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- PDB-6e3h: Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin -

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Basic information

Entry
Database: PDB / ID: 6e3h
TitleCrystal structure of S9-3-37 bound to H5 influenza hemagglutinin
Components
  • (Hemagglutinin ...) x 2
  • (antibody S9-3-37 ...) x 2
Keywordsviral protein/immune system / Antibody / Influenza virus / hemagglutinin / VIRAL PROTEIN / viral protein-immune system complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / 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 / virion membrane / identical protein binding
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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWu, N.C. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI127371 United States
CitationJournal: Cell Host Microbe / Year: 2018
Title: The D3-9 gene segment encodes for recurring and adaptable binding motifs in broadly neutralizing antibodies to influenza virus
Authors: Wu, N.C. / Yamayoshi, S. / Ito, M. / Uraki, R. / Kawaoka, Y. / Wilson, I.A.
History
DepositionJul 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.formula_weight / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity.formula_weight / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Data collection / Structure summary
Category: chem_comp / entity / pdbx_audit_support
Item: _chem_comp.type / _entity.formula_weight / _pdbx_audit_support.funding_organization
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 / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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 11, 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 HA1
B: Hemagglutinin HA2
L: antibody S9-3-37 light chain
H: antibody S9-3-37 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,44810
Polymers106,2034
Non-polymers2,2456
Water27015
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
L: antibody S9-3-37 light chain
H: antibody S9-3-37 heavy chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
L: antibody S9-3-37 light chain
H: antibody S9-3-37 heavy chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
L: antibody S9-3-37 light chain
H: antibody S9-3-37 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,34530
Polymers318,60912
Non-polymers6,73518
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area56660 Å2
ΔGint-137 kcal/mol
Surface area119240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.269, 157.269, 345.167
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1


Mass: 36648.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EP31, UniProt: Q6DQ33*PLUS
#2: Protein Hemagglutinin HA2


Mass: 20200.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EP31, UniProt: Q6DQ33*PLUS

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Antibody , 2 types, 2 molecules LH

#3: Antibody antibody S9-3-37 light chain


Mass: 24023.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody antibody S9-3-37 heavy chain


Mass: 25330.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 3 types, 6 molecules

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


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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.: 3
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, 15 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.87 Å3/Da / Density % sol: 68.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6000, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 36791 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 62 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.05 / Rsym value: 0.23 / Net I/σ(I): 16.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 21 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3616 / CC1/2: 0.8 / Rpim(I) all: 0.28 / Rsym value: 1.26 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000712data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FK0

2fk0


Resolution: 2.9→45.44 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.905 / SU B: 32.359 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.764 / ESU R Free: 0.34 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24774 1787 4.9 %RANDOM
Rwork0.20535 ---
obs0.20737 34961 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.182 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.24 Å20 Å2
2--0.47 Å20 Å2
3----1.54 Å2
Refinement stepCycle: 1 / Resolution: 2.9→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 147 15 7554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0157728
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176727
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.76710493
X-RAY DIFFRACTIONr_angle_other_deg0.3991.72915838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0165937
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41520.871287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.699151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.61537
X-RAY DIFFRACTIONr_chiral_restr0.0450.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218592
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021439
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_it1.0814.5683763
X-RAY DIFFRACTIONr_mcbond_other1.0814.5693764
X-RAY DIFFRACTIONr_mcangle_it1.8726.8494695
X-RAY DIFFRACTIONr_mcangle_other1.8726.8514696
X-RAY DIFFRACTIONr_scbond_it1.6054.8973965
X-RAY DIFFRACTIONr_scbond_other1.6054.8983966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8087.3155799
X-RAY DIFFRACTIONr_long_range_B_refined6.43589.129999
X-RAY DIFFRACTIONr_long_range_B_other6.43589.10230000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 122 -
Rwork0.32 2556 -
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)
10.44680.04230.760.502-0.27621.6247-0.00840.26230.0051-0.0552-0.0659-0.12520.07110.64830.07420.1080.05640.02950.40110.02120.263-56.971243.098218.1456
21.11430.23792.89462.7003-3.357313.51680.15680.4381-0.72370.35710.1856-1.1898-0.20371.0642-0.34241.01730.28730.18270.7202-0.02591.1336-48.464432.3986-14.7062
31.42020.0525-0.14241.3373-0.03981.9604-0.05930.2741-0.101-0.2781-0.0449-0.11980.12370.15180.10430.11470.03240.10150.11660.01780.1177-60.620436.5201-24.4066
41.22860.34910.88610.45240.230713.4331-0.04280.0914-0.0120.06540.0767-0.2001-0.03570.5258-0.03390.13770.03880.0380.17470.01490.295-62.364744.875719.8196
53.0242-0.08583.09990.3744-1.03495.7778-0.1929-0.07550.29840.1726-0.0886-0.0344-0.48970.34580.28140.27330.0266-0.05820.2983-0.03960.3303-61.312344.112251.5911
64.52090.57465.71731.63861.094612.35350.1382-0.1809-0.08070.0124-0.0883-0.02580.4712-0.2407-0.04980.1390.03820.05070.19490.01060.2871-63.540334.978240.5479
74.189-3.60434.96934.0205-3.69926.32910.35980.2195-0.0584-0.4446-0.24750.01860.49960.2338-0.11220.3636-0.0044-0.00050.3059-0.03240.3672-69.133943.3518-3.035
81.7345-0.4364.90721.5542-1.337720.6789-0.09080.02580.1324-0.0328-0.117-0.0373-0.1943-0.03920.20790.1404-0.00030.01540.18660.00590.3059-73.224649.275113.419
92.1199-0.15640.58011.8133-0.89886.5003-0.0197-0.4471-0.11220.36460.104-0.00980.11-0.1539-0.08430.1570.0180.01530.21620.02750.2031-67.015237.634362.881
105.789114.053813.360737.706438.401440.81040.5015-0.66560.3022-0.4727-1.05870.7379-1.7322-0.7060.55711.0114-0.02580.12770.7523-0.06760.5951-69.702945.297180.1158
112.0582-2.0604-1.04824.65122.98356.60880.01620.0655-0.24210.28850.13180.10810.4997-0.2122-0.1480.1616-0.0215-0.05360.12450.03540.2429-60.00518.629929.0356
122.77690.2292.31134.83151.53682.51390.15440.2954-0.3536-0.8468-0.13070.5224-0.1714-0.0661-0.02370.38720.0203-0.10930.5214-0.05950.3981-62.885815.192622.6325
130.7304-0.4831-0.00043.49780.8740.79570.03150.0089-0.13380.1490.0787-0.14270.3037-0.0497-0.11020.25240.0063-0.08080.1126-0.0170.1602-48.2810.747128.0173
146.3149-0.86322.43824.0226-1.39533.51270.4076-0.3397-0.56390.0722-0.2063-0.42361.06770.0309-0.20130.43740.0167-0.16640.1117-0.01970.4123-39.6142-18.776429.4277
1510.9012-2.36456.96661.8676-1.9067.6335-0.0043-0.06850.6719-0.4629-0.0698-0.61320.27940.32030.07420.2491-0.00660.08180.2738-0.03860.3262-34.002519.511525.7973
164.4232-1.1691-0.25682.64180.35672.6370.0743-0.10530.06740.06970.0287-0.18930.02590.2773-0.1030.091-0.0136-0.0480.1649-0.02170.1074-42.495121.508231.1602
173.91143.28251.9625.13581.80035.1448-0.26390.7257-0.9414-0.55420.522-1.18960.30250.6463-0.25820.30010.21550.01850.4224-0.31240.527-28.1475-11.240720.3575
186.38931.48812.09545.40513.17072.63310.08390.3696-0.6097-0.0856-0.0531-0.26310.45970.2355-0.03070.55070.13520.03990.3708-0.00270.569-31.2823-6.429820.4107
192.5223.38462.9985.13283.68563.99210.2120.5467-0.8025-0.39150.371-1.09030.56780.7488-0.5830.9050.25160.0490.9222-0.62181.1097-24.0788-17.185813.7142
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 75
2X-RAY DIFFRACTION2A76 - 82
3X-RAY DIFFRACTION3A83 - 288
4X-RAY DIFFRACTION4A289 - 324
5X-RAY DIFFRACTION5B1 - 28
6X-RAY DIFFRACTION6B29 - 60
7X-RAY DIFFRACTION7B61 - 74
8X-RAY DIFFRACTION8B75 - 106
9X-RAY DIFFRACTION9B107 - 169
10X-RAY DIFFRACTION10B170 - 175
11X-RAY DIFFRACTION11H1 - 42
12X-RAY DIFFRACTION12H43 - 81
13X-RAY DIFFRACTION13H82 - 170
14X-RAY DIFFRACTION14H171 - 214
15X-RAY DIFFRACTION15L1 - 24
16X-RAY DIFFRACTION16L25 - 106
17X-RAY DIFFRACTION17L107 - 151
18X-RAY DIFFRACTION18L152 - 181
19X-RAY DIFFRACTION19L182 - 214

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  • 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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