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- PDB-6bkr: Crystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus ... -

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Basic information

Entry
Database: PDB / ID: 6bkr
TitleCrystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus hemagglutinin in complex with 6'-SLN
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / Influenza / Hemagglutinin / Receptor
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
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
6'-sialyl-N-acetyllactosamine / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsWu, N.C. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI127371 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI114730 United States
CitationJournal: Nat Commun / Year: 2018
Title: A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site.
Authors: Wu, N.C. / Thompson, A.J. / Xie, J. / Lin, C.W. / Nycholat, C.M. / Zhu, X. / Lerner, R.A. / Paulson, J.C. / Wilson, I.A.
History
DepositionNov 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 14, 2018Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry
Item: _atom_site.auth_seq_id / _entity.pdbx_description ..._atom_site.auth_seq_id / _entity.pdbx_description / _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_special_symmetry.auth_seq_id
Revision 2.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / 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 / _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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_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.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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 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 HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,76110
Polymers55,9152
Non-polymers3,8478
Water9,746541
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,28430
Polymers167,7446
Non-polymers11,54024
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area48240 Å2
ΔGint31 kcal/mol
Surface area59120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.458, 100.458, 385.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-538-

HOH

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1 chain


Mass: 35874.480 Da / Num. of mol.: 1 / Mutation: S219F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A4GYF9
#2: Protein Hemagglutinin HA2 chain


Mass: 20040.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B4UPH9

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Sugars , 5 types, 8 molecules

#3: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 1
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
#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.: 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
#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}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 / N-Acetylglucosamine


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, 541 molecules

#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M bicine pH 9 and 42% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 74408 / % possible obs: 99.3 % / Redundancy: 18 % / Biso Wilson estimate: 21 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.09 / Net I/σ(I): 52
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 3.6 / CC1/2: 0.95 / Rpim(I) all: 0.13 / Rsym value: 0.48 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000712data processing
HKL-2000712data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5N

4o5n


Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.244 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18332 3743 5 %RANDOM
Rwork0.15911 ---
obs0.16035 70663 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å2-0 Å2
2--0.5 Å2-0 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 255 543 4667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194300
X-RAY DIFFRACTIONr_bond_other_d0.0020.023960
X-RAY DIFFRACTIONr_angle_refined_deg1.532.015866
X-RAY DIFFRACTIONr_angle_other_deg0.95739180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71924.724199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59315701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8671525
X-RAY DIFFRACTIONr_chiral_restr0.0890.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024756
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02970
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_it0.8451.6331984
X-RAY DIFFRACTIONr_mcbond_other0.8451.6331983
X-RAY DIFFRACTIONr_mcangle_it1.4032.4452483
X-RAY DIFFRACTIONr_mcangle_other1.4022.4452484
X-RAY DIFFRACTIONr_scbond_it1.5132.22316
X-RAY DIFFRACTIONr_scbond_other1.5122.22316
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4943.2463371
X-RAY DIFFRACTIONr_long_range_B_refined6.74318.28718348
X-RAY DIFFRACTIONr_long_range_B_other6.00217.54117765
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.762→1.808 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 281 -
Rwork0.262 5085 -
obs--98.6 %
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)
10.3266-0.03570.22110.2519-0.1061.49020.06720.0894-0.0245-0.10580.03220.11180.0809-0.1944-0.09940.0649-0.0148-0.05530.09710.02790.101730.0315-35.1388-60.6453
22.3110.4039-0.33821.5018-0.29582.12740.05410.4020.1301-0.3669-0.03220.2176-0.0274-0.3352-0.02180.22320.0387-0.11290.33810.05230.076425.6599-27.1599-94.5465
32.1311-0.9801-1.1763.02682.39524.38530.17870.45380.0291-0.47510.0324-0.0619-0.02630.0816-0.2110.26960.02-0.06860.30940.04560.048535.2764-30.257-96.8813
46.73692.04862.497521.45711.39813.57190.07030.18220.125-0.30650.0522-0.2363-0.21050.1593-0.12250.1238-0.01880.00880.23290.08940.070941.8373-19.2482-90.429
52.2295-1.0153-0.44271.39180.65242.00350.12830.36690.029-0.33290.01180.1026-0.0386-0.0339-0.14010.20310.0037-0.0710.25180.04830.046534.6752-28.8646-90.4104
60.2432-0.01910.38870.2505-0.02661.47530.04620.0085-0.0212-0.04090.03080.10530.0734-0.1738-0.0770.051-0.018-0.03770.09040.0330.112832.5356-36.5311-50.2582
712.20314.1472-1.76782.9372-0.19962.34890.0059-0.1651-0.16170.09220.0302-0.05430.22080.0203-0.03620.1026-0.0018-0.00010.08750.01470.103340.9917-40.8477-13.6556
80.6490.7605-1.8241.581-2.27996.60010.02830.00170.03140.0430.00590.1306-0.1459-0.3078-0.03420.0415-0.01080.02020.12520.02760.121131.1555-33.8683-14.514
91.0659-0.178-0.94190.5656-0.21841.86880.01120.0394-0.04390.06790.03530.1099-0.0081-0.192-0.04650.09160.0029-0.02280.10530.02270.113236.5576-31.0902-55.1882
100.3972-0.1088-1.24250.2750.36556.54360.03270.0003-0.0198-0.0110.00470.0244-0.01090.0412-0.03730.0635-0.0131-0.00770.07530.00230.120745.515-33.8001-38.2486
112.30890.35040.65011.94770.4252.1877-0.0011-0.19160.1160.18260.01080.1080.0188-0.0297-0.00970.0669-0.0240.0460.0920.01210.068436.6209-30.93484.9375
1228.1735-5.91595.97753.49181.04115.4345-0.3898-2.4994-0.6470.4780.6434-0.56810.77170.3777-0.25350.63280-0.19820.73040.38080.591845.9801-34.999414.6431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 131
2X-RAY DIFFRACTION2A132 - 174
3X-RAY DIFFRACTION3A175 - 200
4X-RAY DIFFRACTION4A201 - 214
5X-RAY DIFFRACTION5A215 - 258
6X-RAY DIFFRACTION6A259 - 325
7X-RAY DIFFRACTION7B1 - 17
8X-RAY DIFFRACTION8B18 - 53
9X-RAY DIFFRACTION9B54 - 71
10X-RAY DIFFRACTION10B72 - 125
11X-RAY DIFFRACTION11B126 - 168
12X-RAY DIFFRACTION12B169 - 173

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  • 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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