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Basic information

Entry
Database: PDB / ID: 3ubq
TitleInfluenza hemagglutinin from the 2009 pandemic in complex with ligand 3SLN
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 / 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
3'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Influenza a virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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

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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)346,42730
Polymers340,88212
Non-polymers5,54518
Water18,9341051
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)172,62812
Polymers170,4416
Non-polymers2,1876
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32880 Å2
ΔGint-155 kcal/mol
Surface area57420 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)173,79918
Polymers170,4416
Non-polymers3,35812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34360 Å2
ΔGint-138 kcal/mol
Surface area57860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.876, 116.258, 118.366
Angle α, β, γ (deg.)60.96, 77.13, 80.40
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, 18 molecules

#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
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#5: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-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/a3-b2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+2)][a-D-Neup5Ac]{}}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.: 12
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, 1051 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1051 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
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 % / Av σ(I) over netI: 10.69 / Number: 348771 / Rmerge(I) obs: 0.068 / Χ2: 1.04 / D res high: 2 Å / D res low: 50 Å / Num. obs: 172551 / % possible obs: 84.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315099.110.0361.0522.2
3.424.3198.910.0441.0742.2
2.993.4298.310.0720.9632.1
2.712.9995.910.1181.0472
2.522.7192.810.181.0822
2.372.5287.510.2381.0762
2.252.3781.110.2891.0381.9
2.152.257310.3471.0571.9
2.072.1564.210.4041.0061.9
22.0753.710.4590.9491.8
ReflectionResolution: 2→50 Å / Num. obs: 172551 / % possible obs: 84.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.071.80.459153.7
2.07-2.151.90.404164.2
2.15-2.251.90.347173
2.25-2.371.90.289181.1
2.37-2.5220.238187.5
2.52-2.7120.18192.8
2.71-2.9920.118195.9
2.99-3.422.10.072198.3
3.42-4.312.20.044198.9
4.31-502.20.036199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.27 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.24 Å
Translation2.5 Å49.24 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
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→49.238 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.96 / Phase error: 31.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 8648 5.01 %
Rwork0.1993 --
obs0.2019 172491 84.21 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.254 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.5911 Å22.7195 Å25.305 Å2
2--4.3579 Å218.1828 Å2
3---0.2332 Å2
Refinement stepCycle: LAST / Resolution: 2→49.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23264 0 360 1051 24675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524237
X-RAY DIFFRACTIONf_angle_d0.91832808
X-RAY DIFFRACTIONf_dihedral_angle_d15.1278905
X-RAY DIFFRACTIONf_chiral_restr0.0623595
X-RAY DIFFRACTIONf_plane_restr0.0044195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02280.34741430.30143042X-RAY DIFFRACTION47
2.0228-2.04660.33241750.28443422X-RAY DIFFRACTION53
2.0466-2.07150.32851950.26933772X-RAY DIFFRACTION58
2.0715-2.09770.33192220.27123904X-RAY DIFFRACTION61
2.0977-2.12530.29471930.26444114X-RAY DIFFRACTION63
2.1253-2.15450.32392380.26674400X-RAY DIFFRACTION67
2.1545-2.18520.31352450.26144488X-RAY DIFFRACTION70
2.1852-2.21790.31662590.26254760X-RAY DIFFRACTION73
2.2179-2.25250.31792440.26384932X-RAY DIFFRACTION76
2.2525-2.28940.33932680.24145012X-RAY DIFFRACTION78
2.2894-2.32890.30912810.24665227X-RAY DIFFRACTION81
2.3289-2.37130.31632850.24295460X-RAY DIFFRACTION84
2.3713-2.41690.29783190.24755511X-RAY DIFFRACTION85
2.4169-2.46620.30813040.24345715X-RAY DIFFRACTION88
2.4662-2.51980.30483140.24055729X-RAY DIFFRACTION89
2.5198-2.57840.31133140.23565964X-RAY DIFFRACTION91
2.5784-2.64290.32933110.22375982X-RAY DIFFRACTION93
2.6429-2.71440.28562910.21686125X-RAY DIFFRACTION94
2.7144-2.79420.27633300.21996179X-RAY DIFFRACTION95
2.7942-2.88440.27023140.226221X-RAY DIFFRACTION96
2.8844-2.98750.26153170.21216299X-RAY DIFFRACTION97
2.9875-3.10710.26233730.20966278X-RAY DIFFRACTION98
3.1071-3.24850.25873630.19916343X-RAY DIFFRACTION98
3.2485-3.41970.23573600.1966400X-RAY DIFFRACTION99
3.4197-3.63390.22553160.18326415X-RAY DIFFRACTION99
3.6339-3.91440.233320.16186438X-RAY DIFFRACTION99
3.9144-4.30810.20023420.15936395X-RAY DIFFRACTION99
4.3081-4.9310.18723150.14936455X-RAY DIFFRACTION99
4.931-6.21050.21473370.1766439X-RAY DIFFRACTION99
6.2105-49.25280.20423480.18466422X-RAY DIFFRACTION99

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