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- PDB-1ken: INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH AN ANTIBODY THAT PRE... -

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Basic information

Entry
Database: PDB / ID: 1ken
TitleINFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH AN ANTIBODY THAT PREVENTS THE HEMAGGLUTININ LOW PH FUSOGENIC TRANSITION
Components
  • hemagglutinin HA1
  • hemagglutinin HA2
  • influenza virus infectivity neutralizing antibody (heavy chain)
  • influenza virus infectivity neutralizing antibody (light chain)
KeywordsViral protein/Immune system / HEMAGGLUTININ / ENVELOPE PROTEIN / GLYCOPROTEIN / Viral protein-Immune system COMPLEX
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / viral budding from plasma membrane / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / blood microparticle / host cell surface receptor binding / defense response to bacterium / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm
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 / Immunoglobulin/major histocompatibility complex, conserved site ...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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / : / Immunoglobulin kappa constant / Ig gamma-1 chain C region, membrane-bound form / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBarbey-Martin, C. / Gigant, B. / Bizebard, T. / Calder, L.J. / Wharto, S.A. / Skehel, J.J. / Knossow, M.
Citation
Journal: VIROLOGY / Year: 2002
Title: An Antibody that Prevents the Hemagglutinin Low pH Fusogenic Transition
Authors: Barbey-Martin, C. / Gigant, B. / Bizebard, T. / Calder, L.J. / Wharton, S.A. / Skehel, J.J. / Knossow, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: A Neutralizing Antibody Fab-Influenza Haemagglutinin Complex with an Unprecedented 2:1 Stoichiometry:Characterization and Crystallization
Authors: Gigant, B. / Barbey-Martin, C. / Bizebard, T. / Fleury, D. / Daniels, R. / Skehel, J.J. / Knossow, M.
History
DepositionNov 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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
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
B: hemagglutinin HA2
C: hemagglutinin HA1
D: hemagglutinin HA2
E: hemagglutinin HA1
F: hemagglutinin HA2
L: influenza virus infectivity neutralizing antibody (light chain)
H: influenza virus infectivity neutralizing antibody (heavy chain)
U: influenza virus infectivity neutralizing antibody (light chain)
T: influenza virus infectivity neutralizing antibody (heavy chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,84913
Polymers264,08910
Non-polymers1,7603
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48270 Å2
ΔGint-182 kcal/mol
Surface area92230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.041, 315.588, 97.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein hemagglutinin HA1


Mass: 36065.457 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Influenza A virus (A/X-31(H3N2)) / Genus: Influenzavirus A / Species: Influenza A virus / Strain: X31 / References: GenBank: 324239, UniProt: P03438*PLUS
#2: Protein hemagglutinin HA2


Mass: 20212.350 Da / Num. of mol.: 3 / Fragment: FAB fragment of antibody / Source method: isolated from a natural source / Details: BROMELAIN DIGESTED / Source: (natural) Influenza A virus (A/X-31(H3N2)) / Genus: Influenzavirus A / Species: Influenza A virus / Strain: X31 / References: UniProt: P03437
#3: Antibody influenza virus infectivity neutralizing antibody (light chain)


Mass: 23275.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 7209188, UniProt: P01837*PLUS
#4: Antibody influenza virus infectivity neutralizing antibody (heavy chain)


Mass: 24352.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 17977852, UniProt: P01869*PLUS
#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.: 3
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

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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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: peg 20000, calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 291 K
Details: Gigant, B., (2000) Acta Crystallogr., Sect.D, 56, 1067.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.010-0.015 mg/mlprotein1drop
20.15 M1dropNaCl
30.04 %(w/v)1dropNaN3
413-15 %PEG200001reservoir
550 mMTris-HCl1reservoirpH8.0
620 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→25 Å / Num. obs: 54923 / % possible obs: 98.2 % / Redundancy: 3.9 % / Rsym value: 0.128 / Net I/σ(I): 5.3
Reflection shellResolution: 3.5→3.7 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.42 / % possible all: 98.2
Reflection
*PLUS
Rmerge(I) obs: 0.128
Reflection shell
*PLUS
Lowest resolution: 3.69 Å / % possible obs: 98.2 % / Rmerge(I) obs: 0.423

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→25 Å / Rfactor Rfree error: 0.006 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5
Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL, DUE TO THE LIMITED (3.5 ANGSTROMS) RESOLUTION. THE OVERALL COORDINATE ERROR IS ESTIMATED TO BE APPROXIMATELY 0.45-0.60 ANGSTROMS, ...Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL, DUE TO THE LIMITED (3.5 ANGSTROMS) RESOLUTION. THE OVERALL COORDINATE ERROR IS ESTIMATED TO BE APPROXIMATELY 0.45-0.60 ANGSTROMS, BUT THE ERROR IS HIGHER IN REGIONS HAVING HIGH TEMPERATURE FACTORS. PRECISE ASSIGNMENT OF HYDROGEN BONDS, OTHER CONTACTS AND SECONDARY STRUCTURAL ELEMENTS AT THIS RESOLUTION IS NOT POSSIBLE. ATOMS WITH TEMPERATURE FACTORS GREATER THAN 65 ANGSTROMS SQUARED SHOULD BE INTERPRETED WITH CAUTION. RESIDUES 1-8 OF HA1 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflectionSelection details
Rfree0.323 2607 5 %RANDOM
Rwork0.255 ---
obs-51566 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.7473 Å2 / ksol: 0.206359 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.67 Å20 Å20 Å2
2--5.79 Å20 Å2
3----11.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18375 0 117 0 18492
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d1.29
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 404 5.3 %
Rwork0.295 7221 -
obs--82.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor obs: 0.256 / Rfactor Rfree: 0.324 / Rfactor Rwork: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor obs: 0.295

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