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Basic information

Entry
Database: PDB / ID: 4ju0
TitleCrystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E complexed with human receptor analogue LSTc
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / virus attachment / membrane fusion
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; 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 / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.908 Å
AuthorsZhang, W. / Shi, Y. / Qi, J. / Gao, F. / Li, Q. / Fan, Z. / Yan, J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2013
Title: Molecular basis of the receptor binding specificity switch of the hemagglutinins from both the 1918 and 2009 pandemic influenza A viruses by a D225G substitution
Authors: Zhang, W. / Shi, Y. / Qi, J. / Gao, F. / Li, Q. / Fan, Z. / Yan, J. / Gao, G.F.
History
DepositionMar 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_ref_seq_dif / 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_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_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.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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,88825
Polymers327,64312
Non-polymers6,24513
Water3,333185
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,19912
Polymers163,8226
Non-polymers3,3776
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36370 Å2
ΔGint-134 kcal/mol
Surface area56330 Å2
MethodPISA
2
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,68913
Polymers163,8226
Non-polymers2,8687
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35430 Å2
ΔGint-149 kcal/mol
Surface area56260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.871, 116.809, 116.503
Angle α, β, γ (deg.)62.06, 77.76, 81.54
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESSEQ 7:75 OR RESSEQ 78:327 )
21CHAIN C AND (RESSEQ 7:75 OR RESSEQ 78:327 )
31CHAIN E AND (RESSEQ 7:75 OR RESSEQ 78:327 )
41CHAIN G AND (RESSEQ 7:75 OR RESSEQ 78:327 )
51CHAIN I AND (RESSEQ 7:75 OR RESSEQ 78:327 )
61CHAIN K AND (RESSEQ 7:75 OR RESSEQ 78:327 )
12CHAIN B AND (RESSEQ 2:157 )
22CHAIN D AND (RESSEQ 2:157 )
32CHAIN F AND (RESSEQ 2:157 )
42CHAIN H AND (RESSEQ 2:157 )
52CHAIN J AND (RESSEQ 2:157 )
62CHAIN L AND (RESSEQ 2:157 )

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPSERSERCHAIN A AND (RESSEQ 7:75 OR RESSEQ 78:327 )AA7 - 751 - 69
121THRTHRILEILECHAIN A AND (RESSEQ 7:75 OR RESSEQ 78:327 )AA78 - 32772 - 321
211ASPASPSERSERCHAIN C AND (RESSEQ 7:75 OR RESSEQ 78:327 )CC7 - 751 - 69
221THRTHRILEILECHAIN C AND (RESSEQ 7:75 OR RESSEQ 78:327 )CC78 - 32772 - 321
311ASPASPSERSERCHAIN E AND (RESSEQ 7:75 OR RESSEQ 78:327 )EE7 - 751 - 69
321THRTHRILEILECHAIN E AND (RESSEQ 7:75 OR RESSEQ 78:327 )EE78 - 32772 - 321
411ASPASPSERSERCHAIN G AND (RESSEQ 7:75 OR RESSEQ 78:327 )GG7 - 751 - 69
421THRTHRILEILECHAIN G AND (RESSEQ 7:75 OR RESSEQ 78:327 )GG78 - 32772 - 321
511ASPASPSERSERCHAIN I AND (RESSEQ 7:75 OR RESSEQ 78:327 )II7 - 751 - 69
521THRTHRILEILECHAIN I AND (RESSEQ 7:75 OR RESSEQ 78:327 )II78 - 32772 - 321
611ASPASPSERSERCHAIN K AND (RESSEQ 7:75 OR RESSEQ 78:327 )KK7 - 751 - 69
621THRTHRILEILECHAIN K AND (RESSEQ 7:75 OR RESSEQ 78:327 )KK78 - 32772 - 321
112LEULEUTYRTYRCHAIN B AND (RESSEQ 2:157 )BB2 - 1572 - 157
212LEULEUTYRTYRCHAIN D AND (RESSEQ 2:157 )DD2 - 1572 - 157
312LEULEUTYRTYRCHAIN F AND (RESSEQ 2:157 )FF2 - 1572 - 157
412LEULEUTYRTYRCHAIN H AND (RESSEQ 2:157 )HH2 - 1572 - 157
512LEULEUTYRTYRCHAIN J AND (RESSEQ 2:157 )JJ2 - 1572 - 157
612LEULEUTYRTYRCHAIN L AND (RESSEQ 2:157 )LL2 - 1572 - 157

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Hemagglutinin


Mass: 35830.457 Da / Num. of mol.: 6 / Fragment: UNP residues 18-339 / Mutation: D228E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/California/04/2009 H1N1 / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C3W5S1
#2: Protein
Hemagglutinin


Mass: 18776.758 Da / Num. of mol.: 6 / Fragment: UNP residues 345-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/California/04/2009 H1N1 / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C3W5S1

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Sugars , 4 types, 13 molecules

#3: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-3/a3-b1_b4-c1_c6-d2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}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.: 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
#5: 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.: 6
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
#6: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 185 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 6000, 5% MPD, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 62952 / Num. obs: 62952 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.9→3 Å / % possible all: 74.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AL4

3al4


Resolution: 2.908→40.224 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7666 / SU ML: 0.38 / σ(F): 0.07 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2976 5.06 %RANDOM
Rwork0.2405 ---
all0.2427 59949 --
obs0.2427 58849 88.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.808 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 328.43 Å2 / Biso mean: 67.8359 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1--2.858 Å2-1.1501 Å20.8529 Å2
2--4.5963 Å220.0544 Å2
3----1.7383 Å2
Refinement stepCycle: LAST / Resolution: 2.908→40.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22910 0 412 185 23507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323929
X-RAY DIFFRACTIONf_angle_d0.96832414
X-RAY DIFFRACTIONf_chiral_restr0.1343558
X-RAY DIFFRACTIONf_plane_restr0.0034135
X-RAY DIFFRACTIONf_dihedral_angle_d20.0958670
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2489X-RAY DIFFRACTIONPOSITIONAL0.044
12C2489X-RAY DIFFRACTIONPOSITIONAL0.044
13E2489X-RAY DIFFRACTIONPOSITIONAL0.054
14G2492X-RAY DIFFRACTIONPOSITIONAL0.016
15I2489X-RAY DIFFRACTIONPOSITIONAL0.043
16K2489X-RAY DIFFRACTIONPOSITIONAL0.055
21B1248X-RAY DIFFRACTIONPOSITIONAL0.034
22D1248X-RAY DIFFRACTIONPOSITIONAL0.034
23F1253X-RAY DIFFRACTIONPOSITIONAL0.049
24H1253X-RAY DIFFRACTIONPOSITIONAL0.012
25J1248X-RAY DIFFRACTIONPOSITIONAL0.038
26L1253X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.908-2.95570.389860.31281525161152
2.9557-3.00660.39371110.32091872198362
3.0066-3.06130.37321180.3372074219268
3.0613-3.12020.44491120.3182254236675
3.1202-3.18380.38631310.30692484261581
3.1838-3.2530.35691260.28742553267985
3.253-3.32870.30971360.27462704284088
3.3287-3.41190.35481430.26292635277889
3.4119-3.50410.30481620.25732775293791
3.5041-3.60710.29561260.23882774290092
3.6071-3.72340.27991500.24282883303394
3.7234-3.85640.27111630.22632834299795
3.8564-4.01070.25961610.21432876303795
4.0107-4.19310.22791550.20392921307696
4.1931-4.41390.23661470.20612908305597
4.4139-4.690.20821520.19422945309797
4.69-5.05150.25361790.20672934311398
5.0515-5.55870.26321510.19932982313398
5.5587-6.36030.25931670.21912937310498
6.3603-8.00290.24241580.23082989314799
8.0029-40.22770.2311420.2263014315699
Refinement TLS params.Method: refined / Origin x: -21.2394 Å / Origin y: -28.0783 Å / Origin z: -32.2782 Å
111213212223313233
T-0.0503 Å20.04 Å20.019 Å2-0.0573 Å2-0.0182 Å2--0.0252 Å2
L0.2007 °20.0666 °20.0465 °2-0.3676 °2-0.1362 °2--0.3353 °2
S0.0379 Å °-0.0392 Å °-0.03 Å °0.1022 Å °-0.0444 Å °-0.0475 Å °-0.0795 Å °-0.0152 Å °-0.0015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA7 - 328
2X-RAY DIFFRACTION1ALLB1 - 162
3X-RAY DIFFRACTION1ALLC7 - 327
4X-RAY DIFFRACTION1ALLD1 - 164
5X-RAY DIFFRACTION1ALLE7 - 327
6X-RAY DIFFRACTION1ALLF2 - 162
7X-RAY DIFFRACTION1ALLG7 - 328
8X-RAY DIFFRACTION1ALLH1 - 162
9X-RAY DIFFRACTION1ALLI7 - 327
10X-RAY DIFFRACTION1ALLJ1 - 164
11X-RAY DIFFRACTION1ALLK7 - 327
12X-RAY DIFFRACTION1ALLL2 - 162
13X-RAY DIFFRACTION1ALLA801 - 804
14X-RAY DIFFRACTION1ALLC601 - 606
15X-RAY DIFFRACTION1ALLE601 - 606
16X-RAY DIFFRACTION1ALLG401 - 405
17X-RAY DIFFRACTION1ALLI601 - 605
18X-RAY DIFFRACTION1ALLK601 - 603
19X-RAY DIFFRACTION1ALLA901 - 922
20X-RAY DIFFRACTION1ALLB201 - 206
21X-RAY DIFFRACTION1ALLC603 - 720
22X-RAY DIFFRACTION1ALLD201 - 205
23X-RAY DIFFRACTION1ALLE603 - 718
24X-RAY DIFFRACTION1ALLF201 - 211
25X-RAY DIFFRACTION1ALLG401 - 516
26X-RAY DIFFRACTION1ALLH201 - 206
27X-RAY DIFFRACTION1ALLI602 - 726
28X-RAY DIFFRACTION1ALLJ201 - 222
29X-RAY DIFFRACTION1ALLK603 - 726
30X-RAY DIFFRACTION1ALLL201 - 208

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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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