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- PDB-5usr: Crystal structure of human NFS1-ISD11 in complex with E. coli acy... -

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Basic information

Entry
Database: PDB / ID: 5usr
TitleCrystal structure of human NFS1-ISD11 in complex with E. coli acyl-carrier protein at 3.09 angstroms
Components
  • Acyl carrier protein
  • Cysteine desulfurase, mitochondrial
  • LYR motif-containing protein 4
KeywordsTRANSFERASE / LYR / Fe-S cluster assembly / NFS1 / acyl-carrier protein
Function / homology
Function and homology information


molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / L-cysteine desulfurase complex / iron incorporation into metallo-sulfur cluster / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / Maturation of TCA enzymes and regulation of TCA cycle / cysteine desulfurase / cysteine desulfurase activity ...molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / L-cysteine desulfurase complex / iron incorporation into metallo-sulfur cluster / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / Maturation of TCA enzymes and regulation of TCA cycle / cysteine desulfurase / cysteine desulfurase activity / Mo-molybdopterin cofactor biosynthetic process / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / lipid biosynthetic process / lipid A biosynthetic process / iron-sulfur cluster assembly / acyl binding / acyl carrier activity / iron-sulfur cluster binding / phosphopantetheine binding / fatty acid biosynthetic process / pyridoxal phosphate binding / nuclear body / mitochondrial matrix / response to xenobiotic stimulus / lipid binding / centrosome / protein homodimerization activity / mitochondrion / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
LYRM4, LYR domain / : / Cysteine desulfurase IscS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Complex 1 LYR protein domain / Complex 1 protein (LYR family) ...LYRM4, LYR domain / : / Cysteine desulfurase IscS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Acyl carrier protein (ACP) / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8Q1 / Acyl carrier protein / LYR motif-containing protein 4 / Cysteine desulfurase
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsCory, S.A. / Barondeau, D.P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM096100 United States
National Science Foundation (NSF, United States)CHE 1508269 United States
Robert A. Welch FoundationA-1647 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.
Authors: Cory, S.A. / Van Vranken, J.G. / Brignole, E.J. / Patra, S. / Winge, D.R. / Drennan, C.L. / Rutter, J. / Barondeau, D.P.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase, mitochondrial
B: LYR motif-containing protein 4
C: Cysteine desulfurase, mitochondrial
D: LYR motif-containing protein 4
E: Cysteine desulfurase, mitochondrial
F: LYR motif-containing protein 4
G: Cysteine desulfurase, mitochondrial
H: LYR motif-containing protein 4
I: Acyl carrier protein
J: Acyl carrier protein
K: Acyl carrier protein
L: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,29216
Polymers268,12912
Non-polymers2,1634
Water00
1
A: Cysteine desulfurase, mitochondrial
B: LYR motif-containing protein 4
G: Cysteine desulfurase, mitochondrial
H: LYR motif-containing protein 4
J: Acyl carrier protein
K: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1468
Polymers134,0656
Non-polymers1,0812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cysteine desulfurase, mitochondrial
D: LYR motif-containing protein 4
E: Cysteine desulfurase, mitochondrial
F: LYR motif-containing protein 4
I: Acyl carrier protein
L: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1468
Polymers134,0656
Non-polymers1,0812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.484, 147.780, 168.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and resid 4 through 78)
21(chain D and resid 4 through 78)
31chain F
41(chain H and resid 4 through 78)
12(chain A and (resid 56 through 60 or resid 66...
22(chain C and (resid 56 through 60 or resid 66...
32(chain E and (resid 56 through 60 or resid 66...
42(chain G and (resid 56 through 359 or resid 403 through 436))
13(chain I and resid 5 through 73)
23(chain J and resid 5 through 73)
33chain K
43(chain L and resid 5 through 73)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERTHRTHR(chain B and resid 4 through 78)BB4 - 784 - 78
211SERSERTHRTHR(chain D and resid 4 through 78)DD4 - 784 - 78
311SERSERTHRTHRchain FFF4 - 784 - 78
411SERSERTHRTHR(chain H and resid 4 through 78)HH4 - 784 - 78
112LEULEUTYRTYR(chain A and (resid 56 through 60 or resid 66...AA56 - 6025 - 29
122THRTHRGLYGLY(chain A and (resid 56 through 60 or resid 66...AA66 - 8635 - 55
132GLUGLUARGARG(chain A and (resid 56 through 60 or resid 66...AA98 - 27567 - 244
142THRTHRALAALA(chain A and (resid 56 through 60 or resid 66...AA295 - 359264 - 328
152HISHISMETMET(chain A and (resid 56 through 60 or resid 66...AA403 - 436372 - 405
212LEULEUTYRTYR(chain C and (resid 56 through 60 or resid 66...CC56 - 6025 - 29
222THRTHRGLYGLY(chain C and (resid 56 through 60 or resid 66...CC66 - 8635 - 55
232GLUGLUARGARG(chain C and (resid 56 through 60 or resid 66...CC98 - 27567 - 244
242THRTHRALAALA(chain C and (resid 56 through 60 or resid 66...CC295 - 359264 - 328
252HISHISMETMET(chain C and (resid 56 through 60 or resid 66...CC403 - 436372 - 405
312LEULEUTYRTYR(chain E and (resid 56 through 60 or resid 66...EE56 - 6025 - 29
322THRTHRGLYGLY(chain E and (resid 56 through 60 or resid 66...EE66 - 8635 - 55
332GLUGLUALAALA(chain E and (resid 56 through 60 or resid 66...EE98 - 35967 - 328
342HISHISMETMET(chain E and (resid 56 through 60 or resid 66...EE403 - 436372 - 405
412LEULEUALAALA(chain G and (resid 56 through 359 or resid 403 through 436))GG56 - 35925 - 328
422HISHISMETMET(chain G and (resid 56 through 359 or resid 403 through 436))GG403 - 436372 - 405
113GLUGLUILEILE(chain I and resid 5 through 73)II5 - 735 - 73
213GLUGLUILEILE(chain J and resid 5 through 73)JJ5 - 735 - 73
313GLUGLUILEILEchain KKK5 - 735 - 73
413GLUGLUILEILE(chain L and resid 5 through 73)LL5 - 735 - 73

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Cysteine desulfurase, mitochondrial


Mass: 47623.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFS1, NIFS, HUSSY-08 / Plasmid: pET15b / Details (production host): N-terminal his tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y697, cysteine desulfurase
#2: Protein
LYR motif-containing protein 4


Mass: 10763.483 Da / Num. of mol.: 4 / Mutation: S11A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYRM4, C6orf149, ISD11, CGI-203 / Plasmid: pACYCDuet-1 / Details (production host): No affinity tag / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HD34
#3: Protein
Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 8645.460 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: acpP, b1094, JW1080 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6A8
#4: Chemical
ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H45N2O8PS
Nonpolymer detailsS-dodecanoyl-4'-phosphopantetheine, as co-purified from the native source, constitutes a mixture ...S-dodecanoyl-4'-phosphopantetheine, as co-purified from the native source, constitutes a mixture with varying alkyl chain lengths. This was verified by gas chromatography mass spectrometry. In the structure, 12 carbons fitted best into the electron density

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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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 450 uL 0.1 M CBTP (pH = 6.4), 0.3 M CsCl, 0.2 M D,L - allylglycine, 5 mM TCEP, 8 % (wt/vol) PEG 3350 mixed with 50 uL of 40 % (vol/vol) acetone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. obs: 58855 / % possible obs: 99.4 % / Redundancy: 8 % / Biso Wilson estimate: 103.46 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Χ2: 1.424 / Net I/σ(I): 39.6 / Num. measured all: 471007
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.09-3.147.4225680.6190.4161.15188.6
3.14-3.28.229440.7520.3471.1631000.944
3.2-3.268.229130.8130.2931.2161000.7950.848
3.26-3.338.328980.880.2271.2331000.6170.657
3.33-3.48.229300.9190.1781.2781000.4840.517
3.4-3.488.229160.9410.1471.3891000.3990.426
3.48-3.578.229130.9610.121.3181000.3250.346
3.57-3.668.229330.9770.0971.3321000.2620.28
3.66-3.778.229550.9850.071.4131000.190.203
3.77-3.898.229310.9920.0551.3741000.1480.158
3.89-4.038.229540.9940.0451.4391000.1220.13
4.03-4.198.229300.9970.0351.3561000.0940.101
4.19-4.388.229650.9980.0271.3351000.0720.077
4.38-4.618.129580.9980.0231.3251000.0610.065
4.61-4.98.129570.9990.0191.3131000.0520.055
4.9-5.288.129940.9990.0181.2871000.0490.053
5.28-5.817.929580.9980.021.4961000.0530.057
5.81-6.657.830160.9970.0232.1521000.0590.064
6.65-8.387.430380.9990.0162.11399.90.0410.044
8.38-506.831840.9990.0121.87799.60.030.033

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LVM

3lvm


Resolution: 3.09→47.826 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 2000 3.45 %Random
Rwork0.2123 56013 --
obs0.2139 58013 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 294.8 Å2 / Biso mean: 127.153 Å2 / Biso min: 49.54 Å2
Refinement stepCycle: final / Resolution: 3.09→47.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15530 0 136 0 15666
Biso mean--109.25 --
Num. residues----1952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215904
X-RAY DIFFRACTIONf_angle_d0.54721455
X-RAY DIFFRACTIONf_chiral_restr0.0442425
X-RAY DIFFRACTIONf_plane_restr0.0032757
X-RAY DIFFRACTIONf_dihedral_angle_d12.8179824
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B1482X-RAY DIFFRACTION17.28TORSIONAL
12D1482X-RAY DIFFRACTION17.28TORSIONAL
13F1482X-RAY DIFFRACTION17.28TORSIONAL
14H1482X-RAY DIFFRACTION17.28TORSIONAL
21A5708X-RAY DIFFRACTION17.28TORSIONAL
22C5708X-RAY DIFFRACTION17.28TORSIONAL
23E5708X-RAY DIFFRACTION17.28TORSIONAL
24G5708X-RAY DIFFRACTION17.28TORSIONAL
31I1256X-RAY DIFFRACTION17.28TORSIONAL
32J1256X-RAY DIFFRACTION17.28TORSIONAL
33K1256X-RAY DIFFRACTION17.28TORSIONAL
34L1256X-RAY DIFFRACTION17.28TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.09-3.16730.42821410.34139374078100
3.1673-3.25290.34531420.275139624104100
3.2529-3.34860.34651390.25139604099100
3.3486-3.45670.29811420.242639434085100
3.4567-3.58020.31991420.242339694111100
3.5802-3.72350.27581410.213339564097100
3.7235-3.89280.27571420.196239844126100
3.8928-4.0980.26291420.19239714113100
4.098-4.35460.21951420.183739874129100
4.3546-4.69050.23641440.179139944138100
4.6905-5.1620.23261420.182640014143100
5.162-5.90780.26271450.217140554200100
5.9078-7.43870.25791450.236540724217100
7.4387-47.83190.23911510.21044222437399
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)
12.23490.75680.11664.0886-1.03843.0670.3684-0.36290.58540.3516-0.4419-0.261-0.72450.15860.0881.1471-0.1464-0.03940.57630.00261.1125-48.597623.259-10.708
28.88190.29550.78056.02350.46456.0077-0.23330.39280.0513-0.7897-0.0676-1.2075-0.13130.11880.34681.0490.10350.19180.58510.03530.9584-43.92341.058-31.0617
30.85820.6468-0.043.00990.13921.3673-1.3513-1.1562-0.77571.48321.7557-0.3402-0.00530.95320.20281.20750.72130.02611.85850.21511.1371-74.0684-45.529833.6653
44.48673.9501-2.50837.51540.15725.2772-0.22930.1473-1.5802-0.390.08550.1717-0.03860.1220.18170.7021-0.0589-0.07730.7450.21061.3542-94.0376-43.148111.1213
54.6640.3101-1.21262.3414-0.59282.7042-0.17250.646-0.0589-0.1419-0.1623-0.11370.3421-0.30020.19790.5965-0.0821-0.03640.61790.04140.7616-84.7193-18.3114-13.9622
64.65082.1912-1.57852.75690.70655.47760.5797-0.8844-0.27540.3209-0.27680.1583-0.03040.5002-0.21140.7503-0.1852-0.09350.70180.11780.745-74.4648-9.670112.0129
72.1139-0.64270.37073.3647-0.47723.53080.06750.303-0.1908-0.4467-0.14050.04180.2788-0.13690.11911.1328-0.0408-0.12060.6947-0.02760.8801-74.44273.9726-56.7869
87.512-0.09790.15186.56610.08835.2871-0.40330.09780.28720.27560.5137-0.085-0.5128-0.5524-0.18380.80950.2467-0.07120.408-0.03260.4392-81.281114.7066-29.5937
95.7158-0.0489-0.12287.29631.2112.41410.7138-1.8587-0.36532.0297-0.75920.35570.86290.4443-0.21371.0075-0.46-0.23341.19990.24020.9193-53.9699-5.702819.6253
102.2817-0.91950.06271.4023-0.0263-0.0037-0.646-1.0853-0.25131.45090.6037-0.60240.29180.0583-0.4481.99841.1675-0.66381.4237-0.56271.4429-86.094434.4336-21.2977
110.03210.03210.01510.0025-0.014-0.0022-0.0741-0.1925-0.1759-0.0988-0.13760.0830.0514-0.2641-1.20920.89220.43411.21621.66920.21920.2726-30.72962.4697-48.5664
120.5050.16660.81180.8680.78751.6526-0.56190.29370.5679-0.0541-0.30980.5744-0.517-0.3564-1.15361.0597-0.87530.11711.1817-0.52421.0787-95.7337-57.7239-5.3352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 54 through 445)A54 - 445
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 79)B4 - 79
3X-RAY DIFFRACTION3(chain 'C' and resid 56 through 444)C56 - 444
4X-RAY DIFFRACTION4(chain 'D' and resid 4 through 83)D4 - 83
5X-RAY DIFFRACTION5(chain 'E' and resid 47 through 436)E47 - 436
6X-RAY DIFFRACTION6(chain 'F' and resid 4 through 78)F4 - 78
7X-RAY DIFFRACTION7(chain 'G' and resid 54 through 440)G54 - 440
8X-RAY DIFFRACTION8(chain 'H' and resid 3 through 79)H3 - 79
9X-RAY DIFFRACTION9(chain 'I' and resid 2 through 77)I2 - 77
10X-RAY DIFFRACTION10(chain 'J' and resid 3 through 77)J3 - 77
11X-RAY DIFFRACTION11(chain 'K' and resid 5 through 73)K5 - 73
12X-RAY DIFFRACTION12(chain 'L' and resid 3 through 73)L3 - 73

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  • 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

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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

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