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Basic information

Entry
Database: PDB / ID: 4jtv
TitleCrystal structure of 2009 pandemic influenza virus hemagglutinin 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
6'-sialyl-N-acetyllactosamine / N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
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 / 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 / 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 / _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_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_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_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_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
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

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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)331,65926
Polymers325,67912
Non-polymers5,97914
Water4,936274
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,71815
Polymers162,8406
Non-polymers3,8799
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36540 Å2
ΔGint-121 kcal/mol
Surface area56070 Å2
MethodPISA
2
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,94111
Polymers162,8406
Non-polymers2,1015
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33690 Å2
ΔGint-162 kcal/mol
Surface area56120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.722, 117.321, 117.393
Angle α, β, γ (deg.)61.78, 81.82, 77.42
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Hemagglutinin /


Mass: 35719.320 Da / Num. of mol.: 6 / Fragment: UNP residues 18-338
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: 18560.566 Da / Num. of mol.: 6 / Fragment: UNP residues 345-506
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 , 5 types, 14 molecules

#3: 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.: 3
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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: 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.: 2
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
#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: 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.: 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
#7: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / 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, 274 molecules

#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG6000, 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: 53767 / Num. obs: 53767 / % possible obs: 88.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 59.9

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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→38.391 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.764 / SU ML: 0.39 / σ(F): 0.08 / Phase error: 30.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 2509 5.01 %RANDOM
Rwork0.2239 ---
all0.2264 50057 --
obs0.2264 50057 81.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.391 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 362.75 Å2 / Biso mean: 84.6187 Å2 / Biso min: 24.34 Å2
Baniso -1Baniso -2Baniso -3
1--23.9705 Å25.1518 Å2-7.7315 Å2
2--41.2079 Å232.3247 Å2
3----17.2374 Å2
Refinement stepCycle: LAST / Resolution: 2.997→38.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22861 0 393 274 23528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01123857
X-RAY DIFFRACTIONf_angle_d1.13532313
X-RAY DIFFRACTIONf_chiral_restr0.1383542
X-RAY DIFFRACTIONf_plane_restr0.0044126
X-RAY DIFFRACTIONf_dihedral_angle_d21.118623
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 (%)
2.9972-3.05490.3492550.33411068112333
3.0549-3.11720.4305890.3081695178453
3.1172-3.18490.3851990.30251976207560
3.1849-3.2590.36781030.30052043214663
3.259-3.34040.34641260.28652292241870
3.3404-3.43070.31071300.27112335246574
3.4307-3.53160.32841430.26382580272379
3.5316-3.64550.31681530.24172698285184
3.6455-3.77570.2661670.23732880304789
3.7757-3.92670.32461560.21812953310991
3.9267-4.10520.22351340.20672956309092
4.1052-4.32140.23691720.19553086325894
4.3214-4.59170.23611790.17883096327597
4.5917-4.94560.25171580.18873128328697
4.9456-5.4420.26191470.18593189333697
5.442-6.22660.23171710.20043166333798
6.2266-7.83390.26231630.21353215337899
7.8339-38.39370.231640.21093192335698
Refinement TLS params.Method: refined / Origin x: 13.2387 Å / Origin y: 19.5341 Å / Origin z: 17.6542 Å
111213212223313233
T0.2222 Å20.0153 Å20.0296 Å2-0.2045 Å2-0.0034 Å2--0.2607 Å2
L0.3374 °20.0882 °20.0766 °2-0.2462 °2-0.0019 °2--0.3456 °2
S0.0582 Å °0.0197 Å °-0.0622 Å °-0.0234 Å °-0.0688 Å °-0.057 Å °0.1124 Å °-0.0319 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA7 - 327
2X-RAY DIFFRACTION1ALLB1 - 162
3X-RAY DIFFRACTION1ALLC7 - 327
4X-RAY DIFFRACTION1ALLD1 - 162
5X-RAY DIFFRACTION1ALLE7 - 327
6X-RAY DIFFRACTION1ALLF2 - 162
7X-RAY DIFFRACTION1ALLG7 - 327
8X-RAY DIFFRACTION1ALLH1 - 162
9X-RAY DIFFRACTION1ALLI7 - 327
10X-RAY DIFFRACTION1ALLJ1 - 162
11X-RAY DIFFRACTION1ALLK7 - 327
12X-RAY DIFFRACTION1ALLL2 - 162
13X-RAY DIFFRACTION1ALLA601 - 607
14X-RAY DIFFRACTION1ALLC601 - 605
15X-RAY DIFFRACTION1ALLE601 - 606
16X-RAY DIFFRACTION1ALLG601 - 603
17X-RAY DIFFRACTION1ALLI801 - 803
18X-RAY DIFFRACTION1ALLK801 - 803
19X-RAY DIFFRACTION1ALLA701 - 740
20X-RAY DIFFRACTION1ALLB201 - 213
21X-RAY DIFFRACTION1ALLC701 - 729
22X-RAY DIFFRACTION1ALLD201 - 213
23X-RAY DIFFRACTION1ALLE701 - 731
24X-RAY DIFFRACTION1ALLF201 - 207
25X-RAY DIFFRACTION1ALLG701 - 719
26X-RAY DIFFRACTION1ALLH201 - 213
27X-RAY DIFFRACTION1ALLI901 - 935
28X-RAY DIFFRACTION1ALLJ201 - 218
29X-RAY DIFFRACTION1ALLK901 - 924
30X-RAY DIFFRACTION1ALLL201 - 232

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