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- PDB-4juh: Crystal structure of 1918 pandemic influenza virus hemagglutinin ... -

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Basic information

Entry
Database: PDB / ID: 4juh
TitleCrystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G complexed with avian receptor analogue LSTa
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 / 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
3'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 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 / 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_unobs_or_zero_occ_atoms / 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_seq_id / _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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,42910
Polymers165,4826
Non-polymers1,9484
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30920 Å2
ΔGint-123 kcal/mol
Surface area59710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.986, 243.195, 72.208
Angle α, β, γ (deg.)90.00, 119.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin


Mass: 35710.066 Da / Num. of mol.: 3 / Fragment: Hemagglutinin HA1 chain, UNP residues 18-339 / Mutation: D225G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/18 (H1N1) / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9WFX3
#2: Protein Hemagglutinin


Mass: 19450.465 Da / Num. of mol.: 3 / Fragment: Hemagglutinin HA2 chain, UNP residues 345-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/18 (H1N1) / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9WFX3
#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: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-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_b3-c2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3.32 Å3/Da / Density % sol: 62.96 %
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: 2.8→50 Å / Num. all: 52336 / Num. obs: 52336 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 45.71 Å2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99.7

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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: 1RUZ

1ruz


Resolution: 2.805→38.403 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8203 / SU ML: 0.32 / σ(F): 0.06 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2532 5.1 %RANDOM
Rwork0.2014 ---
all0.2037 49662 --
obs0.2037 49662 94.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.909 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 202.79 Å2 / Biso mean: 54.7595 Å2 / Biso min: 16.53 Å2
Baniso -1Baniso -2Baniso -3
1-8.8186 Å2-0 Å27.433 Å2
2---12.4619 Å2-0 Å2
3---3.6433 Å2
Refinement stepCycle: LAST / Resolution: 2.805→38.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11547 0 129 199 11875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511975
X-RAY DIFFRACTIONf_angle_d0.82116234
X-RAY DIFFRACTIONf_chiral_restr0.0811767
X-RAY DIFFRACTIONf_plane_restr0.0052096
X-RAY DIFFRACTIONf_dihedral_angle_d20.1974300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8046-2.85850.31521070.2672180228778
2.8585-2.91680.32611330.25742398253186
2.9168-2.98020.2781220.26092439256188
2.9802-3.04950.25881230.24052500262390
3.0495-3.12570.28671290.23432580270992
3.1257-3.21020.2791400.23022517265793
3.2102-3.30460.27721410.23172640278194
3.3046-3.41120.26851270.22042621274895
3.4112-3.53310.25741370.21612634277196
3.5331-3.67440.25161720.19532708288097
3.6744-3.84150.25571440.1892708285298
3.8415-4.04380.21511510.17592709286098
4.0438-4.29690.23581360.16332732286898
4.2969-4.62810.18881440.14942731287599
4.6281-5.09290.18541610.16012743290499
5.0929-5.82770.20491530.16582729288299
5.8277-7.33390.2371650.19322776294199
7.3339-38.4070.25871470.20322785293299
Refinement TLS params.Method: refined / Origin x: -0.1149 Å / Origin y: -36.1981 Å / Origin z: 19.4559 Å
111213212223313233
T0.1874 Å2-0.0232 Å20.0127 Å2-0.2108 Å2-0.002 Å2--0.1824 Å2
L0.1031 °2-0.0114 °2-0.0084 °2-0.6436 °20.2081 °2--0.255 °2
S-0.0188 Å °0.0089 Å °-0.048 Å °0.1128 Å °-0.0109 Å °0.0731 Å °0.1314 Å °-0.0266 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 327
2X-RAY DIFFRACTION1allB501 - 670
3X-RAY DIFFRACTION1allC5 - 327
4X-RAY DIFFRACTION1allD501 - 664
5X-RAY DIFFRACTION1allE5 - 327
6X-RAY DIFFRACTION1allF501 - 665
7X-RAY DIFFRACTION1allA801 - 805
8X-RAY DIFFRACTION1allC801 - 802
9X-RAY DIFFRACTION1allE801 - 802
10X-RAY DIFFRACTION1allA803 - 953
11X-RAY DIFFRACTION1allB701 - 723
12X-RAY DIFFRACTION1allC901 - 951
13X-RAY DIFFRACTION1allD701 - 709
14X-RAY DIFFRACTION1allE901 - 946
15X-RAY DIFFRACTION1allF701 - 717

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