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- PDB-4k3x: Crystal structure of a subtype H18 hemagglutinin homologue from A... -

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Basic information

Entry
Database: PDB / ID: 4k3x
TitleCrystal structure of a subtype H18 hemagglutinin homologue from A/flat-faced bat/Peru/033/2010 (H18N11)
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / influenza virus / hemagglutinin homologue / H18 / ectodomain
Function / homology
Function and homology information


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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: Plos Pathog. / Year: 2013
Title: New world bats harbor diverse influenza a viruses.
Authors: Tong, S. / Zhu, X. / Li, Y. / Shi, M. / Zhang, J. / Bourgeois, M. / Yang, H. / Chen, X. / Recuenco, S. / Gomez, J. / Chen, L.M. / Johnson, A. / Tao, Y. / Dreyfus, C. / Yu, W. / McBride, R. / ...Authors: Tong, S. / Zhu, X. / Li, Y. / Shi, M. / Zhang, J. / Bourgeois, M. / Yang, H. / Chen, X. / Recuenco, S. / Gomez, J. / Chen, L.M. / Johnson, A. / Tao, Y. / Dreyfus, C. / Yu, W. / McBride, R. / Carney, P.J. / Gilbert, A.T. / Chang, J. / Guo, Z. / Davis, C.T. / Paulson, J.C. / Stevens, J. / Rupprecht, C.E. / Holmes, E.C. / Wilson, I.A. / Donis, R.O.
History
DepositionApr 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_unobs_or_zero_occ_atoms / 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_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 / _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_atom_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_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 2.1Sep 20, 2023Group: 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: Hemagglutinin HA1
C: Hemagglutinin HA1
E: Hemagglutinin HA1
B: Hemagglutinin HA2
D: Hemagglutinin HA2
F: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,46232
Polymers172,4436
Non-polymers11,01926
Water13,421745
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35650 Å2
ΔGint-76 kcal/mol
Surface area62320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.884, 238.884, 160.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1


Mass: 36746.781 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/flat-faced bat/Peru/033/2010(H18N11) / Plasmid: pFastbacHT-A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HI5
#2: Protein Hemagglutinin HA2


Mass: 20734.199 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/flat-faced bat/Peru/033/2010(H18N11) / Plasmid: pFastbacHT-A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HI5

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Sugars , 7 types, 14 molecules

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


Type: oligosaccharide / Mass: 1203.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpb1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-2-1-3-4-4-5/a3-b1_a4-c1_a6-g1_c4-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][beta-L-fucopyranose-(1-6) ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4][LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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.: 5
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
#6: Polysaccharide beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1b_1-5]/1-1-2-2-3/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#7: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1221m-1a_1-5]/1-2-1-3/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#10: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 2 types, 757 molecules

#9: Chemical
ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H18O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.9
Details: 0.1 M MES, pH 6.9, 5% PEG1000, 27.5% PEG600, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.149→50 Å / Num. obs: 121108 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Rsym value: 0.109
Reflection shellResolution: 2.149→2.23 Å / % possible all: 79.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RD8

1rd8


Resolution: 2.149→47.94 Å / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 6093 5.03 %RANDOM
Rwork0.1832 ---
obs0.1851 121054 96.82 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.072 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.2609 Å2-0 Å20 Å2
2---8.2609 Å20 Å2
3---16.5218 Å2
Refinement stepCycle: LAST / Resolution: 2.149→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11730 0 737 745 13212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812776
X-RAY DIFFRACTIONf_angle_d1.07417329
X-RAY DIFFRACTIONf_dihedral_angle_d27.3374914
X-RAY DIFFRACTIONf_chiral_restr0.0742013
X-RAY DIFFRACTIONf_plane_restr0.0042153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.149-2.17340.351570.2872750X-RAY DIFFRACTION71
2.1734-2.1990.33741890.27583064X-RAY DIFFRACTION79
2.199-2.22580.2971660.25273274X-RAY DIFFRACTION83
2.2258-2.2540.29121850.24493457X-RAY DIFFRACTION88
2.254-2.28360.29561900.24793629X-RAY DIFFRACTION93
2.2836-2.31490.30222250.23423680X-RAY DIFFRACTION96
2.3149-2.3480.27641910.23053840X-RAY DIFFRACTION97
2.348-2.3830.27671940.21223909X-RAY DIFFRACTION99
2.383-2.42030.27262060.21723902X-RAY DIFFRACTION100
2.4203-2.45990.2572020.20893948X-RAY DIFFRACTION100
2.4599-2.50230.24481980.20143914X-RAY DIFFRACTION100
2.5023-2.54780.24991940.19783936X-RAY DIFFRACTION100
2.5478-2.59680.23622260.20433943X-RAY DIFFRACTION100
2.5968-2.64990.29761830.2043928X-RAY DIFFRACTION100
2.6499-2.70750.29172190.20713933X-RAY DIFFRACTION100
2.7075-2.77040.26362010.19043951X-RAY DIFFRACTION100
2.7704-2.83970.23781950.19073950X-RAY DIFFRACTION100
2.8397-2.91650.23241980.20093961X-RAY DIFFRACTION100
2.9165-3.00230.24492070.20043926X-RAY DIFFRACTION100
3.0023-3.09920.23142190.1923956X-RAY DIFFRACTION100
3.0992-3.20990.23722130.19683941X-RAY DIFFRACTION100
3.2099-3.33840.21762170.19623978X-RAY DIFFRACTION100
3.3384-3.49030.2252150.19223938X-RAY DIFFRACTION100
3.4903-3.67430.22632360.1753980X-RAY DIFFRACTION100
3.6743-3.90440.18962060.15743969X-RAY DIFFRACTION100
3.9044-4.20570.1671900.14144001X-RAY DIFFRACTION100
4.2057-4.62860.15181940.13174012X-RAY DIFFRACTION100
4.6286-5.29760.16852080.14554046X-RAY DIFFRACTION100
5.2976-6.67160.2022530.18744033X-RAY DIFFRACTION100
6.6716-47.95230.20352160.18584212X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 61.2517 Å / Origin y: 29.2087 Å / Origin z: 66.907 Å
111213212223313233
T0.1957 Å20.0025 Å20.0048 Å2-0.2073 Å20.002 Å2--0.2249 Å2
L0.437 °20.1544 °20.1783 °2-0.186 °20.1613 °2--0.2903 °2
S-0.006 Å °0.0248 Å °0.0643 Å °-0.0117 Å °0.0085 Å °-0.0144 Å °0.0038 Å °0.0493 Å °-0.0004 Å °
Refinement TLS groupSelection details: all

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