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- PDB-4jtx: Crystal structure of 2009 pandemic influenza virus hemagglutinin ... -

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Basic information

Entry
Database: PDB / ID: 4jtx
TitleCrystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E
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 / 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 / metal ion binding / 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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.997 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_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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_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_seq_id / _struct_conn.ptnr2_label_asym_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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 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)332,38821
Polymers329,78812
Non-polymers2,6009
Water2,648147
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,40611
Polymers164,8946
Non-polymers1,5125
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32370 Å2
ΔGint-150 kcal/mol
Surface area57200 Å2
MethodPISA
2
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,98210
Polymers164,8946
Non-polymers1,0884
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31880 Å2
ΔGint-154 kcal/mol
Surface area56990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.688, 119.012, 123.605
Angle α, β, γ (deg.)115.14, 94.96, 96.78
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Hemagglutinin


Mass: 35987.652 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: 18976.951 Da / Num. of mol.: 6 / Fragment: UNP residues 345-510
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
#3: 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.: 3
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
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.15 %
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: 2.997→50 Å / Num. all: 64342 / Num. obs: 64342 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 66.8

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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: 2.997→46.748 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8172 / SU ML: 0.34 / σ(F): 0.08 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 3099 5.11 %RANDOM
Rwork0.21 ---
all0.2117 60635 --
obs0.2117 60635 88.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.496 Å2 / ksol: 0.292 e/Å3
Displacement parametersBiso max: 236.82 Å2 / Biso mean: 60.6506 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1-16.7963 Å2-4.8772 Å2-0.011 Å2
2---2.4652 Å29.012 Å2
3----14.3312 Å2
Refinement stepCycle: LAST / Resolution: 2.997→46.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22962 0 168 147 23277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423771
X-RAY DIFFRACTIONf_angle_d0.95832176
X-RAY DIFFRACTIONf_chiral_restr0.1053485
X-RAY DIFFRACTIONf_plane_restr0.0044137
X-RAY DIFFRACTIONf_dihedral_angle_d17.1158537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9974-3.04430.3101770.31931376145346
3.0443-3.09420.3322950.3071719181457
3.0942-3.14750.3182960.29461951204766
3.1475-3.20470.35251180.29082178229673
3.2047-3.26630.31141300.27132353248380
3.2663-3.3330.3011310.26382487261883
3.333-3.40540.32881450.2572595274088
3.4054-3.48460.31481420.24862679282191
3.4846-3.57180.26811620.23412753291593
3.5718-3.66830.2641400.2212761290193
3.6683-3.77620.251450.21192803294894
3.7762-3.8980.25251380.20182818295696
3.898-4.03730.22571500.18612902305296
4.0373-4.19880.2251570.18432871302896
4.1988-4.38980.19621600.17932834299497
4.3898-4.6210.18461650.15662897306298
4.621-4.91020.19751530.16622902305598
4.9102-5.28890.20831410.17622948308998
5.2889-5.82020.21921510.17782921307298
5.8202-6.66040.22521680.19642905307399
6.6604-8.38350.21641760.19792937311399
8.3835-46.75320.22221590.20742946310599
Refinement TLS params.Method: refined / Origin x: -32.245 Å / Origin y: 83.0986 Å / Origin z: 3.946 Å
111213212223313233
T0.1069 Å20.0045 Å20.0238 Å2-0.1159 Å20.0135 Å2--0.0708 Å2
L0.1074 °2-0.0155 °20.0195 °2-0.2224 °20.08 °2---0.0603 °2
S-0.0079 Å °0.0157 Å °0.0292 Å °-0.0943 Å °-0.0294 Å °-0.0598 Å °-0.0037 Å °-0.0154 Å °-0.0011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA6 - 328
2X-RAY DIFFRACTION1ALLB1 - 162
3X-RAY DIFFRACTION1ALLC7 - 328
4X-RAY DIFFRACTION1ALLD1 - 164
5X-RAY DIFFRACTION1ALLE7 - 327
6X-RAY DIFFRACTION1ALLF2 - 162
7X-RAY DIFFRACTION1ALLG7 - 328
8X-RAY DIFFRACTION1ALLH1 - 162
9X-RAY DIFFRACTION1ALLI7 - 328
10X-RAY DIFFRACTION1ALLJ1 - 166
11X-RAY DIFFRACTION1ALLK7 - 328
12X-RAY DIFFRACTION1ALLL2 - 162
13X-RAY DIFFRACTION1ALLA601 - 603
14X-RAY DIFFRACTION1ALLC601 - 603
15X-RAY DIFFRACTION1ALLE601
16X-RAY DIFFRACTION1ALLG601
17X-RAY DIFFRACTION1ALLI601 - 603
18X-RAY DIFFRACTION1ALLK601
19X-RAY DIFFRACTION1ALLA701 - 718
20X-RAY DIFFRACTION1ALLB201 - 210
21X-RAY DIFFRACTION1ALLC701 - 716
22X-RAY DIFFRACTION1ALLD201 - 209
23X-RAY DIFFRACTION1ALLE701 - 714
24X-RAY DIFFRACTION1ALLF201 - 211
25X-RAY DIFFRACTION1ALLG701 - 714
26X-RAY DIFFRACTION1ALLH201 - 205
27X-RAY DIFFRACTION1ALLI701 - 711
28X-RAY DIFFRACTION1ALLJ201 - 209
29X-RAY DIFFRACTION1ALLK701 - 721
30X-RAY DIFFRACTION1ALLL201 - 209

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