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- PDB-5w42: Crystal structure of human monoclonal antibody H3v-47 in complex ... -

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Basic information

Entry
Database: PDB / ID: 5w42
TitleCrystal structure of human monoclonal antibody H3v-47 in complex with influenza virus hemagglutinin from A/Minnesota/11/2010 (H3N2)
Components
  • (Hemagglutinin) x 2
  • Fab H3v-47 heavy chain
  • Fab H3v-47 light chain
KeywordsIMMUNE SYSTEM / Hemagglutinin / antibody / complex / VIRAL PROTEIN
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / viral budding from plasma membrane / complement activation, classical pathway / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / blood microparticle / host cell surface receptor binding / immune response ...immunoglobulin complex, circulating / immunoglobulin receptor binding / viral budding from plasma membrane / complement activation, classical pathway / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / blood microparticle / host cell surface receptor binding / immune response / 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 / virion membrane / extracellular space / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
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 / Immunoglobulin V-Type ...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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Ig-like domain-containing protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.569 Å
AuthorsZhang, H. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
CitationJournal: Nat Commun / Year: 2018
Title: A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA.
Authors: Bangaru, S. / Zhang, H. / Gilchuk, I.M. / Voss, T.G. / Irving, R.P. / Gilchuk, P. / Matta, P. / Zhu, X. / Lang, S. / Nieusma, T. / Richt, J.A. / Albrecht, R.A. / Vanderven, H.A. / Bombardi, ...Authors: Bangaru, S. / Zhang, H. / Gilchuk, I.M. / Voss, T.G. / Irving, R.P. / Gilchuk, P. / Matta, P. / Zhu, X. / Lang, S. / Nieusma, T. / Richt, J.A. / Albrecht, R.A. / Vanderven, H.A. / Bombardi, R. / Kent, S.J. / Ward, A.B. / Wilson, I.A. / Crowe, J.E.
History
DepositionJun 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_struct_conn_angle / 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_struct_conn_angle.ptnr2_label_asym_id / _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_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
H: Fab H3v-47 heavy chain
L: Fab H3v-47 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,48913
Polymers105,3274
Non-polymers5,1629
Water00
1
A: Hemagglutinin
B: Hemagglutinin
H: Fab H3v-47 heavy chain
L: Fab H3v-47 light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: Fab H3v-47 heavy chain
L: Fab H3v-47 light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: Fab H3v-47 heavy chain
L: Fab H3v-47 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,46839
Polymers315,98212
Non-polymers15,48627
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area63920 Å2
ΔGint-122 kcal/mol
Surface area123300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.622, 194.622, 194.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 36788.191 Da / Num. of mol.: 1 / Fragment: UNP residues 17-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2))
Strain: A/swine/Minnesota/A01134337/2010(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: I0AXC3
#2: Protein Hemagglutinin


Mass: 20055.295 Da / Num. of mol.: 1 / Fragment: UNP residues 346-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/swine/Minnesota/A01134337/2010(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: I0AXC3

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Antibody , 2 types, 2 molecules HL

#3: Antibody Fab H3v-47 heavy chain


Mass: 25227.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686P15220 / Production host: Homo sapiens (human) / References: UniProt: Q6N089
#4: Antibody Fab H3v-47 light chain


Mass: 23256.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0

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Sugars , 6 types, 8 molecules

#5: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[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]/1-1-2-3-3/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)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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
DManpa1-2DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#9: 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.: 1
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
#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 , 1 types, 1 molecules

#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 5.85 Å3/Da / Density % sol: 78.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1M MES (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.569→50 Å / Num. obs: 29479 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.045 / Net I/σ(I): 14.8
Reflection shellResolution: 3.57→3.63 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.784 / Num. unique obs: 1441 / CC1/2: 0.607 / Rpim(I) all: 0.584 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YP2

2yp2


Resolution: 3.569→38.924 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 1980 6.74 %
Rwork0.1958 --
obs0.198 29378 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.569→38.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7234 0 340 0 7574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137768
X-RAY DIFFRACTIONf_angle_d1.98810595
X-RAY DIFFRACTIONf_dihedral_angle_d11.3984662
X-RAY DIFFRACTIONf_chiral_restr0.0951243
X-RAY DIFFRACTIONf_plane_restr0.0181328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5694-3.65860.28821390.28071936X-RAY DIFFRACTION100
3.6586-3.75740.29991390.27081932X-RAY DIFFRACTION100
3.7574-3.86790.26771410.2371942X-RAY DIFFRACTION100
3.8679-3.99260.28541410.23621951X-RAY DIFFRACTION100
3.9926-4.13520.22991460.2071927X-RAY DIFFRACTION100
4.1352-4.30050.21261390.18531960X-RAY DIFFRACTION100
4.3005-4.4960.18571430.16211957X-RAY DIFFRACTION100
4.496-4.73270.16221380.15161919X-RAY DIFFRACTION100
4.7327-5.02860.19481410.15821958X-RAY DIFFRACTION100
5.0286-5.41590.18981430.16011961X-RAY DIFFRACTION100
5.4159-5.95920.25971430.18761969X-RAY DIFFRACTION100
5.9592-6.81750.22051470.20231966X-RAY DIFFRACTION100
6.8175-8.57420.2121340.20552005X-RAY DIFFRACTION100
8.5742-38.92670.24831460.20362015X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -5.9062 Å / Origin y: 12.675 Å / Origin z: -38.1613 Å
111213212223313233
T1.039 Å2-0.0143 Å20.0459 Å2-0.993 Å20.1056 Å2--0.9841 Å2
L0.6501 °20.4786 °2-0.2521 °2-1.4997 °2-0.4233 °2--0.3672 °2
S-0.0987 Å °0.3581 Å °0.2357 Å °-0.4021 Å °0.1305 Å °0.0659 Å °-0.1375 Å °0.1043 Å °-0.0442 Å °
Refinement TLS groupSelection details: all

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