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- PDB-6d96: Structure of influenza neuraminidase from strain A/BrevigMission/... -

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Basic information

Entry
Database: PDB / ID: 6d96
TitleStructure of influenza neuraminidase from strain A/BrevigMission/1/1918(H1N1) expressed in HEK-293E cells
ComponentsNeuraminidase
KeywordsHYDROLASE / 6-BLADED BETA-PROPELLER / GLYCOPROTEIN / GLYCOSIDASE / MEMBRANE / METAL-BINDING / SIGNAL-ANCHOR / TRANSMEMBRANE / VIRION
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCampbell, A.C. / Krause, K.L. / Tanner, J.J.
CitationJournal: To Be Published
Title: Optimisation of neuraminidase expression by HEK-293E cells for use in structural biology
Authors: Campbell, A.C. / Tanner, J.J. / Krause, K.L.
History
DepositionApr 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
E: Neuraminidase
F: Neuraminidase
G: Neuraminidase
H: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,18656
Polymers355,5648
Non-polymers8,62248
Water24,2301345
1
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,91828
Polymers177,7824
Non-polymers4,13624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17380 Å2
ΔGint-124 kcal/mol
Surface area46300 Å2
MethodPISA
2
E: Neuraminidase
F: Neuraminidase
G: Neuraminidase
H: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,26728
Polymers177,7824
Non-polymers4,48624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17840 Å2
ΔGint-119 kcal/mol
Surface area46230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.681, 148.189, 127.166
Angle α, β, γ (deg.)90.000, 94.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 83:146 or (resid 147 and (name...
21(chain B and ((resid 83 and (name N or name...
31(chain C and ((resid 83 and (name N or name...
41(chain D and ((resid 83 and (name N or name...
51(chain E and ((resid 83 and (name N or name...
61(chain F and ((resid 83 and (name N or name...
71(chain H and ((resid 83 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASNASN(chain A and (resseq 83:146 or (resid 147 and (name...AA83 - 14618 - 81
12GLYGLYGLYGLY(chain A and (resseq 83:146 or (resid 147 and (name...AA14782
13VALVALASPASP(chain A and (resseq 83:146 or (resid 147 and (name...AA83 - 46918 - 403
14VALVALASPASP(chain A and (resseq 83:146 or (resid 147 and (name...AA83 - 46918 - 403
21VALVALVALVAL(chain B and ((resid 83 and (name N or name...BB8318
22VALVALASPASP(chain B and ((resid 83 and (name N or name...BB83 - 46918 - 403
23VALVALASPASP(chain B and ((resid 83 and (name N or name...BB83 - 46918 - 403
24VALVALASPASP(chain B and ((resid 83 and (name N or name...BB83 - 46918 - 403
25VALVALASPASP(chain B and ((resid 83 and (name N or name...BB83 - 46918 - 403
31VALVALVALVAL(chain C and ((resid 83 and (name N or name...CC8318
32VALVALASPASP(chain C and ((resid 83 and (name N or name...CC83 - 46918 - 403
33VALVALASPASP(chain C and ((resid 83 and (name N or name...CC83 - 46918 - 403
34VALVALASPASP(chain C and ((resid 83 and (name N or name...CC83 - 46918 - 403
35VALVALASPASP(chain C and ((resid 83 and (name N or name...CC83 - 46918 - 403
41VALVALVALVAL(chain D and ((resid 83 and (name N or name...DD8318
42VALVALASPASP(chain D and ((resid 83 and (name N or name...DD83 - 46918 - 403
43VALVALASPASP(chain D and ((resid 83 and (name N or name...DD83 - 46918 - 403
44VALVALASPASP(chain D and ((resid 83 and (name N or name...DD83 - 46918 - 403
45VALVALASPASP(chain D and ((resid 83 and (name N or name...DD83 - 46918 - 403
51VALVALVALVAL(chain E and ((resid 83 and (name N or name...EE8318
52VALVALASPASP(chain E and ((resid 83 and (name N or name...EE83 - 46918 - 403
53VALVALASPASP(chain E and ((resid 83 and (name N or name...EE83 - 46918 - 403
54VALVALASPASP(chain E and ((resid 83 and (name N or name...EE83 - 46918 - 403
55VALVALASPASP(chain E and ((resid 83 and (name N or name...EE83 - 46918 - 403
61VALVALVALVAL(chain F and ((resid 83 and (name N or name...FF8318
62VALVALASPASP(chain F and ((resid 83 and (name N or name...FF83 - 46918 - 403
63VALVALASPASP(chain F and ((resid 83 and (name N or name...FF83 - 46918 - 403
64VALVALASPASP(chain F and ((resid 83 and (name N or name...FF83 - 46918 - 403
65VALVALASPASP(chain F and ((resid 83 and (name N or name...FF83 - 46918 - 403
71VALVALVALVAL(chain H and ((resid 83 and (name N or name...HH8318
72VALVALASPASP(chain H and ((resid 83 and (name N or name...HH83 - 46918 - 403
73VALVALASPASP(chain H and ((resid 83 and (name N or name...HH83 - 46918 - 403
74VALVALASPASP(chain H and ((resid 83 and (name N or name...HH83 - 46918 - 403
75VALVALASPASP(chain H and ((resid 83 and (name N or name...HH83 - 46918 - 403

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Neuraminidase /


Mass: 44445.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Brevig Mission/1/1918 H1N1 / Gene: NA / Cell line (production host): HEK-293E / Production host: Homo sapiens (human) / References: UniProt: Q9IGQ6, exo-alpha-sialidase

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Sugars , 3 types, 24 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 1369 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1345 / 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: 3.24 Å3/Da / Density % sol: 62.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 12 % PEG 20000, 0.1 M MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→48.15 Å / Num. obs: 242924 / % possible obs: 99.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.19 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.144 / Rrim(I) all: 0.281 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.193.81.183119450.4120.7031.37798.4
11.78-48.153.50.05214940.9930.0330.06295.6

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Processing

Software
NameVersionClassification
Aimless0.5.7data scaling
PHENIX(1.12_2829)refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BEQ

3beq


Resolution: 2.15→38.956 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.98
RfactorNum. reflection% reflection
Rfree0.2151 14387 2.99 %
Rwork0.1858 --
obs0.1866 242924 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.44 Å2 / Biso mean: 26.8387 Å2 / Biso min: 12.28 Å2
Refinement stepCycle: final / Resolution: 2.15→38.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23731 0 530 1345 25606
Biso mean--62.68 31.21 -
Num. residues----3088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00925022
X-RAY DIFFRACTIONf_angle_d0.9734130
X-RAY DIFFRACTIONf_chiral_restr0.0583668
X-RAY DIFFRACTIONf_plane_restr0.0064394
X-RAY DIFFRACTIONf_dihedral_angle_d12.50214609
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12549X-RAY DIFFRACTION6.881TORSIONAL
12B12549X-RAY DIFFRACTION6.881TORSIONAL
13C12549X-RAY DIFFRACTION6.881TORSIONAL
14D12549X-RAY DIFFRACTION6.881TORSIONAL
15E12549X-RAY DIFFRACTION6.881TORSIONAL
16F12549X-RAY DIFFRACTION6.881TORSIONAL
17H12549X-RAY DIFFRACTION6.881TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.17450.32934380.3201152981573698
2.1745-2.20.34014970.31155521604998
2.2-2.22690.31964930.3023155551604899
2.2269-2.2550.28955120.2938153361584899
2.255-2.28470.32384900.289154451593599
2.2847-2.3160.3085060.2864156401614699
2.316-2.34910.29314540.2785154531590799
2.3491-2.38420.32954430.2777155001594399
2.3842-2.42140.29215200.2688153711589199
2.4214-2.46110.29984510.2643156431609499
2.4611-2.50350.30484380.2648155991603799
2.5035-2.5490.31324710.2562154691594099
2.549-2.59810.29385120.2458156211613399
2.5981-2.65110.27215360.2377154281596499
2.6511-2.70870.25944290.2276156591608899
2.7087-2.77170.23654350.2111155831601899
2.7717-2.8410.24784800.1983155881606899
2.841-2.91780.2215100.1938156081611899
2.9178-3.00360.22354780.1852155621604099
3.0036-3.10050.22235050.1761155731607899
3.1005-3.21130.20234770.1626155841606199
3.2113-3.33980.19534150.16121567416089100
3.3398-3.49170.1785160.15051559116107100
3.4917-3.67570.15925780.14241557416152100
3.6757-3.90580.15965180.134155461606499
3.9058-4.2070.1574880.12331565016138100
4.207-4.62980.1225160.1118155711608799
4.6298-5.29830.15184450.1157156511609699
5.2983-6.66980.18064160.14411567016086100
6.6698-38.96280.1674200.1546155881600899
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)
10.41920.0516-0.11430.4733-0.03360.70150.0113-0.06640.0220.0582-0.02150.0106-0.05040.05980.00630.1880.0058-0.0010.19560.00380.161613.305-1.027556.6917
20.58370.0894-0.07940.37080.09330.6074-0.0008-0.0219-0.00730.0221-0.00440.0556-0.00030.01030.00760.19790.01170.01370.1810.03680.2125-16.5962-27.274256.9387
30.40840.1367-0.00850.4707-0.03680.7146-0.02340.0611-0.0104-0.06580.02710.00080.00010.0039-0.00110.18530.01570.01390.2205-0.00320.176116.0223-4.464217.0714
40.72970.0922-0.06880.5277-0.03650.8348-0.02730.1509-0.0933-0.11340.04750.09470.0995-0.0529-0.02410.1908-0.0192-0.02510.1705-0.01620.1745-13.9744-30.634617.3326
50.2992-0.1618-0.18530.6051-0.11410.6083-0.0238-0.0022-0.0137-0.0678-0.0072-0.10310.04550.01060.02950.166-0.00460.01630.1797-0.01260.190787.5082-35.9323-33.069
60.6089-0.0265-0.02660.4665-0.01850.4696-0.0391-0.15-0.01980.11260.043-0.01770.00670.0043-0.00280.19570.0157-0.01260.2193-0.00180.136365.2923-25.9066-1.5192
70.6964-0.0706-0.03440.4169-0.09590.7268-0.0052-0.00470.0745-0.00850.01810.0246-0.06-0.0354-0.01530.2153-0.00050.00480.1866-0.00570.182645.56820.571-23.9485
80.7302-0.2297-0.05220.55440.04520.62910.06260.23230.0688-0.1374-0.0608-0.0409-0.0231-0.0046-0.00270.20620.00180.02470.2450.03820.15567.4874-9.7606-55.5311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 83 through 469)A83 - 469
2X-RAY DIFFRACTION2(chain 'B' and resid 83 through 469)B83 - 469
3X-RAY DIFFRACTION3(chain 'C' and resid 83 through 469)C83 - 469
4X-RAY DIFFRACTION4(chain 'D' and resid 83 through 469)D83 - 469
5X-RAY DIFFRACTION5(chain 'E' and resid 83 through 469)E83 - 469
6X-RAY DIFFRACTION6(chain 'F' and resid 83 through 469)F83 - 469
7X-RAY DIFFRACTION7(chain 'G' and resid 83 through 469)G83 - 469
8X-RAY DIFFRACTION8(chain 'H' and resid 83 through 469)H83 - 469

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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

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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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