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

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Basic information

Entry
Database: PDB / ID: 1qfu
TitleINFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY
Components
  • (PROTEIN (HEMAGGLUTININ ...) x 2
  • (PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY ...) x 2
KeywordsViral protein/Immune system / COMPLEX (HEMAGGLUTININ-IMMMUNOGLOBULIN) / HEMAGGLUTININ / IMMUNOGLOBULIN / 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / 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 / host cell surface receptor binding / defense response to bacterium / immune response / external side of 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 / extracellular space / membrane / metal ion binding / cytoplasm
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 ...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 / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ribbon / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / 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
If kappa light chain / 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: 2.8 Å
AuthorsFleury, D. / Gigant, B. / Bizebard, T. / Daniels, R.S. / Skehel, J.J. / Knossow, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: A complex of influenza hemagglutinin with a neutralizing antibody that binds outside the virus receptor binding site.
Authors: Fleury, D. / Barrere, B. / Bizebard, T. / Daniels, R.S. / Skehel, J.J. / Knossow, M.
#1: Journal: Nature / Year: 1995
Title: Structure of influenza virus haemagglutinin complexed with a neutralizing antibody.
Authors: Bizebard, T. / Gigant, B. / Rigolet, P. / Rasmussen, B. / Diat, O. / Bosecke, P. / Wharton, S.A. / Skehel, J.J. / Knossow, M.
#2: 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.
#3: 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
DepositionApr 14, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 8, 2017Group: Derived calculations
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Nov 27, 2019Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
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 / 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_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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HEMAGGLUTININ (HA1 CHAIN))
B: PROTEIN (HEMAGGLUTININ (HA2 CHAIN))
L: PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))
H: PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3599
Polymers104,6854
Non-polymers1,6755
Water1,26170
1
A: PROTEIN (HEMAGGLUTININ (HA1 CHAIN))
B: PROTEIN (HEMAGGLUTININ (HA2 CHAIN))
L: PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))
H: PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))
hetero molecules

A: PROTEIN (HEMAGGLUTININ (HA1 CHAIN))
B: PROTEIN (HEMAGGLUTININ (HA2 CHAIN))
L: PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))
H: PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))
hetero molecules

A: PROTEIN (HEMAGGLUTININ (HA1 CHAIN))
B: PROTEIN (HEMAGGLUTININ (HA2 CHAIN))
L: PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))
H: PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,07827
Polymers314,05512
Non-polymers5,02415
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)138.000, 138.000, 135.000
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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PROTEIN (HEMAGGLUTININ ... , 2 types, 2 molecules AB

#1: Protein PROTEIN (HEMAGGLUTININ (HA1 CHAIN))


Mass: 36065.457 Da / Num. of mol.: 1 / Fragment: BROMELAIN DIGESTED / 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, UniProt: P03438*PLUS
#2: Protein PROTEIN (HEMAGGLUTININ (HA2 CHAIN))


Mass: 20212.350 Da / Num. of mol.: 1 / Fragment: BROMELAIN DIGESTED / 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 PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (LIGHT CHAIN))


Mass: 23980.707 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDROMAS / Strain: BALB/C / References: UniProt: A2NHM3*PLUS
#4: Antibody PROTEIN (IMMUNOGLOBULIN IGG1-KAPPA ANTIBODY (HEAVY CHAIN))


Mass: 24426.404 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDROMAS / Strain: BALB/C / References: UniProt: P01869*PLUS

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Sugars , 3 types, 5 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-alpha-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
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_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
#7: 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.: 3
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, 70 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.29 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Details: Gigant, B., (1995) Proteins: Struct., Funct., Genet., 23, 115.
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %(w/v)PEG20001reservoir
2100 mMTris-HCl1reservoirpH8.5
3150 mM1reservoirNaCl
40.05 %(w/v)1reservoirNaN3
510-15 mg/mlprotain1drop

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Data collection

DiffractionMean temperature: 276 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.8→7 Å / Num. obs: 36133 / % possible obs: 98 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.327 / % possible all: 95
Reflection
*PLUS
Num. measured all: 159126
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.84refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→7 Å / Cross valid method: RFREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.284 -5 %RANDOM
Rwork0.198 ---
obs-36133 98 %-
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7260 0 109 70 7439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 7 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.6

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