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- PDB-1eo8: INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1eo8
TitleINFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY
Components
  • (HEMAGGLUTININ ...) x 2
  • ANTIBODY (HEAVY CHAIN)
  • ANTIBODY (LIGHT CHAIN)
KeywordsViral protein/Immune system / COMPLEX (HEMAGGLUTININ-IMMMUNOGLOBULIN) / HEMAGGLUTININ / IMMUNOGLOBULIN / VIRAL PROTEIN / IMMUNE SYSTEM COMPLEX / 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 / membrane
Similarity search - Function
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 / Immunoglobulins ...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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFleury, D. / Gigant, B. / Daniels, R.S. / Skehel, J.J. / Knossow, M. / Bizebard, T.
Citation
Journal: Proteins / Year: 2000
Title: Structural evidence for recognition of a single epitope by two distinct antibodies.
Authors: Fleury, D. / Daniels, R.S. / Skehel, J.J. / Knossow, M. / Bizebard, T.
#1: Journal: Proteins / Year: 1995
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Complexes between an Influenza Hemagglutinin and Fab Fragments of Two Different Monoclonal Antibodies
Authors: Gigant, B. / Fleury, D. / Bizebard, T. / Skehel, J.J. / Knossow, M.
#2: Journal: Nature / Year: 1981
Title: Structure of the Haemagglutinin Membrane Glycoprotein of Influenza Virus at 3 A Resolution
Authors: Wilson, I.A. / Skehel, J.J. / Wiley, D.C.
History
DepositionMar 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
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 / database_PDB_caveat / 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_chiral / 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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMAGGLUTININ (HA1 CHAIN)
B: HEMAGGLUTININ (HA2 CHAIN)
L: ANTIBODY (LIGHT CHAIN)
H: ANTIBODY (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2368
Polymers102,7834
Non-polymers1,4534
Water1,964109
1
A: HEMAGGLUTININ (HA1 CHAIN)
B: HEMAGGLUTININ (HA2 CHAIN)
L: ANTIBODY (LIGHT CHAIN)
H: ANTIBODY (HEAVY CHAIN)
hetero molecules

A: HEMAGGLUTININ (HA1 CHAIN)
B: HEMAGGLUTININ (HA2 CHAIN)
L: ANTIBODY (LIGHT CHAIN)
H: ANTIBODY (HEAVY CHAIN)
hetero molecules

A: HEMAGGLUTININ (HA1 CHAIN)
B: HEMAGGLUTININ (HA2 CHAIN)
L: ANTIBODY (LIGHT CHAIN)
H: ANTIBODY (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,70824
Polymers308,34812
Non-polymers4,36012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)138.150, 138.150, 129.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsTHERE IS ONE MONOMER OF THE TRIMERIC HEMAGGLUTININ MOLECULE IN THE ASYMMETRIC UNIT, AND EACH MONOMER IS COMPLEXED WITH ONE FAB FRAGMENT. THE MONOMER OF HEMAGGLUTININ CONSISTS OF TWO CHAINS, IDENTIFIED AS HA1 AND HA2. CHAINS HA1 AND HA2 HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*, RESPECTIVELY. IN THE VIRUS, CHAIN HA1 CONSISTS OF 328 RESIDUES AND CHAIN HA2 CONSISTS OF 220 RESIDUES. HEMAGGLUTININ MAY BE SOLUBILIZED FROM THE VIRAL MEMBRANE BY BROMELAIN DIGESTION, WHICH REMOVES THE C-TERMINAL HYDROPHOBIC (ANCHORING) DOMAIN FROM CHAIN HA2. AFTER BROMELAIN DIGESTION CHAIN HA2 CONSISTS OF 175 RESIDUES, AS PRESENTED IN THIS ENTRY.

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Components

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HEMAGGLUTININ ... , 2 types, 2 molecules AB

#1: Protein HEMAGGLUTININ (HA1 CHAIN)


Mass: 36065.457 Da / Num. of mol.: 1 / Fragment: BROMELAIN RELEASED FRAGMENT / Source method: isolated from a natural source
Details: A RECOMBINANT INFLUENZA STRAIN CONTAINING A/AICHI/68 (H3N2) HEMAGGLUTININ
Source: (natural) Influenza A virus (A/X-31(H3N2)) / Genus: Influenzavirus A / Species: Influenza A virus / Strain: X31 / References: UniProt: P03437
#2: Protein HEMAGGLUTININ (HA2 CHAIN)


Mass: 20212.350 Da / Num. of mol.: 1 / Fragment: BROMELAIN RELEASED FRAGMENT / Source method: isolated from a natural source
Details: A RECOMBINANT INFLUENZA STRAIN CONTAINING A/AICHI/68 (H3N2) HEMAGGLUTININ
Source: (natural) Influenza A virus (A/X-31(H3N2)) / Genus: Influenzavirus A / Species: Influenza A virus / Strain: X31 / References: UniProt: P03437

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Antibody , 2 types, 2 molecules LH

#3: Antibody ANTIBODY (LIGHT CHAIN)


Mass: 23097.604 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT OF ANTIBODY BH151 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDROMAS / Strain: BALB/C / References: GenBank: 7159941
#4: Antibody ANTIBODY (HEAVY CHAIN)


Mass: 23407.254 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT OF ANTIBODY BH151 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDROMAS / Strain: BALB/C / References: GenBank: 7159939

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Sugars , 3 types, 4 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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, 109 molecules

#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 28%(w:v) PEG 600, 100 mM Sodium Phosphate, 150 mM NaCl, 0.05% NaN3 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.5
Details: Gigant, B., (1995) Proteins: Struct., Funct., Genet., 23, 115.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
210 %(w/v)PEG20001reservoir
3100 mMTris-HCl1reservoir
4150 mM1reservoirNaCl
50.05 %(w/v)1reservoirNaN3
6150 mM1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. all: 186998 / Num. obs: 49210 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 7.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.336 / Rsym value: 0.336 / % possible all: 99
Reflection
*PLUS
Num. measured all: 186998
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→7 Å / Cross valid method: RFREE / σ(F): 2
Rfactor% reflectionSelection details
Rfree0.298 5 %RANDOM
Rwork0.196 --
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7153 0 95 109 7357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.9
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.9

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