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- PDB-5anm: Crystal structure of IgE Fc in complex with a neutralizing antibody -

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Basic information

Entry
Database: PDB / ID: 5anm
TitleCrystal structure of IgE Fc in complex with a neutralizing antibody
Components
  • (IMMUNOGLOBULIN ...) x 2
  • IG EPSILON CHAIN C REGION
KeywordsIMMUNE SYSTEM / THERAPEUTIC ANTIBODY / IGG / IGE / ASTHMA
Function / homology
Function and homology information


adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / complement activation, classical pathway / FCERI mediated MAPK activation / antigen binding / B cell receptor signaling pathway / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / inflammatory response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant epsilon
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsCohen, E.S. / Dobson, C.L. / Kack, H. / Wang, B. / Sims, D.A. / Lloyd, C.O. / England, E. / Rees, D.G. / Guo, H. / Karagiannis, S.N. ...Cohen, E.S. / Dobson, C.L. / Kack, H. / Wang, B. / Sims, D.A. / Lloyd, C.O. / England, E. / Rees, D.G. / Guo, H. / Karagiannis, S.N. / O'Brien, S. / Persdotter, S. / Ekdahl, H. / Butler, R. / Keyes, F. / Oakley, S. / Carlsson, M. / Briend, E. / Wilkinson, T. / Anderson, I.K. / Monk, P.D. / vonWachenfeldt, K. / Eriksson, P.O. / Gould, H.J. / Vaughan, T.J. / May, R.D.
CitationJournal: Mabs / Year: 2015
Title: A Novel Ige-Neutralizing Antibody for the Treatment of Severe Uncontrolled Asthma.
Authors: Cohen, E.S. / Dobson, C.L. / Kack, H. / Wang, B. / Sims, D.A. / Lloyd, C.O. / England, E. / Rees, D.G. / Guo, H. / Karagiannis, S.N. / O'Brien, S. / Persdotter, S. / Ekdahl, H. / Butler, R. ...Authors: Cohen, E.S. / Dobson, C.L. / Kack, H. / Wang, B. / Sims, D.A. / Lloyd, C.O. / England, E. / Rees, D.G. / Guo, H. / Karagiannis, S.N. / O'Brien, S. / Persdotter, S. / Ekdahl, H. / Butler, R. / Keyes, F. / Oakley, S. / Carlsson, M. / Briend, E. / Wilkinson, T. / Anderson, I.K. / Monk, P.D. / Von Wachenfeldt, K. / Eriksson, P.F. / Gould, H.J. / Vaughan, T.J. / May, R.D.
History
DepositionSep 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_validate_close_contact / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN G
B: IMMUNOGLOBULIN G
C: IMMUNOGLOBULIN G
D: IMMUNOGLOBULIN G
E: IG EPSILON CHAIN C REGION
F: IG EPSILON CHAIN C REGION
G: IG EPSILON CHAIN C REGION
H: IMMUNOGLOBULIN G
L: IMMUNOGLOBULIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,13112
Polymers225,0749
Non-polymers3,0573
Water3,423190
1
A: IMMUNOGLOBULIN G
B: IMMUNOGLOBULIN G
G: IG EPSILON CHAIN C REGION
hetero molecules

A: IMMUNOGLOBULIN G
B: IMMUNOGLOBULIN G
G: IG EPSILON CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,1958
Polymers150,0506
Non-polymers2,1462
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
MethodPQS
2
C: IMMUNOGLOBULIN G
D: IMMUNOGLOBULIN G
E: IG EPSILON CHAIN C REGION
F: IG EPSILON CHAIN C REGION
H: IMMUNOGLOBULIN G
L: IMMUNOGLOBULIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,0338
Polymers150,0506
Non-polymers1,9842
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)140.957, 140.957, 244.448
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Antibody , 2 types, 6 molecules ACLBDH

#1: Antibody IMMUNOGLOBULIN G


Mass: 22930.264 Da / Num. of mol.: 3 / Fragment: FAB, LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHINESE HAMSTER OVARY-EBNA / Production host: CRICETULUS GRISEUS (Chinese hamster)
#2: Antibody IMMUNOGLOBULIN G


Mass: 24752.887 Da / Num. of mol.: 3 / Fragment: FAB, HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHINESE HAMSTER OVARY-EBNA / Production host: CRICETULUS GRISEUS (Chinese hamster)

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Protein / Non-polymers , 2 types, 193 molecules EFG

#3: Protein IG EPSILON CHAIN C REGION / IMMUNOGLOBULIN E


Mass: 27341.619 Da / Num. of mol.: 3 / Fragment: FC DOMAIN, CE3-CE4, RESIDUES 211-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: P01854
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 3 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpb1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

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Details

Sequence detailsTHIS IS A UNIQUE FAB RAISED AGAINST IGE

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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 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 100 MM MGCL2, 100 MM SODIUM CITRATE PH 5.0 AND 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.85→109.11 Å / Num. obs: 66338 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.2
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 11 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1AQK, 1FP5

1aqk

1fp5


Resolution: 2.85→31.29 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / SU B: 30.044 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 1.133 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25993 3355 5.1 %RANDOM
Rwork0.19553 ---
obs0.1988 62860 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.85→31.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14393 0 205 190 14788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214988
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.97220459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.96451865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10523.574568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.743152314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.441581
X-RAY DIFFRACTIONr_chiral_restr0.1120.22360
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02111159
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_it2.1713.2557526
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.7244.8659369
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4843.4197459
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 227 -
Rwork0.275 4564 -
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)
11.5525-0.1138-0.14142.2729-0.7251.42740.0776-0.0966-0.19420.05120.01730.21650.198-0.1143-0.0950.1885-0.10880.04770.2236-0.04360.1052-38.954128.470261.1058
21.57410.33280.15232.52080.02171.59870.1433-0.09970.21830.0361-0.103-0.2023-0.33080.1288-0.04030.2155-0.0860.00510.2374-0.01860.0837-78.578699.009440.5424
32.2860.720.6531.8351-0.844.33280.4682-0.35410.11980.294-0.21940.7227-0.6307-0.5595-0.24880.4145-0.20640.32490.5802-0.47730.7247-112.9354112.269683.7606
40.9963-0.6602-0.1571.50070.02392.09410.1071-0.0914-0.09410.04980.0445-0.0196-0.36190.1449-0.15160.2189-0.11770.06840.1972-0.00290.0644-21.727558.504372.3046
51.00970.27240.21673.39880.17923.45890.402-0.49270.16650.3362-0.257-0.3244-0.3780.877-0.14510.2408-0.34070.04690.9769-0.13510.2375-78.9835103.392275.7987
61.9120.3049-0.48961.86610.76513.80120.1388-0.5320.02980.2543-0.16530.1310.51280.08520.02650.2042-0.14680.05820.4329-0.03010.0299-97.952984.070267.396
72.11440.793-0.03563.8318-0.30331.9030.0061-0.1224-0.3047-0.0485-0.0320.7086-0.0497-0.35540.0260.0140.00140.00010.328-0.02040.2603-68.499348.325950.7023
82.29610.3292-0.05823.705-0.92071.03540.02710.30450.3075-0.276-0.2825-0.14090.03320.18350.25530.13830.0638-0.00190.38120.10770.1106-50.581174.932941.5971
93.4689-0.4803-0.82455.7904-0.77151.6474-0.0809-0.4591-0.78830.01420.20.90540.15450.6389-0.1190.2525-0.13760.22940.5138-0.13060.5496-111.650690.3077112.461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION1B1 - 121
3X-RAY DIFFRACTION2C1 - 113
4X-RAY DIFFRACTION2D1 - 121
5X-RAY DIFFRACTION3L1 - 113
6X-RAY DIFFRACTION3H1 - 121
7X-RAY DIFFRACTION4G1 - 999
8X-RAY DIFFRACTION5E1 - 999
9X-RAY DIFFRACTION6F1 - 999
10X-RAY DIFFRACTION7A114 - 999
11X-RAY DIFFRACTION7B122 - 999
12X-RAY DIFFRACTION8C114 - 999
13X-RAY DIFFRACTION8D122 - 999
14X-RAY DIFFRACTION9L114 - 999
15X-RAY DIFFRACTION9H122 - 999

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Yorodumi

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  • 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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