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Basic information

Entry
Database: PDB / ID: 3ubn
TitleInfluenza hemagglutinin from the 2009 pandemic in complex with ligand 6SLN
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral envelope protein / hemagglutinin / viral fusion protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
6'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Influenza a virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5079 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2012
Title: Structural Characterization of the Hemagglutinin Receptor Specificity from the 2009 H1N1 Influenza Pandemic.
Authors: Xu, R. / McBride, R. / Nycholat, C.M. / Paulson, J.C. / Wilson, I.A.
History
DepositionOct 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / _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 / _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 2.1Sep 13, 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 9, 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 HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: Hemagglutinin HA1
J: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,14228
Polymers340,88212
Non-polymers6,26016
Water8,737485
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,01316
Polymers170,4416
Non-polymers3,57210
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35810 Å2
ΔGint-125 kcal/mol
Surface area57350 Å2
MethodPISA
2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: Hemagglutinin HA1
J: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,12812
Polymers170,4416
Non-polymers2,6876
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34630 Å2
ΔGint-149 kcal/mol
Surface area56950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.00, 116.71, 119.66
Angle α, β, γ (deg.)60.61, 77.05, 80.38
Int Tables number1
Space group name H-MP1

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Components

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Hemagglutinin ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Hemagglutinin HA1


Mass: 36535.281 Da / Num. of mol.: 6 / Fragment: Ectodomain HA1, residues 18-344 / Mutation: G205C, R220C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: SW1 A/CALIFORNIA/04/2009 / Gene: HA, hemagglutinin / Plasmid: pFastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C3W5S1
#2: Protein
Hemagglutinin HA2


Mass: 20278.383 Da / Num. of mol.: 6 / Fragment: Ectodomain HA2, residues 345-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza a virus / Strain: SW1 A/CALIFORNIA/04/2009 / Gene: HA, hemagglutinin / Plasmid: pFASTbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C3W5S1

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Sugars , 4 types, 16 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.: 5
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
[][b-D-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


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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

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Non-polymers , 1 types, 485 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 27% PEG-MME 2000, 0.1M Tris pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2010
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionRedundancy: 2.1 % / Av σ(I) over netI: 9.23 / Number: 207943 / Rmerge(I) obs: 0.087 / Χ2: 1.03 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 99231 / % possible obs: 94.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385099.510.0380.9722.2
4.275.3899.110.0490.9522.2
3.734.279910.0661.0382.2
3.393.7398.810.0931.0762.2
3.153.399810.1421.1032.2
2.963.1596.910.2121.0652.2
2.822.9695.610.3041.0842.1
2.692.8294.310.3641.0482
2.592.6988.910.4280.9581.9
2.52.5975.710.4650.9911.7
ReflectionResolution: 2.5→50 Å / Num. obs: 99231 / % possible obs: 94.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.033 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.591.70.46579600.991175.7
2.59-2.691.90.42893260.958188.9
2.69-2.8220.36498891.048194.3
2.82-2.962.10.304100241.084195.6
2.96-3.152.20.212101831.065196.9
3.15-3.392.20.142102571.103198
3.39-3.732.20.093103751.076198.8
3.73-4.272.20.066103721.038199
4.27-5.382.20.049104060.952199.1
5.38-502.20.038104390.972199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.02 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.37 Å
Translation2.5 Å47.37 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LZG

3lzg


Resolution: 2.5079→49.682 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 1.97 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 4908 4.95 %
Rwork0.2049 --
obs0.2073 99186 94.22 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.775 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 115.93 Å2 / Biso mean: 48.8788 Å2 / Biso min: 22.23 Å2
Baniso -1Baniso -2Baniso -3
1--2.0158 Å20.7936 Å25.7018 Å2
2---0.0177 Å214.0085 Å2
3---2.0335 Å2
Refinement stepCycle: LAST / Resolution: 2.5079→49.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23303 0 415 485 24203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224331
X-RAY DIFFRACTIONf_angle_d0.61432947
X-RAY DIFFRACTIONf_chiral_restr0.0423623
X-RAY DIFFRACTIONf_plane_restr0.0024206
X-RAY DIFFRACTIONf_dihedral_angle_d15.1318960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5079-2.59750.33863770.29317322769973
2.5975-2.70150.36694440.28318886933089
2.7015-2.82450.31025140.25629412992694
2.8245-2.97340.324990.251195231002295
2.9734-3.15960.30554820.238897361021897
3.1596-3.40350.27714820.219797931027598
3.4035-3.74590.24375080.193499271043599
3.7459-4.28770.21045510.166798521040399
4.2877-5.4010.20485250.167298961042199
5.401-49.69210.2375260.198999311045799

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