[English] 日本語
Yorodumi
- PDB-6nhr: Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza viru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nhr
TitleCrystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin HA2 I45F mutant
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN
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 / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Science / Year: 2020
Title: Different genetic barriers for resistance to HA stem antibodies in influenza H3 and H1 viruses.
Authors: Wu, N.C. / Thompson, A.J. / Lee, J.M. / Su, W. / Arlian, B.M. / Xie, J. / Lerner, R.A. / Yen, H.L. / Bloom, J.D. / Wilson, I.A.
History
DepositionDec 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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 / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,72419
Polymers166,6566
Non-polymers5,06813
Water15,241846
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38290 Å2
ΔGint-59 kcal/mol
Surface area57320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.378, 131.409, 72.280
Angle α, β, γ (deg.)90.00, 98.07, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPROAA9 - 3241 - 316
21PROPROPROPROCC9 - 3241 - 316
12PROPROPROPROAA9 - 3241 - 316
22PROPROPROPROEE9 - 3241 - 316
13GLYGLYARGARGBB1 - 1701 - 170
23GLYGLYARGARGDD1 - 1701 - 170
14GLYGLYARGARGBB1 - 1701 - 170
24GLYGLYARGARGFF1 - 1701 - 170
15PROPROGLUGLUCC9 - 3251 - 317
25PROPROGLUGLUEE9 - 3251 - 317
16GLYGLYPHEPHEDD1 - 1711 - 171
26GLYGLYPHEPHEFF1 - 1711 - 171

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 35320.781 Da / Num. of mol.: 3 / Fragment: residues 27-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H9XC94
#2: Protein Hemagglutinin HA2 chain


Mass: 20231.330 Da / Num. of mol.: 3 / Fragment: residues 346-521 / Mutation: I45F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7

-
Sugars , 5 types, 13 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 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
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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: 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.: 7
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

-
Non-polymers , 1 types, 846 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 846 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 38% 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 110282 / % possible obs: 97.4 % / Redundancy: 5.6 % / CC1/2: 1 / Rpim(I) all: 0.05 / Rsym value: 0.1 / Net I/σ(I): 20
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 13871 / CC1/2: 0.77 / Rpim(I) all: 0.4 / Rsym value: 0.83 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000712data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNK
Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.6 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21614 5420 5 %RANDOM
Rwork0.18432 ---
obs0.18588 103850 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å20.87 Å2
2--0.32 Å20 Å2
3----1.59 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11529 0 332 846 12707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912170
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210756
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.96916553
X-RAY DIFFRACTIONr_angle_other_deg0.941325114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95151467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28424.724580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.553151976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4141570
X-RAY DIFFRACTIONr_chiral_restr0.0860.21857
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022418
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_it0.9942.675877
X-RAY DIFFRACTIONr_mcbond_other0.9942.675876
X-RAY DIFFRACTIONr_mcangle_it1.6143.9997338
X-RAY DIFFRACTIONr_mcangle_other1.61347339
X-RAY DIFFRACTIONr_scbond_it1.6183.0556292
X-RAY DIFFRACTIONr_scbond_other1.6183.0556293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.754.5229215
X-RAY DIFFRACTIONr_long_range_B_refined5.42352.40149508
X-RAY DIFFRACTIONr_long_range_B_other5.32652.14849025
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A202240.05
12C202240.05
21A200180.07
22E200180.07
31B107200.06
32D107200.06
41B107160.06
42F107160.06
51C200620.07
52E200620.07
61D109120.05
62F109120.05
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 404 -
Rwork0.267 7726 -
obs--98.19 %
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)
11.03250.06770.01111.63520.31190.5126-0.0418-0.2316-0.30890.0798-0.0398-0.01250.2116-0.13980.08160.1486-0.0640.02710.23190.08350.123-26.36650.730125.8376
216.7845-1.9963-0.34911.36270.56022.24330.03610.2109-0.2809-0.1919-0.14540.05760.09-0.34170.10930.2998-0.0806-0.01310.16010.0270.1646-29.0783-11.87579.7288
30.85170.38810.12131.48580.19110.3416-0.0313-0.20770.02670.0996-0.02670.03010.0591-0.17430.0580.0618-0.0211-0.00460.26040.020.0319-25.546115.017929.1594
42.64420.70420.67051.02521.30076.4055-0.0638-0.28680.37730.25490.0264-0.1903-0.2698-0.04460.03730.18860.0706-0.15430.2088-0.20420.2672-16.488260.730448.1441
54.52425.72673.276212.67849.10169.78460.1243-0.2625-0.03980.8348-0.0771-0.14490.4245-0.2117-0.04720.13970.0939-0.06680.2759-0.05710.1066-28.13244.412243.9112
68.1409-1.2937-6.37122.67992.078911.2102-0.0692-0.27790.06940.16340.0760.02760.1315-0.0223-0.00680.0677-0.0133-0.03970.15390.0420.0726-25.423614.074321.6652
70.4059-0.1777-0.01753.32312.212.0918-0.1095-0.23510.26430.13220.1333-0.1324-0.1822-0.0427-0.02370.14950.1044-0.09720.2565-0.16250.2123-25.077557.728540.3109
80.42740.48130.2962.05091.4291.4536-0.0783-0.12710.0332-0.0285-0.08180.37330.0225-0.36730.16010.04320.0212-0.04210.33530.0140.1933-52.053225.484813.922
91.1499-0.07670.62922.8066-1.36173.74620.03780.04890.0578-0.3696-0.3422-0.13870.58610.33660.30440.1553-0.02050.01310.21870.06130.1152-47.0424-2.365-9.3551
100.54160.31950.4271.81341.28371.1578-0.0863-0.14750.0652-0.0614-0.05040.3498-0.0969-0.23870.13670.07950.0348-0.02410.30270.01380.1984-49.7831.541817.6086
111.5634-0.3528-0.82553.24251.89663.6713-0.0569-0.33980.3155-0.0327-0.13080.3001-0.4205-0.5210.18760.16490.2252-0.0780.3618-0.1560.2842-46.582462.811633.5589
120.01110.10870.036339.158323.146213.97350.04580.0745-0.0088-1.32750.0777-0.4989-0.6182-0.4965-0.12350.6755-0.20390.03141.1418-0.11360.5049-44.031640.524513.2359
130.4746-0.16870.03622.29180.82150.8743-0.1375-0.21620.24850.09190.07970.1944-0.2273-0.24680.05770.14330.1583-0.05580.2758-0.10910.2322-39.286955.414529.5769
140.5314-0.3905-0.27281.3810.86741.01580.02350.11840.0772-0.14460.0024-0.0651-0.037-0.0851-0.0260.0308-0.0186-0.01310.13220.04270.0589-16.950522.9821-4.4738
151.76440.07550.34830.65630.15061.7707-0.03160.0329-0.30420.0205-0.00990.07710.317-0.13520.04140.1228-0.07050.01980.08560.00110.0776-17.9791-4.4868-4.911
160.7996-0.8689-0.41582.14361.25571.22460.01010.05090.2313-0.18160.0851-0.1162-0.2347-0.0187-0.09520.08040.008-0.01020.10060.03860.1353-21.023739.24253.0336
170.939-0.6019-0.05914.0492-0.01511.21430.0382-0.04960.4405-0.41240.0433-0.3835-0.52070.0349-0.08150.28890.00730.0020.04-0.0860.345-20.476268.124419.6001
185.25753.12641.04454.05761.76732.0232-0.1147-0.12950.0954-0.19420.0639-0.038-0.27490.0320.05070.1133-0.01750.00110.18650.00990.0499-21.684926.49235.2466
190.60960.64330.38033.70281.68121.3381-0.0689-0.06940.3465-0.03250.1233-0.1098-0.3507-0.0911-0.05450.23920.0888-0.03470.1119-0.08290.3297-24.554763.132924.9105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 200
2X-RAY DIFFRACTION2A201 - 231
3X-RAY DIFFRACTION3A232 - 329
4X-RAY DIFFRACTION4B1 - 35
5X-RAY DIFFRACTION5B36 - 58
6X-RAY DIFFRACTION6B59 - 75
7X-RAY DIFFRACTION7B76 - 172
8X-RAY DIFFRACTION8C9 - 119
9X-RAY DIFFRACTION9C120 - 258
10X-RAY DIFFRACTION10C259 - 325
11X-RAY DIFFRACTION11D1 - 55
12X-RAY DIFFRACTION12D56 - 60
13X-RAY DIFFRACTION13D61 - 171
14X-RAY DIFFRACTION14E9 - 155
15X-RAY DIFFRACTION15E156 - 263
16X-RAY DIFFRACTION16E264 - 325
17X-RAY DIFFRACTION17F1 - 56
18X-RAY DIFFRACTION18F57 - 72
19X-RAY DIFFRACTION19F73 - 171

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • 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

-
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

Read more