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- PDB-3m6s: Crystal structure of H1N1pdm Hemagglutinin -

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Basic information

Entry
Database: PDB / ID: 3m6s
TitleCrystal structure of H1N1pdm Hemagglutinin
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / Influenza virus / Hemagglutinin / pandemic / Envelope protein / Fusion protein / Host cell membrane / Host membrane / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYang, H. / Carney, P.J. / Stevens, J.
CitationJournal: PLoS Curr / Year: 2010
Title: Structure and Receptor binding properties of a pandemic H1N1 virus hemagglutinin
Authors: Yang, H. / Carney, P. / Stevens, J.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 19, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 6, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,69121
Polymers344,52212
Non-polymers3,1699
Water0
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,1289
Polymers172,2616
Non-polymers8673
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31290 Å2
ΔGint-147 kcal/mol
Surface area59210 Å2
MethodPISA
2
G: Hemagglutinin
H: Hemagglutinin
hetero molecules

I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,56312
Polymers172,2616
Non-polymers2,3026
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
identity operation1_555x,y,z1
Buried area32590 Å2
ΔGint-126 kcal/mol
Surface area59850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.984, 109.709, 129.896
Angle α, β, γ (deg.)86.25, 74.68, 75.10
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11F
21D
31B
41H
51J
61L
12E
22C
32G
42A
52I
62K

NCS ensembles :
ID
1
2
DetailsThe biological unit is a trimer.

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Components

#1: Protein
Hemagglutinin /


Mass: 36661.324 Da / Num. of mol.: 6 / Fragment: Hemagglutinin HA1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Darwin/2001/2009(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C5MV42
#2: Protein
Hemagglutinin /


Mass: 20759.008 Da / Num. of mol.: 6 / Fragment: Hemagglutinin HA2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Darwin/2001/2009(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C5MV42
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 4
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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 7.5
Details: 22% PEG2000MME, 0.1M HEPES at pH7.5, microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 96521 / Num. obs: 94645 / % possible obs: 98.1 % / Redundancy: 2 % / Rsym value: 0.076
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.442 / % possible all: 95.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KU3
Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.889 / SU B: 36.705 / SU ML: 0.32 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25588 4608 5 %RANDOM
Rwork0.22978 ---
obs0.23109 87344 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.604 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.94 Å21.83 Å2
2--2.55 Å2-1.87 Å2
3----3.72 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23380 0 207 0 23587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02224181
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.95132795
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07752946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77625.0621130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.275154086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4621584
X-RAY DIFFRACTIONr_chiral_restr0.1250.23565
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118340
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_it0.661.514671
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.332223685
X-RAY DIFFRACTIONr_scbond_it2.10739510
X-RAY DIFFRACTIONr_scangle_it3.6514.59110
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11F676tight positional0.050.05
12D676tight positional0.060.05
13B676tight positional0.060.05
14H676tight positional0.060.05
15J676tight positional0.10.05
16L676tight positional0.060.05
21E1280tight positional0.050.05
22C1280tight positional0.060.05
23G1280tight positional0.070.05
24A1280tight positional0.070.05
25I1280tight positional0.060.05
26K1280tight positional0.070.05
11F687loose positional0.085
12D687loose positional0.085
13B687loose positional0.085
14H687loose positional0.075
15J687loose positional0.115
16L687loose positional0.075
21E1219loose positional0.065
22C1219loose positional0.075
23G1219loose positional0.085
24A1219loose positional0.085
25I1219loose positional0.065
26K1219loose positional0.085
11F676tight thermal0.080.5
12D676tight thermal0.090.5
13B676tight thermal0.090.5
14H676tight thermal0.090.5
15J676tight thermal0.10.5
16L676tight thermal0.090.5
21E1280tight thermal0.090.5
22C1280tight thermal0.110.5
23G1280tight thermal0.120.5
24A1280tight thermal0.10.5
25I1280tight thermal0.090.5
26K1280tight thermal0.10.5
11F687loose thermal0.0910
12D687loose thermal0.1110
13B687loose thermal0.0910
14H687loose thermal0.0910
15J687loose thermal0.1310
16L687loose thermal0.110
21E1219loose thermal0.1110
22C1219loose thermal0.1310
23G1219loose thermal0.1410
24A1219loose thermal0.1110
25I1219loose thermal0.110
26K1219loose thermal0.1210
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 301 -
Rwork0.314 6322 -
obs--95.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.2636-0.1568-0.0910.37460.19173.15460.06990.07470.0871-0.00130.018-0.1042-0.58650.385-0.08780.2713-0.14490.07060.163-0.05050.2958-20.3997-12.5839-34.3041
20.97410.39771.32521.44233.51110.8841-0.0265-0.14-0.05650.2050.0674-0.0523-0.2095-0.0649-0.04090.52310.05160.06350.04410.00170.1584-28.0342-4.971117.3059
30.386-0.03620.3810.79521.22262.6770.1411-0.0291-0.15630.03880.08940.0540.09310.1175-0.23060.1091-0.0074-0.0320.0197-0.02570.341-36.6417-42.1848-28.5966
40.66820.0418-0.36320.23290.481311.12440.181-0.1284-0.08310.02130.03280.0482-0.5841-0.7118-0.21380.1530.03320.07050.11540.06210.1983-37.3934-23.43921.6924
50.5635-0.17010.90740.4090.06133.53930.0073-0.17560.0162-0.00160.11370.1646-0.4748-0.7234-0.1210.23630.14180.04380.20690.08290.3478-54.4456-13.7762-35.4145
60.5362-0.252-1.12851.35031.95898.74060.1142-0.24150.04030.14940.18650.0417-1.3844-0.6824-0.30070.63150.39490.14450.49880.0180.2205-49.6245-6.054617.599
70.92720.11560.81150.59060.03374.28250.0388-0.1212-0.1262-0.0214-0.04930.07620.4621-0.13890.01060.0942-0.018-0.020.0242-0.00580.191-18.2701-78.8485-50.1068
81.4507-0.1511-1.86660.7984-0.11217.89110.1193-0.74430.07150.331-0.00250.0096-0.67660.8828-0.11680.249-0.102-0.03380.523-0.02950.1356-10.8808-69.63842.3853
90.77340.04890.28540.65420.59774.34550.05070.1578-0.262-0.0912-0.0045-0.29320.5211.3717-0.04610.17270.23530.05230.63760.02480.3189-58.0768-80.9825-50.4158
100.4003-0.09772.35690.2171-0.685815.2046-0.04580.07470.02190.0253-0.1504-0.1252-0.00060.29720.19620.0749-0.0176-0.04590.55960.07560.1171-63.3914-69.87122.2438
110.78970.1450.25440.8560.62375.2118-0.07680.05770.2107-0.18640.1412-0.035-0.62520.6515-0.06440.1408-0.1589-0.02170.19590.00080.2465-73.4443-50.5896-53.8326
121.6680.35010.45141.61971.67396.51690.1842-0.84330.250.7925-0.1554-0.06530.37960.5687-0.02890.4566-0.1862-0.07010.6072-0.12040.1868-73.3476-51.69330.2944
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 322
2X-RAY DIFFRACTION1A328
3X-RAY DIFFRACTION2B2 - 170
4X-RAY DIFFRACTION3C0 - 322
5X-RAY DIFFRACTION3C328 - 329
6X-RAY DIFFRACTION4D2 - 172
7X-RAY DIFFRACTION5E0 - 322
8X-RAY DIFFRACTION5E328
9X-RAY DIFFRACTION6F2 - 172
10X-RAY DIFFRACTION7G1 - 322
11X-RAY DIFFRACTION7G328 - 332
12X-RAY DIFFRACTION8H2 - 171
13X-RAY DIFFRACTION9I0 - 321
14X-RAY DIFFRACTION9I328 - 329
15X-RAY DIFFRACTION10J2 - 171
16X-RAY DIFFRACTION11K2 - 322
17X-RAY DIFFRACTION11K328 - 331
18X-RAY DIFFRACTION12L2 - 172

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