34323.529748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.493152810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6515110
X-RAY DIFFRACTIONr_chiral_restr0.1990.22574
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113158
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6091.510608
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.437217044
X-RAY DIFFRACTIONr_scbond_it7.31536815
X-RAY DIFFRACTIONr_scangle_it10.4194.56550
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å
RfactorNum. reflection% reflection
Rfree0.399 83 -
Rwork0.346 6096 -
obs--100 %
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)
10.20960.06-0.18280.12630.09270.401-0.0082-0.04380.0084-0.01360.0308-0.02550.0257-0.0237-0.02260.3809-0.00980.01380.50610.00020.48179.1129.2167-11.1191
20.20330.013-0.02830.0209-0.05180.1911-0.10610.07540.2196-0.07730.0339-0.03540.1462-0.0920.07220.3617-0.03450.05790.4135-0.04060.376713.736819.2879-36.1144
30.0952-0.0253-0.18930.18880.05160.42540.01850.04550.0659-0.1892-0.0113-0.04030.0309-0.1008-0.00720.5287-0.02740.0910.4355-0.00820.37227.174820.315-63.1735
40.2145-0.063-0.20940.14150.19040.3485-0.09780.028-0.0743-0.0388-0.01490.01390.0907-0.06290.11280.5576-0.02160.15970.363-0.01350.41633.798311.0946-65.8347
50.56331.0184-0.40221.9661-0.78850.33790.29850.09450.29410.66830.12960.6297-0.3437-0.0631-0.42810.9781-0.04760.67390.09310.00250.614213.6469-47.2521-18.6945
60.710.5268-0.26591.5084-0.88050.51840.51130.15820.10410.79-0.20640.4911-0.42810.1264-0.30490.892-0.06470.38420.1831-0.0220.452730.4994-31.5302-33.2189
70.23060.3483-0.43030.739-0.63980.81760.08360.03470.03770.1311-0.00820.0399-0.0846-0.0227-0.07530.5265-0.02380.17920.39720.00280.51345.7441-25.9245-58.39
80.18610.0231-0.15191.1277-0.1980.155-0.01770.0663-0.05390.02840.03530.22810.0103-0.0393-0.01760.5543-0.00410.19520.3439-0.00980.507643.5225-15.7689-63.5744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 576
2X-RAY DIFFRACTION2B1 - 243
3X-RAY DIFFRACTION3C1 - 130
4X-RAY DIFFRACTION4D0 - 118
5X-RAY DIFFRACTION5M0 - 576
6X-RAY DIFFRACTION6N1 - 243
7X-RAY DIFFRACTION7O1 - 130
8X-RAY DIFFRACTION8P0 - 118

+
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